From 8d2172c834e3534ce7a1582b171c2f7a248e10b5 Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Fri, 8 Mar 2024 21:23:34 +0100
Subject: [PATCH 01/14] All data in data/
Both simulation.py and plot_com.py look for data in data/
Transcript data in /data
- Closes Tango/tango_models#2
Remove copy of data from pipeline/
---
{pipeline => data}/TANGO_MTA_WF_310320.xlsx | Bin
.../DataNormLL_RPKM_meaned.tsv | 0
.../DataNormLP_RPKM_meaned.tsv | 0
.../DataNormPF_RPKM_meaned.tsv | 0
.../exchanged_metabolites_smetana.xlsx | Bin
.../freudenreichii_lactose.csv | 0
.../data_transcript/lactis_lactose.csv | 0
.../data_transcript/plantarum_lactose.csv | 0
pipeline/com_DM.tsv | 8 --
pipeline/com_time.tsv | 8 --
pipeline/community_data_tango.tsv | 21 -----
pipeline/data_GrowthExp.csv | 89 ------------------
pipeline/data_metabolites_freud.tsv | 9 --
scripts/plot_com.py | 2 +-
src/tango_models/simulation.py | 2 +-
tango_models.cwl | 6 +-
16 files changed, 5 insertions(+), 140 deletions(-)
rename {pipeline => data}/TANGO_MTA_WF_310320.xlsx (100%)
rename {pipeline => data}/data_transcript/DataNormLL_RPKM_meaned.tsv (100%)
rename {pipeline => data}/data_transcript/DataNormLP_RPKM_meaned.tsv (100%)
rename {pipeline => data}/data_transcript/DataNormPF_RPKM_meaned.tsv (100%)
rename {pipeline => data}/data_transcript/exchanged_metabolites_smetana.xlsx (100%)
rename {pipeline => data}/data_transcript/freudenreichii_lactose.csv (100%)
rename {pipeline => data}/data_transcript/lactis_lactose.csv (100%)
rename {pipeline => data}/data_transcript/plantarum_lactose.csv (100%)
delete mode 100644 pipeline/com_DM.tsv
delete mode 100644 pipeline/com_time.tsv
delete mode 100644 pipeline/community_data_tango.tsv
delete mode 100644 pipeline/data_GrowthExp.csv
delete mode 100644 pipeline/data_metabolites_freud.tsv
diff --git a/pipeline/TANGO_MTA_WF_310320.xlsx b/data/TANGO_MTA_WF_310320.xlsx
similarity index 100%
rename from pipeline/TANGO_MTA_WF_310320.xlsx
rename to data/TANGO_MTA_WF_310320.xlsx
diff --git a/pipeline/data_transcript/DataNormLL_RPKM_meaned.tsv b/data/data_transcript/DataNormLL_RPKM_meaned.tsv
similarity index 100%
rename from pipeline/data_transcript/DataNormLL_RPKM_meaned.tsv
rename to data/data_transcript/DataNormLL_RPKM_meaned.tsv
diff --git a/pipeline/data_transcript/DataNormLP_RPKM_meaned.tsv b/data/data_transcript/DataNormLP_RPKM_meaned.tsv
similarity index 100%
rename from pipeline/data_transcript/DataNormLP_RPKM_meaned.tsv
rename to data/data_transcript/DataNormLP_RPKM_meaned.tsv
diff --git a/pipeline/data_transcript/DataNormPF_RPKM_meaned.tsv b/data/data_transcript/DataNormPF_RPKM_meaned.tsv
similarity index 100%
rename from pipeline/data_transcript/DataNormPF_RPKM_meaned.tsv
rename to data/data_transcript/DataNormPF_RPKM_meaned.tsv
diff --git a/pipeline/data_transcript/exchanged_metabolites_smetana.xlsx b/data/data_transcript/exchanged_metabolites_smetana.xlsx
similarity index 100%
rename from pipeline/data_transcript/exchanged_metabolites_smetana.xlsx
rename to data/data_transcript/exchanged_metabolites_smetana.xlsx
diff --git a/pipeline/data_transcript/freudenreichii_lactose.csv b/data/data_transcript/freudenreichii_lactose.csv
similarity index 100%
rename from pipeline/data_transcript/freudenreichii_lactose.csv
rename to data/data_transcript/freudenreichii_lactose.csv
diff --git a/pipeline/data_transcript/lactis_lactose.csv b/data/data_transcript/lactis_lactose.csv
similarity index 100%
rename from pipeline/data_transcript/lactis_lactose.csv
rename to data/data_transcript/lactis_lactose.csv
diff --git a/pipeline/data_transcript/plantarum_lactose.csv b/data/data_transcript/plantarum_lactose.csv
similarity index 100%
rename from pipeline/data_transcript/plantarum_lactose.csv
rename to data/data_transcript/plantarum_lactose.csv
diff --git a/pipeline/com_DM.tsv b/pipeline/com_DM.tsv
deleted file mode 100644
index db81330..0000000
--- a/pipeline/com_DM.tsv
+++ /dev/null
@@ -1,8 +0,0 @@
-State DM
-Linoc 11.65
-Finoc 11.65
-Moul 40.53
-Demoul 51.44
-AS 52.28
-Aff4s 53.41
-Aff7s 53.55
diff --git a/pipeline/com_time.tsv b/pipeline/com_time.tsv
deleted file mode 100644
index 2363b94..0000000
--- a/pipeline/com_time.tsv
+++ /dev/null
@@ -1,8 +0,0 @@
-State time
-Linoc 0
-Finoc 18
-Moul 19.5
-Demoul 40
-AS 60
-Aff4s 732
-Aff7s 1236
diff --git a/pipeline/community_data_tango.tsv b/pipeline/community_data_tango.tsv
deleted file mode 100644
index 74b2abe..0000000
--- a/pipeline/community_data_tango.tsv
+++ /dev/null
@@ -1,21 +0,0 @@
-bacteria density_com step time
-lactis 5.7 Linoc 0
-lactis 7.5 Before_Moul 19.5
-lactis 8.78 Moul 40
-lactis 9.12 Demoul 60
-lactis 9.06 before_ripening 60
-lactis 8.95 Aff4s 672
-lactis 8.45 Aff7s 1176
-plantarum 5.2 Linoc 0
-plantarum 5.4 Before_Moul 19.5
-plantarum 6.49 Moul 40
-plantarum 7.53 Demoul 60
-plantarum 7.92 before_ripening 60
-plantarum 8.47 Aff4s 672
-plantarum 8.47 Aff7s 1176
-freudenreichii 6.1 Before_Moul 19.5
-freudenreichii 7.16 Moul 40
-freudenreichii 8.04 Demoul 60
-freudenreichii 8.11 before_ripening 60
-freudenreichii 8.56 Aff4s 672
-freudenreichii 8.59 Aff7s 1176
\ No newline at end of file
diff --git a/pipeline/data_GrowthExp.csv b/pipeline/data_GrowthExp.csv
deleted file mode 100644
index 6ef60b0..0000000
--- a/pipeline/data_GrowthExp.csv
+++ /dev/null
@@ -1,89 +0,0 @@
-species,experiment,replicate,time,type,unit,value
-lactis,GrowthExp,1,0,pH,[-],6.7
-lactis,GrowthExp,1,3,pH,[-],6.63
-lactis,GrowthExp,1,4,pH,[-],6.55
-lactis,GrowthExp,1,5,pH,[-],6.49
-lactis,GrowthExp,1,6,pH,[-],6.45
-lactis,GrowthExp,1,7,pH,[-],6.33
-lactis,GrowthExp,1,8,pH,[-],6.25
-lactis,GrowthExp,1,9,pH,[-],6.07
-lactis,GrowthExp,1,10,pH,[-],6
-lactis,GrowthExp,1,11,pH,[-],5.99
-lactis,GrowthExp,1,12,pH,[-],5.94
-lactis,GrowthExp,1,13,pH,[-],5.92
-lactis,GrowthExp,1,14,pH,[-],5.93
-lactis,GrowthExp,1,15,pH,[-],5.82
-lactis,GrowthExp,1,16,pH,[-],5.88
-lactis,GrowthExp,1,17,pH,[-],5.8
-lactis,GrowthExp,1,79,pH,[-],5.12
-lactis,GrowthExp,2,0,pH,[-],6.7
-lactis,GrowthExp,2,3,pH,[-],6.61
-lactis,GrowthExp,2,4,pH,[-],6.54
-lactis,GrowthExp,2,5,pH,[-],6.49
-lactis,GrowthExp,2,6,pH,[-],6.43
-lactis,GrowthExp,2,7,pH,[-],6.3
-lactis,GrowthExp,2,8,pH,[-],6.23
-lactis,GrowthExp,2,9,pH,[-],6.08
-lactis,GrowthExp,2,10,pH,[-],6
-lactis,GrowthExp,2,11,pH,[-],6.01
-lactis,GrowthExp,2,12,pH,[-],5.93
-lactis,GrowthExp,2,13,pH,[-],5.95
-lactis,GrowthExp,2,14,pH,[-],5.94
-lactis,GrowthExp,2,15,pH,[-],5.85
-lactis,GrowthExp,2,16,pH,[-],5.85
-lactis,GrowthExp,2,17,pH,[-],5.81
-lactis,GrowthExp,2,79,pH,[-],5.11
-lactis,GrowthExp,1,0,numbering,CFU.g^-1,1000000
-lactis,GrowthExp,1,5,numbering,CFU.g^-1,165000000
-lactis,GrowthExp,1,7,numbering,CFU.g^-1,177000000
-lactis,GrowthExp,1,9,numbering,CFU.g^-1,186000000
-lactis,GrowthExp,1,14,numbering,CFU.g^-1,173000000
-lactis,GrowthExp,1,16,numbering,CFU.g^-1,155000000
-lactis,GrowthExp,1,79,numbering,CFU.g^-1,248500000
-lactis,GrowthExp,2,0,numbering,CFU.g^-1,4000000
-lactis,GrowthExp,2,5,numbering,CFU.g^-1,152000000
-lactis,GrowthExp,2,7,numbering,CFU.g^-1,237000000
-lactis,GrowthExp,2,9,numbering,CFU.g^-1,217000000
-lactis,GrowthExp,2,14,numbering,CFU.g^-1,219000000
-lactis,GrowthExp,2,16,numbering,CFU.g^-1,132000000
-lactis,GrowthExp,2,79,numbering,CFU.g^-1,125000000
-plantarum,GrowthExp,1,0,pH,[-],6.7
-plantarum,GrowthExp,1,5,pH,[-],6.68
-plantarum,GrowthExp,1,7,pH,[-],6.67
-plantarum,GrowthExp,1,8,pH,[-],6.64
-plantarum,GrowthExp,1,9,pH,[-],6.57
-plantarum,GrowthExp,1,14,pH,[-],6.55
-plantarum,GrowthExp,1,16,pH,[-],6.52
-plantarum,GrowthExp,1,79,pH,[-],5.7
-plantarum,GrowthExp,2,0,pH,[-],6.7
-plantarum,GrowthExp,2,5,pH,[-],6.68
-plantarum,GrowthExp,2,7,pH,[-],6.65
-plantarum,GrowthExp,2,8,pH,[-],6.65
-plantarum,GrowthExp,2,9,pH,[-],6.54
-plantarum,GrowthExp,2,14,pH,[-],6.53
-plantarum,GrowthExp,2,16,pH,[-],6.5
-plantarum,GrowthExp,2,79,pH,[-],5.71
-plantarum,GrowthExp,1,0,numbering,CFU.g^-1,3000000
-plantarum,GrowthExp,1,5,numbering,CFU.g^-1,9000000
-plantarum,GrowthExp,1,7,numbering,CFU.g^-1,17000000
-plantarum,GrowthExp,1,9,numbering,CFU.g^-1,26000000
-plantarum,GrowthExp,1,14,numbering,CFU.g^-1,44000000
-plantarum,GrowthExp,1,16,numbering,CFU.g^-1,84000000
-plantarum,GrowthExp,1,79,numbering,CFU.g^-1,110000000
-plantarum,GrowthExp,2,0,numbering,CFU.g^-1,6000000
-plantarum,GrowthExp,2,5,numbering,CFU.g^-1,14000000
-plantarum,GrowthExp,2,7,numbering,CFU.g^-1,15000000
-plantarum,GrowthExp,2,9,numbering,CFU.g^-1,25000000
-plantarum,GrowthExp,2,14,numbering,CFU.g^-1,40000000
-plantarum,GrowthExp,2,16,numbering,CFU.g^-1,59000000
-plantarum,GrowthExp,2,79,numbering,CFU.g^-1,117000000
-freudenreichii,GrowthExp,1,0,numbering,CFU.g^-1,4400000
-freudenreichii,GrowthExp,1,23,numbering,CFU.g^-1,230000000
-freudenreichii,GrowthExp,1,40,numbering,CFU.g^-1,1700000000
-freudenreichii,GrowthExp,1,48,numbering,CFU.g^-1,1200000000
-freudenreichii,GrowthExp,1,122,numbering,CFU.g^-1,2300000000
-freudenreichii,GrowthExp,2,0,numbering,CFU.g^-1,3000000
-freudenreichii,GrowthExp,2,23,numbering,CFU.g^-1,370000000
-freudenreichii,GrowthExp,2,40,numbering,CFU.g^-1,1700000000
-freudenreichii,GrowthExp,2,48,numbering,CFU.g^-1,1300000000
-freudenreichii,GrowthExp,2,122,numbering,CFU.g^-1,2000000000
diff --git a/pipeline/data_metabolites_freud.tsv b/pipeline/data_metabolites_freud.tsv
deleted file mode 100644
index b83d438..0000000
--- a/pipeline/data_metabolites_freud.tsv
+++ /dev/null
@@ -1,9 +0,0 @@
-,time,mean,std,metabolite
-0,0.0,16.5,0.08,EX_lac__L_e
-1,89.0,7.88,0.08,EX_lac__L_e
-2,0.0,0,0.02,EX_ac_e
-3,89.0,3.07,0.02,EX_ac_e
-4,0.0,0,0.063,EX_succ_e
-5,89.0,0.371,0.063,EX_succ_e
-6,0.0,0,0.02,EX_ppa_e
-7,89.0,8.31,0.02,EX_ppa_e
diff --git a/scripts/plot_com.py b/scripts/plot_com.py
index dfc0fe8..40c0afe 100644
--- a/scripts/plot_com.py
+++ b/scripts/plot_com.py
@@ -23,7 +23,7 @@ def get_data_com():
time = time_o.loc[simulation.index]
- experiments = pd.read_excel('pipeline/TANGO_MTA_WF_310320.xlsx').set_index('Stade')
+ experiments = pd.read_excel('data/TANGO_MTA_WF_310320.xlsx').set_index('Stade')
diff --git a/src/tango_models/simulation.py b/src/tango_models/simulation.py
index 2a1033c..51c032a 100644
--- a/src/tango_models/simulation.py
+++ b/src/tango_models/simulation.py
@@ -265,7 +265,7 @@ def sim(sp_reac,media_reac,param_sp,model_list,args_c):
print('mod',mod)
for p in param['theta_param'][mod]:
print(p,param[p])
- std,times,DM = preprocessing_data.get_experimental_data(param['path_time_data_com'],param['path_DM_data_com'],'pipeline/TANGO_MTA_WF_310320.xlsx', interest_value = param['interest_value'])
+ std,times,DM = preprocessing_data.get_experimental_data(param['path_time_data_com'],param['path_DM_data_com'],'data/TANGO_MTA_WF_310320.xlsx', interest_value = param['interest_value'])
res=dFBA.DFBA(param,times=times,DM=DM,com=True,transcrip=False,opt=None,VERBOSE=args_c.verbose,lactic_acid=args_c.lactic_acid_model)
print(pd.DataFrame(res))
time_dFBA_end=time.time()
diff --git a/tango_models.cwl b/tango_models.cwl
index 3a7942a..fb0193f 100644
--- a/tango_models.cwl
+++ b/tango_models.cwl
@@ -20,9 +20,9 @@ requirements:
listing: []
- basename: "pipeline"
class: Directory
- listing:
- - class: File
- location: pipeline/TANGO_MTA_WF_310320.xlsx
+ listing: []
+ # - class: File
+ # location: pipeline/TANGO_MTA_WF_310320.xlsx
NetworkAccess:
class: NetworkAccess
networkAccess: true
--
GitLab
From 21290ae6ce70dc65ba8d747028f656af2d541f70 Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Sat, 9 Mar 2024 12:02:55 +0100
Subject: [PATCH 02/14] tango_plot stage models, optional, needed for
transcripts
---
tango_plots.cwl | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/tango_plots.cwl b/tango_plots.cwl
index 21f761c..e4807a4 100644
--- a/tango_plots.cwl
+++ b/tango_plots.cwl
@@ -14,6 +14,8 @@ requirements:
- $(inputs.data)
- entry: $(inputs.results)
entryname: results
+ - entry: $(inputs.models)
+ entryname: metabolic_models
NetworkAccess:
class: NetworkAccess
networkAccess: true
@@ -35,6 +37,12 @@ inputs:
{indiv,flux,com,goodness_of_fit,switch_pathways}
default: "indiv"
+ models:
+ type: Directory?
+ doc: |-
+ Directory containing experimental data, referenced in optimize
+ configuration
+
results:
type: Directory
doc: |-
--
GitLab
From 2580554eb772248b2c573768dbb54cf4205d18d9 Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Sat, 9 Mar 2024 12:05:51 +0100
Subject: [PATCH 03/14] CWL use enum to limit possible options
---
tango_models.cwl | 53 +++++++++++++++++++++++++++++++++++++++++-------
tango_plots.cwl | 11 +++++++++-
2 files changed, 56 insertions(+), 8 deletions(-)
diff --git a/tango_models.cwl b/tango_models.cwl
index fb0193f..566fe20 100644
--- a/tango_models.cwl
+++ b/tango_models.cwl
@@ -38,18 +38,32 @@ hints:
inputs:
cobra_solver:
- type: string
doc: |-
solver used for FBA computation by Cobra
{glpk,glpk_exact,cplex,scipy}
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - "glpk"
+ - "glpk_exact"
+ - "cplex"
+ - "scipy"
+ default: "glpk"
inputBinding:
position: 5
prefix: "-CobraSolver"
community_scale:
- type: string
doc: |-
dFBA at the community scale {True,False}
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - "True"
+ - "False"
+ default: "False"
inputBinding:
position: 5
prefix: "-com"
@@ -83,22 +97,32 @@ inputs:
prefix: "-dp"
freud_sim:
- type: string?
doc: |-
different initial conditions for lactate where defined in the
experiments for growth and metabolite dosage => this parameter
allows to switch between both situations {growth,metabolites}
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - "growth"
+ - "metabolites"
default: "growth"
inputBinding:
position: 5
prefix: "-fsim"
lactic_acid_model:
- type: string?
doc: |-
lactic acid model use total if lactate represents total lactic
acid concentration, or dissociated if lactate represents the
dissociated lactic acid {total,dissociated}
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - "total"
+ - "dissociated"
default: "total"
inputBinding:
position: 5
@@ -116,19 +140,29 @@ inputs:
prefix: "-mp"
optimize:
- type: string?
doc: |-
activatee or not the optimization on parameters {True,False}
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - "True"
+ - "False"
default: "False"
inputBinding:
position: 5
prefix: "-optim"
recovery:
- type: string?
doc: |-
activate or not recovery of the optimization on parameters
{True,False}
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - "True"
+ - "False"
default: "False"
inputBinding:
position: 6
@@ -152,9 +186,14 @@ inputs:
prefix: "-sp"
verbose:
- type: string?
doc: |-
active or not verbose reporting {True,False}
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - "True"
+ - "False"
default: "False"
inputBinding:
position: 6
diff --git a/tango_plots.cwl b/tango_plots.cwl
index e4807a4..592c4c8 100644
--- a/tango_plots.cwl
+++ b/tango_plots.cwl
@@ -31,10 +31,19 @@ inputs:
location: ./data
figure:
- type: string
doc: |-
Which predefined figure to make
{indiv,flux,com,goodness_of_fit,switch_pathways}
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - "com"
+ - "flux"
+ - "goodness_of_fit"
+ - "indiv"
+ - "switch_pathways"
+ - "transcripts"
default: "indiv"
models:
--
GitLab
From 3741a121d483ed4c38a50721ae38aca55dcb0e0b Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Tue, 12 Mar 2024 07:10:58 +0100
Subject: [PATCH 04/14] workflow
---
figures_monoculture_inline.cwl | 138 ++++++++++++++++
mock/data | 1 +
mock/pipeline | 1 +
mock/tango_models.cwl | 280 +++++++++++++++++++++++++++++++++
mock/tango_models_mock.py | 84 ++++++++++
pipeline/combine_files.cwl | 22 +++
pipeline/combine_res_optim.cwl | 21 +++
pipeline/flatten_array.cwl | 29 ++++
tango_models.cwl | 42 +++--
tango_workflow.cwl | 148 +++++++++++++++++
10 files changed, 752 insertions(+), 14 deletions(-)
create mode 100644 figures_monoculture_inline.cwl
create mode 120000 mock/data
create mode 120000 mock/pipeline
create mode 100644 mock/tango_models.cwl
create mode 100755 mock/tango_models_mock.py
create mode 100644 pipeline/combine_files.cwl
create mode 100644 pipeline/combine_res_optim.cwl
create mode 100644 pipeline/flatten_array.cwl
create mode 100644 tango_workflow.cwl
diff --git a/figures_monoculture_inline.cwl b/figures_monoculture_inline.cwl
new file mode 100644
index 0000000..38fd4ba
--- /dev/null
+++ b/figures_monoculture_inline.cwl
@@ -0,0 +1,138 @@
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+ MultipleInputFeatureRequirement: {}
+ StepInputExpressionRequirement: {}
+ ScatterFeatureRequirement: {}
+ InlineJavascriptRequirement: {}
+
+inputs:
+ model_list:
+ type: File[]
+ default:
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/lactis.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/plantarum.sbml"
+ format: http://edamontology.org/format_2585
+ freud_sim_list:
+ type: string[]
+ default:
+ - "metabolites"
+ - "growth"
+ - "growth"
+ - "growth"
+
+outputs:
+ scattered_results:
+ type: Directory
+ outputSource: flatten/flattened
+ plots:
+ type: File[]
+ outputSource:
+ - plot_indiv/plots
+ # standard_output:
+ # type: File
+ # outputSource: plot_indiv/standard_output
+ # standard_error:
+ # type: File
+ # outputSource: plot_indiv/standard_error
+
+steps:
+ run_indiv:
+ doc: |-
+ For each model file in the input model_list, run an individual
+ simulation.
+ run: tango_models.cwl
+ scatter: [model, freud_sim]
+ scatterMethod: dotproduct
+ in:
+ model:
+ source: model_list
+ valueFrom: $([self]) # wrap in singleton array
+ freud_sim:
+ source: freud_sim_list
+ cobra_solver:
+ valueFrom: "glpk"
+ community_scale:
+ valueFrom: "False"
+ culture:
+ default:
+ class: File
+ location: "pipeline/config_file/config_culture.yml"
+ format: http://edamontology.org/format_3750
+ dynamics:
+ default:
+ class: File
+ location: "pipeline/config_file/config_dynamic.yml"
+ format: http://edamontology.org/format_3750
+ solver:
+ default:
+ class: File
+ location: "pipeline/config_file/config_optim.yml"
+ format: http://edamontology.org/format_3750
+ out: [results]
+
+ plot_indiv:
+ doc: |-
+ Use the combined simulation results to generate figure plots.
+ run: tango_plots.cwl
+ in:
+ figure:
+ valueFrom: "indiv"
+ results:
+ source: flatten/flattened
+ out: [plots, standard_output, standard_error]
+
+ flatten:
+ doc: |-
+ Each individual simulation creates a separate results directory,
+ but plot_indiv expects a single directory. This step combines
+ the results into a single directory. Since a result file might
+ be generated several times by different runs, skip duplicates to
+ avoid a CWL file staging conflict.
+ run:
+ class: ExpressionTool
+ requirements:
+ InlineJavascriptRequirement: {}
+ LoadListingRequirement: { loadListing: shallow_listing }
+ inputs:
+ nested: Directory[]
+ outputs:
+ flattened: Directory
+ expression: |
+ ${
+ var flat = [];
+ for (var i = 0; i < inputs.nested.length; i++) {
+ flat =
+ flat.concat(
+ inputs.nested[i].listing.filter(
+ // This ES5.1 filtering is very ugly
+ function(item) {
+ return ! flat.find(
+ function(x) {
+ return x.basename ===
+ item.basename;
+ });
+ }));
+ }
+ return {
+ "flattened": {
+ "class": "Directory",
+ "basename": "results",
+ "listing": flat
+ }
+ };
+ }
+ in:
+ nested:
+ source: run_indiv/results
+ out: [flattened]
diff --git a/mock/data b/mock/data
new file mode 120000
index 0000000..eed2d0b
--- /dev/null
+++ b/mock/data
@@ -0,0 +1 @@
+../data/
\ No newline at end of file
diff --git a/mock/pipeline b/mock/pipeline
new file mode 120000
index 0000000..32aee15
--- /dev/null
+++ b/mock/pipeline
@@ -0,0 +1 @@
+../pipeline
\ No newline at end of file
diff --git a/mock/tango_models.cwl b/mock/tango_models.cwl
new file mode 100644
index 0000000..b40b82c
--- /dev/null
+++ b/mock/tango_models.cwl
@@ -0,0 +1,280 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+label: Numerical reconciliation of bacterial fermentation in cheese production
+doc: |-
+ TANGO uses a numerical strategy to reconcile multi-omics data and
+ metabolic networks for characterising bacterial fermentation in
+ cheese production composed of 3 species:
+ *P. freudenreichii*, *L. lactis* and *L. plantarum*
+
+requirements:
+ ShellCommandRequirement: {}
+ InlineJavascriptRequirement: {}
+ InitialWorkDirRequirement:
+ listing:
+ - $(inputs.data)
+ - $(inputs.initial_res_optim)
+ - basename: "results"
+ class: Directory
+ listing: []
+ - basename: "pipeline"
+ class: Directory
+ listing: []
+ NetworkAccess:
+ class: NetworkAccess
+ networkAccess: true
+
+hints:
+ DockerRequirement:
+ dockerImageId: tango_models
+ dockerFile: |-
+ FROM continuumio/miniconda
+ WORKDIR /usr/src/app
+ COPY ./ ./
+ RUN conda env create -f env-minimal.yml
+
+inputs:
+ cobra_solver:
+ doc: |-
+ solver used for FBA computation by Cobra
+ {glpk,glpk_exact,cplex,scipy}
+ type:
+ # - "null"
+ - type: enum
+ symbols:
+ - "glpk"
+ - "glpk_exact"
+ - "cplex"
+ - "scipy"
+ default: "glpk"
+ inputBinding:
+ position: 5
+ prefix: "-CobraSolver"
+
+ community_scale:
+ doc: |-
+ dFBA at the community scale {True,False}
+ type:
+ # - "null"
+ - type: enum
+ symbols:
+ - "True"
+ - "False"
+ default: "False"
+ inputBinding:
+ position: 5
+ prefix: "-com"
+
+ culture:
+ type: File
+ format: edam:format_3750
+ doc: |-
+ specific media and/or specif modification applied to the FBA
+ models
+ default:
+ class: File
+ location: "pipeline/config_file/config_culture.yml"
+ format: http://edamontology.org/format_3750
+ inputBinding:
+ position: 2
+ prefix: "-cp"
+
+ data:
+ type: Directory
+ doc: |-
+ Directory containing experimental data, referenced in optimize
+ configuration
+ default:
+ class: Directory
+ location: ./data
+
+ dynamics:
+ type: File
+ format: edam:format_3750
+ doc: |-
+ specific paramters for your dFBA analysis
+ default:
+ class: File
+ location: "pipeline/config_file/config_dynamic.yml"
+ format: http://edamontology.org/format_3750
+ inputBinding:
+ position: 3
+ prefix: "-dp"
+
+ freud_sim:
+ doc: |-
+ different initial conditions for lactate where defined in the
+ experiments for growth and metabolite dosage => this parameter
+ allows to switch between both situations {growth,metabolites}
+ type:
+ # - "null"
+ - type: enum
+ symbols:
+ - "growth"
+ - "metabolites"
+ default: "growth"
+ inputBinding:
+ position: 5
+ prefix: "-fsim"
+
+ lactic_acid_model:
+ doc: |-
+ lactic acid model use total if lactate represents total lactic
+ acid concentration, or dissociated if lactate represents the
+ dissociated lactic acid {total,dissociated}
+ type:
+ # - "null"
+ - type: enum
+ symbols:
+ - "total"
+ - "dissociated"
+ default: "total"
+ inputBinding:
+ position: 5
+ prefix: "-lam"
+
+ model:
+ type:
+ type: array
+ items: File
+ format: edam:format_2585
+ doc: |-
+ SBML model
+ inputBinding:
+ position: 1
+ prefix: "-mp"
+
+ optimize:
+ doc: |-
+ activatee or not the optimization on parameters {True,False}
+ type:
+ # - "null"
+ - type: enum
+ symbols:
+ - "True"
+ - "False"
+ default: "False"
+ inputBinding:
+ position: 5
+ prefix: "-optim"
+
+ recovery:
+ doc: |-
+ activate or not recovery of the optimization on parameters
+ {True,False}
+ type:
+ # - "null"
+ - type: enum
+ symbols:
+ - "True"
+ - "False"
+ default: "False"
+ inputBinding:
+ position: 6
+ prefix: "-r"
+
+ initial_res_optim:
+ type: File?
+ doc: |-
+ Per-species optimization results
+ # default:
+ # class: File
+ # location: ./res_optim.txt
+
+ solver:
+ type: File
+ format: edam:format_3750
+ doc: |-
+ configuration file for optimization
+ default:
+ class: File
+ location: "pipeline/config_file/config_optim.yml"
+ format: http://edamontology.org/format_3750
+ inputBinding:
+ position: 4
+ prefix: "-sp"
+
+ verbose:
+ doc: |-
+ active or not verbose reporting {True,False}
+ type:
+ # - "null"
+ - type: enum
+ symbols:
+ - "True"
+ - "False"
+ default: "False"
+ inputBinding:
+ position: 6
+ prefix: "-v"
+
+baseCommand:
+ - ./tango_models_mock
+ - sim
+
+outputs:
+ results:
+ type: File[]
+ outputBinding:
+ glob: "results/*.pkz"
+ outputEval: |
+ ${
+ return self.filter(function(i) { return -1 == i.basename.indexOf("_t_") })
+ }
+ doc: |
+ Pickled Pandas data frames containing simulation results
+ format: edam:format_2333
+ recovery_optimisation:
+ type: File?
+ outputBinding:
+ glob: "recover_optim*yml"
+ doc: |-
+ Pickle file of recovery optimization
+ format: edam:format_2333
+ result_optimization:
+ type: File
+ outputBinding:
+ glob: "res_optim.txt"
+ doc: |-
+ optimization results
+ format: edam:format_3475
+ standard_output:
+ type: stdout
+ format: edam:format_1964
+ standard_error:
+ type: stderr
+ format: edam:format_1964
+
+stdout: stdout.txt
+stderr: stderr.txt
+
+s:author:
+ - class: s:Person
+ s:name: Simon Labarthe
+ s:identifier: https://orcid.org/0000-0003-2114-0697
+ - class: s:Person
+ s:name: Clémence Frioux
+ s:identifier: https://orcid.org/0000-0003-2114-0697
+ - class: s:Person
+ s:name: David James Sherman
+ s:identifier: https://orcid.org/0000-0002-2316-1005
+ - class: s:Person
+ s:name: Maxime Lecomte
+ s:identifier: https://orcid.org/0000-0002-4558-6151
+ - class: s:Person
+ s:name: Hélène Falentin
+ s:identifier: https://orcid.org/0000-0001-6254-5303
+ - class: s:Person
+ s:name: Julie Aubert
+ s:identifier: https://orcid.org/0000-0001-5203-5748
+
+s:dateCreated: "2024-03-02"
+s:license: https://spdx.org/licenses/LGPL-3.0-or-later
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-http.rdf
+ - http://edamontology.org/EDAM_1.23.owl
diff --git a/mock/tango_models_mock.py b/mock/tango_models_mock.py
new file mode 100755
index 0000000..282f4d1
--- /dev/null
+++ b/mock/tango_models_mock.py
@@ -0,0 +1,84 @@
+#!/usr/bin/env python3
+
+import click
+import sys
+from pathlib import Path
+
+
+@click.command()
+@click.option(
+ "--cobra_solver", help="solver used for FBA computation by Cobra", default="glpk"
+)
+@click.option("--community_scale", help="dFBA at the community scale", default="False")
+@click.option(
+ "--freud_sim", help="different initial conditions for lactate", default="growth"
+)
+@click.option("--lactic_acid_model", help="lactic acid model", default="total")
+@click.option("--optimize", help="type: array", default="False")
+@click.option(
+ "--recovery", help="activate or not recovery of the optimization", default="False"
+)
+@click.option(
+ "--verbose", help="active or not verbose reporting {True,False}", default="False"
+)
+@click.argument(
+ "culture",
+ # help="specific media and/or specif modification",
+ type=click.File("rb"),
+ default="pipeline/config_file/config_culture.yml",
+)
+@click.argument(
+ "dynamics",
+ # help="specific paramters for your dFBA analysis",
+ type=click.File("rb"),
+ default="pipeline/config_file/config_dynamic.yml",
+)
+@click.argument(
+ "solver",
+ # help="configuration file for optimization",
+ type=click.File("rb"),
+ default="pipeline/config_file/config_optim.yml",
+)
+@click.argument(
+ "data",
+ # help="experimental data",
+ type=click.Path("rb"),
+ default="./data",
+)
+@click.argument(
+ "initial_res_optim",
+ # help="Per-species optimization results",
+ type=click.Path(exists=False),
+ default="./res_optim.txt",
+)
+@click.argument(
+ "model",
+ # help="SBML model",
+ nargs=-1,
+)
+def tango_models(
+ cobra_solver,
+ community_scale,
+ freud_sim,
+ lactic_acid_model,
+ optimize,
+ recovery,
+ verbose,
+ culture,
+ dynamics,
+ solver,
+ data,
+ initial_res_optim,
+ model,
+):
+ """Mock TANGO models."""
+ click.echo(f"TANGO")
+
+ results = Path("results/")
+ results.mkdir(parents=True, exist_ok=True)
+
+ click.echo(f'Models { ", ".join(model) }')
+
+
+if __name__ == "__main__":
+ tango_models()
diff --git a/pipeline/combine_files.cwl b/pipeline/combine_files.cwl
new file mode 100644
index 0000000..b1dc9aa
--- /dev/null
+++ b/pipeline/combine_files.cwl
@@ -0,0 +1,22 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+ InlineJavascriptRequirement: {}
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: $(inputs.name)
+ entry: ${ return inputs.file_list.map(function(f) {return f.contents}).join("") }
+inputs:
+ name: string
+ file_list:
+ type:
+ type: array
+ items: File
+ inputBinding:
+ loadContents: true
+outputs:
+ concat:
+ type: File
+ outputBinding:
+ glob: $(inputs.name)
+baseCommand: ["true"]
diff --git a/pipeline/combine_res_optim.cwl b/pipeline/combine_res_optim.cwl
new file mode 100644
index 0000000..d0f479b
--- /dev/null
+++ b/pipeline/combine_res_optim.cwl
@@ -0,0 +1,21 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+ InlineJavascriptRequirement: {}
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: res_optim.txt
+ entry: ${ return inputs.file_list.map(function(f) {return f.contents}).join("") }
+inputs:
+ file_list:
+ type:
+ type: array
+ items: File
+ inputBinding:
+ loadContents: true
+outputs:
+ concat:
+ type: File
+ outputBinding:
+ glob: "res_optim.txt"
+baseCommand: ["true"]
diff --git a/pipeline/flatten_array.cwl b/pipeline/flatten_array.cwl
new file mode 100644
index 0000000..9b701a9
--- /dev/null
+++ b/pipeline/flatten_array.cwl
@@ -0,0 +1,29 @@
+cwlVersion: v1.2
+class: ExpressionTool
+doc: "Flatten a nested array of 'Any' type into an array."
+requirements:
+ InlineJavascriptRequirement: {}
+inputs:
+ nested:
+ type:
+ type: array
+ items:
+ type: array
+ items: ["null", Any]
+outputs:
+ flattened:
+ type:
+ type: array
+ items: Any
+expression: |
+ ${
+ var flattened = [];
+ for (var i = 0; i < inputs.nested.length; i++) {
+ for (var j = 0; j < inputs.nested[i].length; j++) {
+ if (inputs.nested[i][j] != null) {
+ flattened.push(inputs.nested[i][j]);
+ }
+ }
+ }
+ return {"flattened": flattened};
+ }
diff --git a/tango_models.cwl b/tango_models.cwl
index 566fe20..54ecc16 100644
--- a/tango_models.cwl
+++ b/tango_models.cwl
@@ -21,8 +21,6 @@ requirements:
- basename: "pipeline"
class: Directory
listing: []
- # - class: File
- # location: pipeline/TANGO_MTA_WF_310320.xlsx
NetworkAccess:
class: NetworkAccess
networkAccess: true
@@ -42,7 +40,7 @@ inputs:
solver used for FBA computation by Cobra
{glpk,glpk_exact,cplex,scipy}
type:
- - "null"
+ # - "null"
- type: enum
symbols:
- "glpk"
@@ -58,7 +56,7 @@ inputs:
doc: |-
dFBA at the community scale {True,False}
type:
- - "null"
+ # - "null"
- type: enum
symbols:
- "True"
@@ -74,6 +72,10 @@ inputs:
doc: |-
specific media and/or specif modification applied to the FBA
models
+ default:
+ class: File
+ location: "pipeline/config_file/config_culture.yml"
+ format: http://edamontology.org/format_3750
inputBinding:
position: 2
prefix: "-cp"
@@ -92,6 +94,10 @@ inputs:
format: edam:format_3750
doc: |-
specific paramters for your dFBA analysis
+ default:
+ class: File
+ location: "pipeline/config_file/config_dynamic.yml"
+ format: http://edamontology.org/format_3750
inputBinding:
position: 3
prefix: "-dp"
@@ -102,7 +108,7 @@ inputs:
experiments for growth and metabolite dosage => this parameter
allows to switch between both situations {growth,metabolites}
type:
- - "null"
+ # - "null"
- type: enum
symbols:
- "growth"
@@ -118,7 +124,7 @@ inputs:
acid concentration, or dissociated if lactate represents the
dissociated lactic acid {total,dissociated}
type:
- - "null"
+ # - "null"
- type: enum
symbols:
- "total"
@@ -143,7 +149,7 @@ inputs:
doc: |-
activatee or not the optimization on parameters {True,False}
type:
- - "null"
+ # - "null"
- type: enum
symbols:
- "True"
@@ -158,7 +164,7 @@ inputs:
activate or not recovery of the optimization on parameters
{True,False}
type:
- - "null"
+ # - "null"
- type: enum
symbols:
- "True"
@@ -172,15 +178,19 @@ inputs:
type: File?
doc: |-
Per-species optimization results
- default:
- class: File
- location: ./res_optim.txt
+ # default:
+ # class: File
+ # location: ./res_optim.txt
solver:
type: File
format: edam:format_3750
doc: |-
configuration file for optimization
+ default:
+ class: File
+ location: "pipeline/config_file/config_optim.yml"
+ format: http://edamontology.org/format_3750
inputBinding:
position: 4
prefix: "-sp"
@@ -189,7 +199,7 @@ inputs:
doc: |-
active or not verbose reporting {True,False}
type:
- - "null"
+ # - "null"
- type: enum
symbols:
- "True"
@@ -205,9 +215,13 @@ baseCommand:
outputs:
results:
- type: Directory
+ type: File[]
outputBinding:
- glob: "results"
+ glob: "results/*.pkz"
+ outputEval: |
+ ${
+ return self.filter(function(i) { return -1 == i.basename.indexOf("_t_") })
+ }
doc: |
Pickled Pandas data frames containing simulation results
format: edam:format_2333
diff --git a/tango_workflow.cwl b/tango_workflow.cwl
new file mode 100644
index 0000000..81a0274
--- /dev/null
+++ b/tango_workflow.cwl
@@ -0,0 +1,148 @@
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+ MultipleInputFeatureRequirement: {}
+ StepInputExpressionRequirement: {}
+ ScatterFeatureRequirement: {}
+ InlineJavascriptRequirement: {}
+ SubworkflowFeatureRequirement: {}
+
+inputs:
+ model_list:
+ type: File[]
+ default:
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/lactis.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/plantarum.sbml"
+ format: http://edamontology.org/format_2585
+ combo_model_list:
+ type: File[]
+ default:
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/lactis.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/plantarum.sbml"
+ format: http://edamontology.org/format_2585
+ combo_freud_sim_list:
+ type: {"type": "array", "items": [{"type": "enum", "symbols": ["file:///Users/sherman/work/tango_models/tango_models.cwl#freud_sim/growth", "file:///Users/sherman/work/tango_models/tango_models.cwl#freud_sim/metabolites"]}]}
+ default:
+ - "metabolites"
+ - "growth"
+ - "growth"
+ - "growth"
+
+outputs:
+ results:
+ type: File[]
+ outputSource: [individual/results, community/results]
+ linkMerge: merge_flattened
+
+steps:
+ optimize:
+ doc: |-
+ For each model file in the input model_list, run an individual
+ optimization. Return combined result_optimization.
+ run:
+ class: Workflow
+ inputs:
+ model_list: File[]
+ outputs:
+ result_optimization:
+ type: File
+ outputSource: combine/concat
+ steps:
+ optimize_each:
+ run: tango_models.cwl
+ scatter: model
+ in:
+ model:
+ source: model_list
+ valueFrom: $([self]) # wrap in singleton array
+ optimize:
+ valueFrom: "True"
+ community_scale:
+ valueFrom: "False"
+ out: [result_optimization]
+ combine:
+ run: pipeline/combine_files.cwl
+ in:
+ name:
+ valueFrom: "res_optim.txt"
+ file_list:
+ source: optimize_each/result_optimization
+ out: [concat]
+ in:
+ model_list:
+ source: model_list
+ out: [result_optimization]
+
+ individual:
+ doc: |-
+ For each model file in the input model_list, run an individual
+ simulation.
+ run:
+ class: Workflow
+ inputs:
+ model_list: File[]
+ outputs:
+ results:
+ type: File[]
+ outputSource: combine/flattened
+ steps:
+ individual_each:
+ run: tango_models.cwl
+ scatter: [model, freud_sim]
+ scatterMethod: dotproduct
+ in:
+ model:
+ source: combo_model_list
+ valueFrom: $([self]) # wrap in singleton array
+ freud_sim:
+ source: combo_freud_sim_list
+ optimize:
+ valueFrom: "False"
+ community_scale:
+ valueFrom: "False"
+ initial_res_optim:
+ source: [optimize/result_optimization]
+ out: [results]
+ combine:
+ run: pipeline/flatten_array.cwl
+ in:
+ nested:
+ source: individual_each/results
+ out: [flattened]
+ in:
+ combo_model_list:
+ source: combo_model_list
+ combo_freud_sim_list:
+ source: combo_freud_sim_list
+ out: [results]
+
+ community:
+ doc: |-
+ Simulate the community.
+ run: tango_models.cwl
+ in:
+ model:
+ source: model_list
+ optimize:
+ valueFrom: "False"
+ community_scale:
+ valueFrom: "True"
+ initial_res_optim:
+ source: [optimize/result_optimization]
+ out: [results]
--
GitLab
From 25428824549a33ff22c086b4567a922524893eb7 Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Wed, 13 Mar 2024 17:34:57 +0100
Subject: [PATCH 05/14] tango_experiments_job.yml defines pure cultures and
communities
---
tango_dynamics_wf.cwl | 105 ++++++++++++++++++++++++++++++++++++++
tango_experiments_job.yml | 50 ++++++++++++++++++
tango_optimization_wf.cwl | 67 ++++++++++++++++++++++++
3 files changed, 222 insertions(+)
create mode 100644 tango_dynamics_wf.cwl
create mode 100644 tango_experiments_job.yml
create mode 100644 tango_optimization_wf.cwl
diff --git a/tango_dynamics_wf.cwl b/tango_dynamics_wf.cwl
new file mode 100644
index 0000000..6c9c3e3
--- /dev/null
+++ b/tango_dynamics_wf.cwl
@@ -0,0 +1,105 @@
+---
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+ MultipleInputFeatureRequirement: {}
+ StepInputExpressionRequirement: {}
+ ScatterFeatureRequirement: {}
+ InlineJavascriptRequirement: {}
+
+inputs:
+ pure_culture:
+ type:
+ type: array
+ items:
+ type: record
+ fields:
+ models: File[]
+ freud_sim: string
+ community:
+ type:
+ type: array
+ items:
+ type: record
+ fields:
+ models: File[]
+
+outputs:
+ results:
+ type: Directory
+ outputSource: combine/results
+
+doc: |-
+ For each model file in the input model_list, run an individual
+ simulation.
+
+steps:
+
+ individual_each:
+ run: "pipeline/tango_mock.cwl"
+ scatter: [model, freud_sim]
+ scatterMethod: dotproduct
+ in:
+ model:
+ source: pure_culture
+ valueFrom: $([self.models[0]]) # wrap model in singleton array
+ freud_sim:
+ source: pure_culture
+ valueFrom: $(self.freud_sim)
+ optimize:
+ valueFrom: "False"
+ community_scale:
+ valueFrom: "False"
+ out: [results]
+
+ community:
+ run: "pipeline/tango_mock.cwl"
+ scatter: model
+ in:
+ model:
+ source: community
+ valueFrom: $(self.models)
+ optimize:
+ valueFrom: "False"
+ community_scale:
+ valueFrom: "True"
+ out: [results]
+
+ combine:
+ run:
+ class: ExpressionTool
+ requirements:
+ InlineJavascriptRequirement: {}
+ MultipleInputFeatureRequirement: {}
+ LoadListingRequirement: { loadListing: shallow_listing }
+ inputs:
+ results_list:
+ type:
+ type: array
+ items:
+ type: array
+ items: File
+ outputs:
+ results: Directory
+ expression: |
+ ${
+ var flat = []
+ for (var i=0; i<inputs.results_list.length; i++) {
+ for (var j=0; j<inputs.results_list[i].length; j++) {
+ flat = flat.concat(inputs.results_list[i][j])
+ }
+ }
+ return {
+ "results": {
+ "class": "Directory",
+ "basename": "results",
+ "listing": flat
+ }
+ }
+ }
+ in:
+ results_list:
+ source: [individual_each/results, community/results]
+ linkMerge: merge_flattened
+ out: [results]
diff --git a/tango_experiments_job.yml b/tango_experiments_job.yml
new file mode 100644
index 0000000..1d593cb
--- /dev/null
+++ b/tango_experiments_job.yml
@@ -0,0 +1,50 @@
+pure_culture:
+ - models:
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ freud_sim: "metabolites"
+ - models:
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ freud_sim: "growth"
+ - models:
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ freud_sim: "growth"
+ - models:
+ - class: File
+ path: "metabolic_models/lactis.sbml"
+ format: http://edamontology.org/format_2585
+ freud_sim: "growth"
+ - models:
+ - class: File
+ path: "metabolic_models/plantarum.sbml"
+ format: http://edamontology.org/format_2585
+ freud_sim: "growth"
+
+community:
+ - models:
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/lactis.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/plantarum.sbml"
+ format: http://edamontology.org/format_2585
+ dynamics:
+ class: File
+ location: "pipeline/config_file/config_dynamic.yml"
+ format: http://edamontology.org/format_3750
+ culture:
+ class: File
+ location: "pipeline/config_file/config_culture.yml"
+ format: http://edamontology.org/format_3750
+ solver:
+ class: File
+ location: "pipeline/config_file/config_optim.yml"
+ format: http://edamontology.org/format_3750
diff --git a/tango_optimization_wf.cwl b/tango_optimization_wf.cwl
new file mode 100644
index 0000000..ec0c542
--- /dev/null
+++ b/tango_optimization_wf.cwl
@@ -0,0 +1,67 @@
+---
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+ MultipleInputFeatureRequirement: {}
+ StepInputExpressionRequirement: {}
+ ScatterFeatureRequirement: {}
+ InlineJavascriptRequirement: {}
+
+inputs:
+ pure_culture:
+ type:
+ type: array
+ items:
+ type: record
+ fields:
+ models: File[]
+ freud_sim: string
+
+outputs:
+ result_optimization:
+ type: File
+ outputSource: combine/result_optimization
+
+doc: |-
+ For each model file in the input model_list, run an individual
+ optimization. Return combined result_optimization.
+
+steps:
+
+ optimize_each:
+ run: "pipeline/tango_mock.cwl"
+ scatter: [model, freud_sim]
+ scatterMethod: dotproduct
+ in:
+ model:
+ source: pure_culture
+ valueFrom: $([self.models[0]]) # wrap model in singleton array
+ freud_sim:
+ source: pure_culture
+ valueFrom: $(self.freud_sim)
+ optimize:
+ valueFrom: "True"
+ community_scale:
+ valueFrom: "False"
+ out: [result_optimization]
+
+ combine:
+ in:
+ file_list:
+ source: optimize_each/result_optimization
+ out: [result_optimization]
+ run:
+ class: CommandLineTool
+ baseCommand: ["cat"]
+ inputs:
+ file_list:
+ type: File[]
+ inputBinding:
+ position: 1
+ outputs:
+ result_optimization:
+ type: File
+ streamable: true
+ outputBinding: {glob: "res_optim.txt"}
+ stdout: "res_optim.txt"
--
GitLab
From d9eeb341d52444cd1b99a05acf9e7f36f9db9b9f Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Mon, 18 Mar 2024 08:51:40 +0100
Subject: [PATCH 06/14] Tango workflow with plots
per-community parameters
---
pipeline/mkdir_files.cwl | 28 ++++++
tango_dynamics_wf.cwl | 62 +++++--------
tango_experiments_job.yml | 25 +++--
tango_optimization_wf.cwl | 2 +-
tango_plots.cwl | 20 ++--
tango_workflow.cwl | 186 +++++++++++++-------------------------
6 files changed, 135 insertions(+), 188 deletions(-)
create mode 100644 pipeline/mkdir_files.cwl
diff --git a/pipeline/mkdir_files.cwl b/pipeline/mkdir_files.cwl
new file mode 100644
index 0000000..b6f8da9
--- /dev/null
+++ b/pipeline/mkdir_files.cwl
@@ -0,0 +1,28 @@
+---
+cwlVersion: v1.2
+class: ExpressionTool
+requirements:
+ InlineJavascriptRequirement: {}
+ MultipleInputFeatureRequirement: {}
+ LoadListingRequirement: { loadListing: shallow_listing }
+inputs:
+ name:
+ type: string
+ default: "results"
+ file_list: File[]
+outputs:
+ results: Directory
+expression: |
+ ${
+ var flat = []
+ for (var i=0; i<inputs.file_list.length; i++) {
+ flat = flat.concat(inputs.file_list[i])
+ }
+ return {
+ "results": {
+ "class": "Directory",
+ "basename": inputs.name,
+ "listing": flat
+ }
+ }
+ }
diff --git a/tango_dynamics_wf.cwl b/tango_dynamics_wf.cwl
index 6c9c3e3..66f4624 100644
--- a/tango_dynamics_wf.cwl
+++ b/tango_dynamics_wf.cwl
@@ -9,6 +9,7 @@ requirements:
InlineJavascriptRequirement: {}
inputs:
+ initial_res_optim: File
pure_culture:
type:
type: array
@@ -24,11 +25,12 @@ inputs:
type: record
fields:
models: File[]
+
outputs:
results:
- type: Directory
- outputSource: combine/results
+ type: File[]
+ outputSource: combine/flattened
doc: |-
For each model file in the input model_list, run an individual
@@ -37,7 +39,7 @@ doc: |-
steps:
individual_each:
- run: "pipeline/tango_mock.cwl"
+ run: tango_models.cwl
scatter: [model, freud_sim]
scatterMethod: dotproduct
in:
@@ -51,11 +53,14 @@ steps:
valueFrom: "False"
community_scale:
valueFrom: "False"
+ initial_res_optim:
+ source: initial_res_optim
out: [results]
community:
- run: "pipeline/tango_mock.cwl"
- scatter: model
+ run: tango_models.cwl
+ scatter: [model, culture, dynamics, solver]
+ scatterMethod: dotproduct
in:
model:
source: community
@@ -64,42 +69,23 @@ steps:
valueFrom: "False"
community_scale:
valueFrom: "True"
+ initial_res_optim:
+ source: initial_res_optim
+ culture:
+ source: community
+ valueFrom: $(self.culture || null)
+ dynamics:
+ source: community
+ valueFrom: $(self.dynamics || null)
+ solver:
+ source: community
+ valueFrom: $(self.solver || null)
out: [results]
combine:
- run:
- class: ExpressionTool
- requirements:
- InlineJavascriptRequirement: {}
- MultipleInputFeatureRequirement: {}
- LoadListingRequirement: { loadListing: shallow_listing }
- inputs:
- results_list:
- type:
- type: array
- items:
- type: array
- items: File
- outputs:
- results: Directory
- expression: |
- ${
- var flat = []
- for (var i=0; i<inputs.results_list.length; i++) {
- for (var j=0; j<inputs.results_list[i].length; j++) {
- flat = flat.concat(inputs.results_list[i][j])
- }
- }
- return {
- "results": {
- "class": "Directory",
- "basename": "results",
- "listing": flat
- }
- }
- }
+ run: pipeline/flatten_array.cwl
in:
- results_list:
+ nested:
source: [individual_each/results, community/results]
linkMerge: merge_flattened
- out: [results]
+ out: [flattened]
diff --git a/tango_experiments_job.yml b/tango_experiments_job.yml
index 1d593cb..150e9b5 100644
--- a/tango_experiments_job.yml
+++ b/tango_experiments_job.yml
@@ -9,11 +9,6 @@ pure_culture:
path: "metabolic_models/freudenreichii.sbml"
format: http://edamontology.org/format_2585
freud_sim: "growth"
- - models:
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- freud_sim: "growth"
- models:
- class: File
path: "metabolic_models/lactis.sbml"
@@ -38,13 +33,15 @@ community:
format: http://edamontology.org/format_2585
dynamics:
class: File
- location: "pipeline/config_file/config_dynamic.yml"
- format: http://edamontology.org/format_3750
- culture:
- class: File
- location: "pipeline/config_file/config_culture.yml"
- format: http://edamontology.org/format_3750
- solver:
- class: File
- location: "pipeline/config_file/config_optim.yml"
+ location: "pipeline/config_file/config_dynamic_com.yml"
format: http://edamontology.org/format_3750
+
+figures: ["com", "flux"]
+
+initial_res_optim:
+ class: File
+ location: ./res_optim.txt
+
+models_dir:
+ class: Directory
+ location: ./models
diff --git a/tango_optimization_wf.cwl b/tango_optimization_wf.cwl
index ec0c542..3af2e68 100644
--- a/tango_optimization_wf.cwl
+++ b/tango_optimization_wf.cwl
@@ -30,7 +30,7 @@ doc: |-
steps:
optimize_each:
- run: "pipeline/tango_mock.cwl"
+ run: tango_models.cwl
scatter: [model, freud_sim]
scatterMethod: dotproduct
in:
diff --git a/tango_plots.cwl b/tango_plots.cwl
index 592c4c8..ca4179a 100644
--- a/tango_plots.cwl
+++ b/tango_plots.cwl
@@ -34,16 +34,16 @@ inputs:
doc: |-
Which predefined figure to make
{indiv,flux,com,goodness_of_fit,switch_pathways}
- type:
- - "null"
- - type: enum
- symbols:
- - "com"
- - "flux"
- - "goodness_of_fit"
- - "indiv"
- - "switch_pathways"
- - "transcripts"
+ type: string
+ # - "null"
+ # - type: enum
+ # symbols:
+ # - "com"
+ # - "flux"
+ # - "goodness_of_fit"
+ # - "indiv"
+ # - "switch_pathways"
+ # - "transcripts"
default: "indiv"
models:
diff --git a/tango_workflow.cwl b/tango_workflow.cwl
index 81a0274..ee5d386 100644
--- a/tango_workflow.cwl
+++ b/tango_workflow.cwl
@@ -9,140 +9,76 @@ requirements:
SubworkflowFeatureRequirement: {}
inputs:
- model_list:
- type: File[]
- default:
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/lactis.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/plantarum.sbml"
- format: http://edamontology.org/format_2585
- combo_model_list:
- type: File[]
- default:
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/lactis.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/plantarum.sbml"
- format: http://edamontology.org/format_2585
- combo_freud_sim_list:
- type: {"type": "array", "items": [{"type": "enum", "symbols": ["file:///Users/sherman/work/tango_models/tango_models.cwl#freud_sim/growth", "file:///Users/sherman/work/tango_models/tango_models.cwl#freud_sim/metabolites"]}]}
- default:
- - "metabolites"
- - "growth"
- - "growth"
- - "growth"
+ # Choose experiments to include in simulations
+ pure_culture:
+ type:
+ type: array
+ items:
+ type: record
+ fields:
+ models: File[]
+ freud_sim: string
+ community:
+ type:
+ type: array
+ items:
+ type: record
+ fields:
+ models: File[]
+
+ # Choose plots to make from silumation results
+ figures: string[]
+ models_dir: Directory
outputs:
results:
+ type: Directory
+ outputSource: combine/results
+ figures:
type: File[]
- outputSource: [individual/results, community/results]
- linkMerge: merge_flattened
+ outputSource: flatten/flattened
steps:
optimize:
- doc: |-
- For each model file in the input model_list, run an individual
- optimization. Return combined result_optimization.
- run:
- class: Workflow
- inputs:
- model_list: File[]
- outputs:
- result_optimization:
- type: File
- outputSource: combine/concat
- steps:
- optimize_each:
- run: tango_models.cwl
- scatter: model
- in:
- model:
- source: model_list
- valueFrom: $([self]) # wrap in singleton array
- optimize:
- valueFrom: "True"
- community_scale:
- valueFrom: "False"
- out: [result_optimization]
- combine:
- run: pipeline/combine_files.cwl
- in:
- name:
- valueFrom: "res_optim.txt"
- file_list:
- source: optimize_each/result_optimization
- out: [concat]
in:
- model_list:
- source: model_list
+ pure_culture:
+ source: pure_culture
out: [result_optimization]
-
- individual:
- doc: |-
- For each model file in the input model_list, run an individual
- simulation.
- run:
- class: Workflow
- inputs:
- model_list: File[]
- outputs:
- results:
- type: File[]
- outputSource: combine/flattened
- steps:
- individual_each:
- run: tango_models.cwl
- scatter: [model, freud_sim]
- scatterMethod: dotproduct
- in:
- model:
- source: combo_model_list
- valueFrom: $([self]) # wrap in singleton array
- freud_sim:
- source: combo_freud_sim_list
- optimize:
- valueFrom: "False"
- community_scale:
- valueFrom: "False"
- initial_res_optim:
- source: [optimize/result_optimization]
- out: [results]
- combine:
- run: pipeline/flatten_array.cwl
- in:
- nested:
- source: individual_each/results
- out: [flattened]
- in:
- combo_model_list:
- source: combo_model_list
- combo_freud_sim_list:
- source: combo_freud_sim_list
- out: [results]
-
- community:
- doc: |-
- Simulate the community.
- run: tango_models.cwl
+ run: tango_optimization_wf.cwl
+
+ dynamics:
in:
- model:
- source: model_list
- optimize:
- valueFrom: "False"
- community_scale:
- valueFrom: "True"
initial_res_optim:
- source: [optimize/result_optimization]
+ source: optimize/result_optimization
+ pure_culture:
+ source: pure_culture
+ community:
+ source: community
out: [results]
+ run: tango_dynamics_wf.cwl
+
+ combine:
+ in:
+ file_list:
+ source: dynamics/results
+ out: [results]
+ run: pipeline/mkdir_files.cwl
+
+ figures:
+ scatter: [figure]
+ in:
+ results:
+ source: combine/results
+ figure:
+ source: figures
+ models:
+ source: models_dir
+ out: [plots]
+ run: tango_plots.cwl
+
+ flatten:
+ in:
+ nested:
+ source: figures/plots
+ out: [flattened]
+ run: pipeline/flatten_array.cwl
--
GitLab
From a87be0ba287322e0827ea8fd1d02810dcd92d955 Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Tue, 26 Mar 2024 08:39:10 +0100
Subject: [PATCH 07/14] Working, array outputs
---
scripts/plot_com.py | 2 +-
tango_dynamics_wf.cwl | 1 -
tango_experiments+types_job.yml | 46 +++++++++++++++++++++++++++++++++
tango_experiments_job.yml | 2 +-
tango_models.cwl | 4 ++-
tango_plots.cwl | 25 +++++++++++-------
tango_workflow.cwl | 27 +++++++++----------
7 files changed, 81 insertions(+), 26 deletions(-)
create mode 100644 tango_experiments+types_job.yml
diff --git a/scripts/plot_com.py b/scripts/plot_com.py
index 40c0afe..52b3e28 100644
--- a/scripts/plot_com.py
+++ b/scripts/plot_com.py
@@ -19,7 +19,7 @@ def get_data_com():
results_w = pd.DataFrame(results_w,columns=[param['Y_output_id_inv'][i] for i in range(results_w.shape[1])])
simulation = pd.read_csv('results/result_dfba_com_without_optim.csv',sep='\t').set_index('State')
- time_o = pd.read_csv('pipeline/com_time.tsv',sep='\t').set_index('State')
+ time_o = pd.read_csv('data/com_time.tsv',sep='\t').set_index('State')
time = time_o.loc[simulation.index]
diff --git a/tango_dynamics_wf.cwl b/tango_dynamics_wf.cwl
index 66f4624..3bbae37 100644
--- a/tango_dynamics_wf.cwl
+++ b/tango_dynamics_wf.cwl
@@ -25,7 +25,6 @@ inputs:
type: record
fields:
models: File[]
-
outputs:
results:
diff --git a/tango_experiments+types_job.yml b/tango_experiments+types_job.yml
new file mode 100644
index 0000000..bb64016
--- /dev/null
+++ b/tango_experiments+types_job.yml
@@ -0,0 +1,46 @@
+pure_culture:
+ - models:
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ freud_sim: "metabolites"
+ - models:
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ freud_sim: "growth"
+ - models:
+ - class: File
+ path: "metabolic_models/lactis.sbml"
+ format: http://edamontology.org/format_2585
+ freud_sim: "growth"
+ - models:
+ - class: File
+ path: "metabolic_models/plantarum.sbml"
+ format: http://edamontology.org/format_2585
+ freud_sim: "growth"
+
+community:
+ - models:
+ - class: File
+ path: "metabolic_models/freudenreichii.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/lactis.sbml"
+ format: http://edamontology.org/format_2585
+ - class: File
+ path: "metabolic_models/plantarum.sbml"
+ format: http://edamontology.org/format_2585
+
+dynamics:
+ class: File
+ location: "pipeline/config_file/config_dynamic.yml"
+ format: http://edamontology.org/format_3750
+culture:
+ class: File
+ location: "pipeline/config_file/config_culture.yml"
+ format: http://edamontology.org/format_3750
+solver:
+ class: File
+ location: "pipeline/config_file/config_optim.yml"
+ format: http://edamontology.org/format_3750
diff --git a/tango_experiments_job.yml b/tango_experiments_job.yml
index 150e9b5..18d83c4 100644
--- a/tango_experiments_job.yml
+++ b/tango_experiments_job.yml
@@ -36,7 +36,7 @@ community:
location: "pipeline/config_file/config_dynamic_com.yml"
format: http://edamontology.org/format_3750
-figures: ["com", "flux"]
+which_figures: ["com", "flux"]
initial_res_optim:
class: File
diff --git a/tango_models.cwl b/tango_models.cwl
index 54ecc16..a282e9a 100644
--- a/tango_models.cwl
+++ b/tango_models.cwl
@@ -217,7 +217,9 @@ outputs:
results:
type: File[]
outputBinding:
- glob: "results/*.pkz"
+ glob:
+ - "results/*.pkz"
+ - "results/*.csv"
outputEval: |
${
return self.filter(function(i) { return -1 == i.basename.indexOf("_t_") })
diff --git a/tango_plots.cwl b/tango_plots.cwl
index ca4179a..f846fa0 100644
--- a/tango_plots.cwl
+++ b/tango_plots.cwl
@@ -10,12 +10,22 @@ requirements:
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
listing:
- - $(inputs.scripts)
- - $(inputs.data)
- - entry: $(inputs.results)
- entryname: results
+ - entry: $(inputs.scripts)
+ entryname: scripts
+ - entry: $(inputs.data)
+ entryname: data
- entry: $(inputs.models)
entryname: metabolic_models
+ - |
+ ${
+ return {
+ "class": "Directory",
+ "basename": "results",
+ "listing": inputs.results
+ }
+ }
+
+ # LoadListingRequirement: { loadListing: shallow_listing }
NetworkAccess:
class: NetworkAccess
networkAccess: true
@@ -53,12 +63,9 @@ inputs:
configuration
results:
- type: Directory
+ type: File[]
doc: |-
- Directory containing TANGO results
- default:
- class: Directory
- location: ./results
+ Array of TANGO result files
scripts:
type: Directory
diff --git a/tango_workflow.cwl b/tango_workflow.cwl
index ee5d386..7fccfd4 100644
--- a/tango_workflow.cwl
+++ b/tango_workflow.cwl
@@ -27,13 +27,13 @@ inputs:
models: File[]
# Choose plots to make from silumation results
- figures: string[]
+ which_figures: string[]
models_dir: Directory
outputs:
results:
- type: Directory
- outputSource: combine/results
+ type: File[]
+ outputSource: dynamics/results
figures:
type: File[]
outputSource: flatten/flattened
@@ -57,20 +57,21 @@ steps:
out: [results]
run: tango_dynamics_wf.cwl
- combine:
- in:
- file_list:
- source: dynamics/results
- out: [results]
- run: pipeline/mkdir_files.cwl
+ # combine:
+ # in:
+ # file_list:
+ # source: dynamics/results
+ # out: [results]
+ # run: pipeline/mkdir_files.cwl
- figures:
+ plot_figures:
scatter: [figure]
in:
results:
- source: combine/results
+ source: dynamics/results
+ # source: combine/results
figure:
- source: figures
+ source: which_figures
models:
source: models_dir
out: [plots]
@@ -79,6 +80,6 @@ steps:
flatten:
in:
nested:
- source: figures/plots
+ source: plot_figures/plots
out: [flattened]
run: pipeline/flatten_array.cwl
--
GitLab
From e5e0d36482e1a375be4c5e5449d2cedf3e750477 Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Tue, 26 Mar 2024 08:40:40 +0100
Subject: [PATCH 08/14] plot jobs
tango_plots is scatter workflow that calls tango_one_plot
Call plot scripts using module
Use tango_plots for scatter. Combine outputs into directories
---
pipeline/mkdir_files.cwl | 2 +-
plot_transcripts_job.yml | 7 ++
tango_one_plot.cwl | 119 +++++++++++++++++++++++++++++
tango_plots.cwl | 159 ++++++++-------------------------------
tango_workflow.cwl | 46 +++++------
5 files changed, 184 insertions(+), 149 deletions(-)
create mode 100644 plot_transcripts_job.yml
create mode 100644 tango_one_plot.cwl
diff --git a/pipeline/mkdir_files.cwl b/pipeline/mkdir_files.cwl
index b6f8da9..7a9e0c5 100644
--- a/pipeline/mkdir_files.cwl
+++ b/pipeline/mkdir_files.cwl
@@ -11,7 +11,7 @@ inputs:
default: "results"
file_list: File[]
outputs:
- results: Directory
+ out_dir: Directory
expression: |
${
var flat = []
diff --git a/plot_transcripts_job.yml b/plot_transcripts_job.yml
new file mode 100644
index 0000000..fba36c6
--- /dev/null
+++ b/plot_transcripts_job.yml
@@ -0,0 +1,7 @@
+figure: "transcripts"
+results:
+ class: Directory
+ path: "./results"
+models:
+ class: Directory
+ path: "./metabolic_models"
diff --git a/tango_one_plot.cwl b/tango_one_plot.cwl
new file mode 100644
index 0000000..2de3440
--- /dev/null
+++ b/tango_one_plot.cwl
@@ -0,0 +1,119 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+label: Plot TANGO results
+doc: |-
+ Use plot_* scripts to make figures from TANGO results
+
+requirements:
+ ShellCommandRequirement: {}
+ InlineJavascriptRequirement: {}
+ InitialWorkDirRequirement:
+ listing:
+ - entry: $(inputs.scripts)
+ entryname: scripts
+ - entry: $(inputs.data)
+ entryname: data
+ - entry: $(inputs.models)
+ entryname: metabolic_models
+ - entry: $(inputs.results)
+ entryname: results
+ NetworkAccess:
+ class: NetworkAccess
+ networkAccess: true
+
+inputs:
+ data:
+ type: Directory
+ doc: |-
+ Directory containing experimental data, referenced in optimize
+ configuration
+ default:
+ class: Directory
+ location: ./data
+
+ figure:
+ doc: |-
+ Which predefined figure to make
+ {indiv,flux,com,goodness_of_fit,switch_pathways}
+ type: string
+ default: "indiv"
+
+ models:
+ type: Directory?
+ doc: |-
+ Directory containing experimental data, referenced in optimize
+ configuration
+
+ results:
+ # type: File[]
+ type: Directory
+ doc: |-
+ Array of TANGO result files
+
+ scripts:
+ type: Directory
+ doc: |-
+ Scripts for predefined figures
+ default:
+ class: Directory
+ location: ./scripts
+
+baseCommand:
+ - python
+ - "-m"
+
+arguments:
+ - valueFrom: $("scripts.plot_" + inputs.figure)
+
+outputs:
+ plots:
+ type:
+ type: array
+ items: File
+ outputBinding:
+ glob:
+ - "*.pdf"
+ - "*.svg"
+ doc: |-
+ Figure in PDF format
+ format: edam:format_3508
+ standard_output:
+ type: stdout
+ format: edam:format_1964
+ standard_error:
+ type: stderr
+ format: edam:format_1964
+
+stdout: stdout.txt
+stderr: stderr.txt
+
+s:author:
+ - class: s:Person
+ s:name: Simon Labarthe
+ s:identifier: https://orcid.org/0000-0003-2114-0697
+ - class: s:Person
+ s:name: Clémence Frioux
+ s:identifier: https://orcid.org/0000-0003-2114-0697
+ - class: s:Person
+ s:name: David James Sherman
+ s:identifier: https://orcid.org/0000-0002-2316-1005
+ - class: s:Person
+ s:name: Maxime Lecomte
+ s:identifier: https://orcid.org/0000-0002-4558-6151
+ - class: s:Person
+ s:name: Hélène Falentin
+ s:identifier: https://orcid.org/0000-0001-6254-5303
+ - class: s:Person
+ s:name: Julie Aubert
+ s:identifier: https://orcid.org/0000-0001-5203-5748
+
+s:dateCreated: "2024-03-04"
+s:license: https://spdx.org/licenses/LGPL-3.0-or-later
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-http.rdf
+ - http://edamontology.org/EDAM_1.23.owl
diff --git a/tango_plots.cwl b/tango_plots.cwl
index f846fa0..d0ed96b 100644
--- a/tango_plots.cwl
+++ b/tango_plots.cwl
@@ -1,134 +1,39 @@
cwlVersion: v1.2
-class: CommandLineTool
-
-label: Plot TANGO results
-doc: |-
- Use plot_* scripts to make figures from TANGO results
+class: Workflow
requirements:
- ShellCommandRequirement: {}
+ MultipleInputFeatureRequirement: {}
+ StepInputExpressionRequirement: {}
+ ScatterFeatureRequirement: {}
InlineJavascriptRequirement: {}
- InitialWorkDirRequirement:
- listing:
- - entry: $(inputs.scripts)
- entryname: scripts
- - entry: $(inputs.data)
- entryname: data
- - entry: $(inputs.models)
- entryname: metabolic_models
- - |
- ${
- return {
- "class": "Directory",
- "basename": "results",
- "listing": inputs.results
- }
- }
-
- # LoadListingRequirement: { loadListing: shallow_listing }
- NetworkAccess:
- class: NetworkAccess
- networkAccess: true
+ SubworkflowFeatureRequirement: {}
inputs:
- data:
- type: Directory
- doc: |-
- Directory containing experimental data, referenced in optimize
- configuration
- default:
- class: Directory
- location: ./data
-
- figure:
- doc: |-
- Which predefined figure to make
- {indiv,flux,com,goodness_of_fit,switch_pathways}
- type: string
- # - "null"
- # - type: enum
- # symbols:
- # - "com"
- # - "flux"
- # - "goodness_of_fit"
- # - "indiv"
- # - "switch_pathways"
- # - "transcripts"
- default: "indiv"
-
- models:
- type: Directory?
- doc: |-
- Directory containing experimental data, referenced in optimize
- configuration
-
- results:
- type: File[]
- doc: |-
- Array of TANGO result files
-
- scripts:
- type: Directory
- doc: |-
- Scripts for predefined figures
- default:
- class: Directory
- location: ./scripts
-
-baseCommand:
- - python
-
-arguments:
- - valueFrom: $("scripts/plot_" + inputs.figure + ".py")
-
+ results: Directory
+ which_figures: string[]
+ models: Directory
+
outputs:
- plots:
- type:
- type: array
- items: File
- outputBinding:
- glob:
- - "*.pdf"
- - "*.svg"
- doc: |-
- Figure in PDF format
- format: edam:format_3508
- standard_output:
- type: stdout
- format: edam:format_1964
- standard_error:
- type: stderr
- format: edam:format_1964
-
-stdout: stdout.txt
-stderr: stderr.txt
-
-s:author:
- - class: s:Person
- s:name: Simon Labarthe
- s:identifier: https://orcid.org/0000-0003-2114-0697
- - class: s:Person
- s:name: Clémence Frioux
- s:identifier: https://orcid.org/0000-0003-2114-0697
- - class: s:Person
- s:name: David James Sherman
- s:identifier: https://orcid.org/0000-0002-2316-1005
- - class: s:Person
- s:name: Maxime Lecomte
- s:identifier: https://orcid.org/0000-0002-4558-6151
- - class: s:Person
- s:name: Hélène Falentin
- s:identifier: https://orcid.org/0000-0001-6254-5303
- - class: s:Person
- s:name: Julie Aubert
- s:identifier: https://orcid.org/0000-0001-5203-5748
-
-s:dateCreated: "2024-03-04"
-s:license: https://spdx.org/licenses/LGPL-3.0-or-later
-
-$namespaces:
- s: https://schema.org/
- edam: http://edamontology.org/
-$schemas:
- - https://schema.org/version/latest/schemaorg-current-http.rdf
- - http://edamontology.org/EDAM_1.23.owl
+ figures:
+ type: File[]
+ outputSource: flatten/flattened
+
+steps:
+ plot_figures:
+ scatter: [figure]
+ in:
+ results:
+ source: results
+ figure:
+ source: which_figures
+ models:
+ source: models
+ out: [plots]
+ run: tango_one_plot.cwl
+
+ flatten:
+ in:
+ nested:
+ source: plot_figures/plots
+ out: [flattened]
+ run: pipeline/flatten_array.cwl
diff --git a/tango_workflow.cwl b/tango_workflow.cwl
index 7fccfd4..55584d8 100644
--- a/tango_workflow.cwl
+++ b/tango_workflow.cwl
@@ -26,17 +26,19 @@ inputs:
fields:
models: File[]
- # Choose plots to make from silumation results
+ # Choose plots to make from simulation results
which_figures: string[]
+
+ # Transcripts plot need input SBML models
models_dir: Directory
outputs:
results:
- type: File[]
- outputSource: dynamics/results
+ type: Directory
+ outputSource: mkdir_results/out_dir
figures:
- type: File[]
- outputSource: flatten/flattened
+ type: Directory
+ outputSource: mkdir_figures/out_dir
steps:
optimize:
@@ -57,29 +59,31 @@ steps:
out: [results]
run: tango_dynamics_wf.cwl
- # combine:
- # in:
- # file_list:
- # source: dynamics/results
- # out: [results]
- # run: pipeline/mkdir_files.cwl
+ mkdir_results:
+ in:
+ file_list:
+ source: dynamics/results
+ name:
+ valueFrom: "results"
+ out: [out_dir]
+ run: pipeline/mkdir_files.cwl
plot_figures:
- scatter: [figure]
in:
results:
- source: dynamics/results
- # source: combine/results
- figure:
+ source: mkdir_results/out_dir
+ which_figures:
source: which_figures
models:
source: models_dir
- out: [plots]
+ out: [figures]
run: tango_plots.cwl
- flatten:
+ mkdir_figures:
in:
- nested:
- source: plot_figures/plots
- out: [flattened]
- run: pipeline/flatten_array.cwl
+ file_list:
+ source: plot_figures/figures
+ name:
+ valueFrom: "figures"
+ out: [out_dir]
+ run: pipeline/mkdir_files.cwl
--
GitLab
From 9f2212583a9f1a1506b654641df454ad72d911e0 Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Tue, 26 Mar 2024 16:29:10 +0100
Subject: [PATCH 09/14] Make figures
.gitignore figures
---
.gitignore | 1 +
tango_experiments_job.yml | 8 +++++++-
tango_plots_job.yml | 13 +++++++++++++
3 files changed, 21 insertions(+), 1 deletion(-)
create mode 100644 tango_plots_job.yml
diff --git a/.gitignore b/.gitignore
index abb4b30..5c480d1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,6 +13,7 @@ commandline*
/result*
/pipeline/dfba_trajectory*.png
/pipeline/result_pure_culture*.csv
+/figures
ro-crate
diff --git a/tango_experiments_job.yml b/tango_experiments_job.yml
index 18d83c4..f26459d 100644
--- a/tango_experiments_job.yml
+++ b/tango_experiments_job.yml
@@ -36,7 +36,13 @@ community:
location: "pipeline/config_file/config_dynamic_com.yml"
format: http://edamontology.org/format_3750
-which_figures: ["com", "flux"]
+which_figures:
+ - com
+ - flux
+ - indiv
+ - goodness_of_fit
+ # - switch_pathways
+ - transcripts
initial_res_optim:
class: File
diff --git a/tango_plots_job.yml b/tango_plots_job.yml
new file mode 100644
index 0000000..be08f30
--- /dev/null
+++ b/tango_plots_job.yml
@@ -0,0 +1,13 @@
+results:
+ class: Directory
+ location: ./results
+models:
+ class: Directory
+ location: ./metabolic_models
+which_figures:
+ - com
+ - flux
+ - indiv
+ - goodness_of_fit
+ # - switch_pathways
+ - transcripts
--
GitLab
From 07f1d452c7918938722837c439d80b31895c6f69 Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Tue, 26 Mar 2024 17:18:17 +0100
Subject: [PATCH 10/14] Shuttle time-series results to plot_switch_pathway
Output of mkdir_files is "out_dir"
---
pipeline/mkdir_files.cwl | 6 +++++-
tango_dynamics_wf.cwl | 17 ++++++++++++++---
tango_experiments_job.yml | 2 +-
tango_models.cwl | 12 ++++++++++++
tango_plots.cwl | 15 ++++++++++++---
tango_plots_job.yml | 17 ++++++++++++++---
tango_workflow.cwl | 5 +++--
7 files changed, 61 insertions(+), 13 deletions(-)
diff --git a/pipeline/mkdir_files.cwl b/pipeline/mkdir_files.cwl
index 7a9e0c5..2c8738a 100644
--- a/pipeline/mkdir_files.cwl
+++ b/pipeline/mkdir_files.cwl
@@ -1,17 +1,21 @@
---
cwlVersion: v1.2
class: ExpressionTool
+
requirements:
InlineJavascriptRequirement: {}
MultipleInputFeatureRequirement: {}
LoadListingRequirement: { loadListing: shallow_listing }
+
inputs:
name:
type: string
default: "results"
file_list: File[]
+
outputs:
out_dir: Directory
+
expression: |
${
var flat = []
@@ -19,7 +23,7 @@ expression: |
flat = flat.concat(inputs.file_list[i])
}
return {
- "results": {
+ "out_dir": {
"class": "Directory",
"basename": inputs.name,
"listing": flat
diff --git a/tango_dynamics_wf.cwl b/tango_dynamics_wf.cwl
index 3bbae37..d829bef 100644
--- a/tango_dynamics_wf.cwl
+++ b/tango_dynamics_wf.cwl
@@ -30,6 +30,9 @@ outputs:
results:
type: File[]
outputSource: combine/flattened
+ time_series:
+ type: File[]
+ outputSource: combine_time_series/flattened
doc: |-
For each model file in the input model_list, run an individual
@@ -54,9 +57,9 @@ steps:
valueFrom: "False"
initial_res_optim:
source: initial_res_optim
- out: [results]
+ out: [results, time_series]
- community:
+ community_together:
run: tango_models.cwl
scatter: [model, culture, dynamics, solver]
scatterMethod: dotproduct
@@ -85,6 +88,14 @@ steps:
run: pipeline/flatten_array.cwl
in:
nested:
- source: [individual_each/results, community/results]
+ source: [individual_each/results, community_together/results]
+ linkMerge: merge_flattened
+ out: [flattened]
+
+ combine_time_series:
+ run: pipeline/flatten_array.cwl
+ in:
+ nested:
+ source: [individual_each/time_series]
linkMerge: merge_flattened
out: [flattened]
diff --git a/tango_experiments_job.yml b/tango_experiments_job.yml
index f26459d..0ecad9f 100644
--- a/tango_experiments_job.yml
+++ b/tango_experiments_job.yml
@@ -41,7 +41,7 @@ which_figures:
- flux
- indiv
- goodness_of_fit
- # - switch_pathways
+ - switch_pathways
- transcripts
initial_res_optim:
diff --git a/tango_models.cwl b/tango_models.cwl
index a282e9a..46100c4 100644
--- a/tango_models.cwl
+++ b/tango_models.cwl
@@ -247,6 +247,18 @@ outputs:
standard_error:
type: stderr
format: edam:format_1964
+ time_series:
+ type: File[]
+ outputBinding:
+ glob:
+ - "results/*.pkz"
+ outputEval: |
+ ${
+ return self.filter(function(i) { return -1 != i.basename.indexOf("_t_") })
+ }
+ doc: |
+ Pickled Pandas data frames containing time series of simulation results
+ format: edam:format_2333
stdout: stdout.txt
stderr: stderr.txt
diff --git a/tango_plots.cwl b/tango_plots.cwl
index d0ed96b..c3f2911 100644
--- a/tango_plots.cwl
+++ b/tango_plots.cwl
@@ -9,7 +9,7 @@ requirements:
SubworkflowFeatureRequirement: {}
inputs:
- results: Directory
+ results: File[]
which_figures: string[]
models: Directory
@@ -18,12 +18,21 @@ outputs:
type: File[]
outputSource: flatten/flattened
-steps:
+steps:
+ prepare:
+ in:
+ file_list:
+ source: results
+ name:
+ valueFrom: "results"
+ out: [out_dir]
+ run: pipeline/mkdir_files.cwl
+
plot_figures:
scatter: [figure]
in:
results:
- source: results
+ source: prepare/out_dir
figure:
source: which_figures
models:
diff --git a/tango_plots_job.yml b/tango_plots_job.yml
index be08f30..bcbb122 100644
--- a/tango_plots_job.yml
+++ b/tango_plots_job.yml
@@ -1,6 +1,17 @@
results:
- class: Directory
- location: ./results
+ - class: File
+ path: "results/result_community_model_whole.pkz"
+ - class: File
+ path: "results/result_dfba_com_without_optim.csv"
+ - class: File
+ path: "results/result_pure_culture_model_freudenreichii_growth.pkz"
+ - class: File
+ path: "results/result_pure_culture_model_freudenreichii_metabolites.pkz"
+ - class: File
+ path: "results/result_pure_culture_model_lactis.pkz"
+ - class: File
+ path: "results/result_pure_culture_model_plantarum.pkz"
+
models:
class: Directory
location: ./metabolic_models
@@ -9,5 +20,5 @@ which_figures:
- flux
- indiv
- goodness_of_fit
- # - switch_pathways
+ - switch_pathways
- transcripts
diff --git a/tango_workflow.cwl b/tango_workflow.cwl
index 55584d8..d82f655 100644
--- a/tango_workflow.cwl
+++ b/tango_workflow.cwl
@@ -56,7 +56,7 @@ steps:
source: pure_culture
community:
source: community
- out: [results]
+ out: [results, time_series]
run: tango_dynamics_wf.cwl
mkdir_results:
@@ -71,7 +71,8 @@ steps:
plot_figures:
in:
results:
- source: mkdir_results/out_dir
+ source: [dynamics/results, dynamics/time_series]
+ linkMerge: merge_flattened
which_figures:
source: which_figures
models:
--
GitLab
From 60e47a6185944c49d5148cbc5057833de578d97d Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Mon, 22 Apr 2024 14:36:48 +0200
Subject: [PATCH 11/14] ExpressionTool mkdir_files: skip files with duplicate
basename
Correct location models_dir
---
pipeline/mkdir_files.cwl | 12 +++++++++++-
tango_experiments_job.yml | 2 +-
2 files changed, 12 insertions(+), 2 deletions(-)
diff --git a/pipeline/mkdir_files.cwl b/pipeline/mkdir_files.cwl
index 2c8738a..d0e1bf8 100644
--- a/pipeline/mkdir_files.cwl
+++ b/pipeline/mkdir_files.cwl
@@ -2,6 +2,11 @@
cwlVersion: v1.2
class: ExpressionTool
+doc: |
+ Combine an array of Files into a single named directory. If
+ files with duplicate basenames are provided, only the first
+ one is included, whether or not their contents are the same.
+
requirements:
InlineJavascriptRequirement: {}
MultipleInputFeatureRequirement: {}
@@ -19,8 +24,13 @@ outputs:
expression: |
${
var flat = []
+ var seen = {}
for (var i=0; i<inputs.file_list.length; i++) {
- flat = flat.concat(inputs.file_list[i])
+ var key = inputs.file_list[i].basename
+ if (!seen.hasOwnProperty(key)) {
+ flat = flat.concat(inputs.file_list[i])
+ }
+ seen[key] = true
}
return {
"out_dir": {
diff --git a/tango_experiments_job.yml b/tango_experiments_job.yml
index 0ecad9f..0736985 100644
--- a/tango_experiments_job.yml
+++ b/tango_experiments_job.yml
@@ -50,4 +50,4 @@ initial_res_optim:
models_dir:
class: Directory
- location: ./models
+ location: ./metabolic_models
--
GitLab
From 749650b18e30d4d3b8731521d404c7d37f4c4fc1 Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Mon, 22 Apr 2024 15:09:08 +0200
Subject: [PATCH 12/14] Cleanup: move CWL tools to pipeline/
Default location for data/
---
figures_monoculture.cwl | 118 ---------------
figures_monoculture_inline.cwl | 138 ------------------
figures_monoculture_job.yml | 18 ---
indiv_freud_job.yml | 18 ---
.../tango_dynamics_wf.cwl | 4 +-
tango_models.cwl => pipeline/tango_models.cwl | 8 +-
.../tango_one_plot.cwl | 4 +-
.../tango_optimization_wf.cwl | 0
tango_plots.cwl => pipeline/tango_plots.cwl | 4 +-
tango_experiments+types_job.yml | 46 ------
tango_plots_job.yml | 24 ---
tango_workflow.cwl | 6 +-
12 files changed, 13 insertions(+), 375 deletions(-)
delete mode 100644 figures_monoculture.cwl
delete mode 100644 figures_monoculture_inline.cwl
delete mode 100644 figures_monoculture_job.yml
delete mode 100644 indiv_freud_job.yml
rename tango_dynamics_wf.cwl => pipeline/tango_dynamics_wf.cwl (96%)
rename tango_models.cwl => pipeline/tango_models.cwl (97%)
rename tango_one_plot.cwl => pipeline/tango_one_plot.cwl (98%)
rename tango_optimization_wf.cwl => pipeline/tango_optimization_wf.cwl (100%)
rename tango_plots.cwl => pipeline/tango_plots.cwl (92%)
delete mode 100644 tango_experiments+types_job.yml
delete mode 100644 tango_plots_job.yml
diff --git a/figures_monoculture.cwl b/figures_monoculture.cwl
deleted file mode 100644
index 8cb6018..0000000
--- a/figures_monoculture.cwl
+++ /dev/null
@@ -1,118 +0,0 @@
-cwlVersion: v1.2
-class: Workflow
-
-requirements:
- MultipleInputFeatureRequirement: {}
- StepInputExpressionRequirement: {}
- ScatterFeatureRequirement: {}
- InlineJavascriptRequirement: {}
-
-inputs:
- model_list: File[]
- freud_sim_list: string[]
-
-outputs:
- scattered_results:
- type: Directory
- outputSource: flatten/flattened
- plots:
- type: File[]
- outputSource:
- - plot_indiv/plots
- # standard_output:
- # type: File
- # outputSource: plot_indiv/standard_output
- # standard_error:
- # type: File
- # outputSource: plot_indiv/standard_error
-
-steps:
- run_indiv:
- doc: |-
- For each model file in the input model_list, run an individual
- simulation.
- run: tango_models.cwl
- scatter: [model, freud_sim]
- scatterMethod: dotproduct
- in:
- model:
- source: model_list
- valueFrom: $([self]) # wrap in singleton array
- freud_sim:
- source: freud_sim_list
- cobra_solver:
- valueFrom: "glpk"
- community_scale:
- valueFrom: "False"
- culture:
- default:
- class: File
- location: "pipeline/config_file/config_culture.yml"
- format: http://edamontology.org/format_3750
- dynamics:
- default:
- class: File
- location: "pipeline/config_file/config_dynamic.yml"
- format: http://edamontology.org/format_3750
- solver:
- default:
- class: File
- location: "pipeline/config_file/config_optim.yml"
- format: http://edamontology.org/format_3750
- out: [results]
-
- plot_indiv:
- doc: |-
- Use the combined simulation results to generate figure plots.
- run: tango_plots.cwl
- in:
- figure:
- valueFrom: "indiv"
- results:
- source: flatten/flattened
- out: [plots, standard_output, standard_error]
-
- flatten:
- doc: |-
- Each individual simulation creates a separate results directory,
- but plot_indiv expects a single directory. This step combines
- the results into a single directory. Since a result file might
- be generated several times by different runs, skip duplicates to
- avoid a CWL file staging conflict.
- run:
- class: ExpressionTool
- requirements:
- InlineJavascriptRequirement: {}
- LoadListingRequirement: { loadListing: shallow_listing }
- inputs:
- nested: Directory[]
- outputs:
- flattened: Directory
- expression: |
- ${
- var flat = [];
- for (var i = 0; i < inputs.nested.length; i++) {
- flat =
- flat.concat(
- inputs.nested[i].listing.filter(
- // This ES5.1 filtering is very ugly
- function(item) {
- return ! flat.find(
- function(x) {
- return x.basename ===
- item.basename;
- });
- }));
- }
- return {
- "flattened": {
- "class": "Directory",
- "basename": "results",
- "listing": flat
- }
- };
- }
- in:
- nested:
- source: run_indiv/results
- out: [flattened]
diff --git a/figures_monoculture_inline.cwl b/figures_monoculture_inline.cwl
deleted file mode 100644
index 38fd4ba..0000000
--- a/figures_monoculture_inline.cwl
+++ /dev/null
@@ -1,138 +0,0 @@
-cwlVersion: v1.2
-class: Workflow
-
-requirements:
- MultipleInputFeatureRequirement: {}
- StepInputExpressionRequirement: {}
- ScatterFeatureRequirement: {}
- InlineJavascriptRequirement: {}
-
-inputs:
- model_list:
- type: File[]
- default:
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/lactis.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/plantarum.sbml"
- format: http://edamontology.org/format_2585
- freud_sim_list:
- type: string[]
- default:
- - "metabolites"
- - "growth"
- - "growth"
- - "growth"
-
-outputs:
- scattered_results:
- type: Directory
- outputSource: flatten/flattened
- plots:
- type: File[]
- outputSource:
- - plot_indiv/plots
- # standard_output:
- # type: File
- # outputSource: plot_indiv/standard_output
- # standard_error:
- # type: File
- # outputSource: plot_indiv/standard_error
-
-steps:
- run_indiv:
- doc: |-
- For each model file in the input model_list, run an individual
- simulation.
- run: tango_models.cwl
- scatter: [model, freud_sim]
- scatterMethod: dotproduct
- in:
- model:
- source: model_list
- valueFrom: $([self]) # wrap in singleton array
- freud_sim:
- source: freud_sim_list
- cobra_solver:
- valueFrom: "glpk"
- community_scale:
- valueFrom: "False"
- culture:
- default:
- class: File
- location: "pipeline/config_file/config_culture.yml"
- format: http://edamontology.org/format_3750
- dynamics:
- default:
- class: File
- location: "pipeline/config_file/config_dynamic.yml"
- format: http://edamontology.org/format_3750
- solver:
- default:
- class: File
- location: "pipeline/config_file/config_optim.yml"
- format: http://edamontology.org/format_3750
- out: [results]
-
- plot_indiv:
- doc: |-
- Use the combined simulation results to generate figure plots.
- run: tango_plots.cwl
- in:
- figure:
- valueFrom: "indiv"
- results:
- source: flatten/flattened
- out: [plots, standard_output, standard_error]
-
- flatten:
- doc: |-
- Each individual simulation creates a separate results directory,
- but plot_indiv expects a single directory. This step combines
- the results into a single directory. Since a result file might
- be generated several times by different runs, skip duplicates to
- avoid a CWL file staging conflict.
- run:
- class: ExpressionTool
- requirements:
- InlineJavascriptRequirement: {}
- LoadListingRequirement: { loadListing: shallow_listing }
- inputs:
- nested: Directory[]
- outputs:
- flattened: Directory
- expression: |
- ${
- var flat = [];
- for (var i = 0; i < inputs.nested.length; i++) {
- flat =
- flat.concat(
- inputs.nested[i].listing.filter(
- // This ES5.1 filtering is very ugly
- function(item) {
- return ! flat.find(
- function(x) {
- return x.basename ===
- item.basename;
- });
- }));
- }
- return {
- "flattened": {
- "class": "Directory",
- "basename": "results",
- "listing": flat
- }
- };
- }
- in:
- nested:
- source: run_indiv/results
- out: [flattened]
diff --git a/figures_monoculture_job.yml b/figures_monoculture_job.yml
deleted file mode 100644
index 44c2101..0000000
--- a/figures_monoculture_job.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-model_list:
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/lactis.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/plantarum.sbml"
- format: http://edamontology.org/format_2585
-freud_sim_list:
- - "growth"
- - "metabolites"
- - "growth"
- - "growth"
diff --git a/indiv_freud_job.yml b/indiv_freud_job.yml
deleted file mode 100644
index 0dd70b6..0000000
--- a/indiv_freud_job.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-cobra_solver: "glpk"
-community_scale: "False"
-culture:
- class: File
- path: "pipeline/config_file/config_culture.yml"
- format: http://edamontology.org/format_3750
-dynamics:
- class: File
- path: "pipeline/config_file/config_dynamic.yml"
- format: http://edamontology.org/format_3750
-model:
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
-solver:
- class: File
- path: "pipeline/config_file/config_optim.yml"
- format: http://edamontology.org/format_3750
diff --git a/tango_dynamics_wf.cwl b/pipeline/tango_dynamics_wf.cwl
similarity index 96%
rename from tango_dynamics_wf.cwl
rename to pipeline/tango_dynamics_wf.cwl
index d829bef..0b7a050 100644
--- a/tango_dynamics_wf.cwl
+++ b/pipeline/tango_dynamics_wf.cwl
@@ -85,7 +85,7 @@ steps:
out: [results]
combine:
- run: pipeline/flatten_array.cwl
+ run: flatten_array.cwl
in:
nested:
source: [individual_each/results, community_together/results]
@@ -93,7 +93,7 @@ steps:
out: [flattened]
combine_time_series:
- run: pipeline/flatten_array.cwl
+ run: flatten_array.cwl
in:
nested:
source: [individual_each/time_series]
diff --git a/tango_models.cwl b/pipeline/tango_models.cwl
similarity index 97%
rename from tango_models.cwl
rename to pipeline/tango_models.cwl
index 46100c4..20be795 100644
--- a/tango_models.cwl
+++ b/pipeline/tango_models.cwl
@@ -74,7 +74,7 @@ inputs:
models
default:
class: File
- location: "pipeline/config_file/config_culture.yml"
+ location: "config_file/config_culture.yml"
format: http://edamontology.org/format_3750
inputBinding:
position: 2
@@ -87,7 +87,7 @@ inputs:
configuration
default:
class: Directory
- location: ./data
+ location: ../data
dynamics:
type: File
@@ -96,7 +96,7 @@ inputs:
specific paramters for your dFBA analysis
default:
class: File
- location: "pipeline/config_file/config_dynamic.yml"
+ location: "config_file/config_dynamic.yml"
format: http://edamontology.org/format_3750
inputBinding:
position: 3
@@ -189,7 +189,7 @@ inputs:
configuration file for optimization
default:
class: File
- location: "pipeline/config_file/config_optim.yml"
+ location: "config_file/config_optim.yml"
format: http://edamontology.org/format_3750
inputBinding:
position: 4
diff --git a/tango_one_plot.cwl b/pipeline/tango_one_plot.cwl
similarity index 98%
rename from tango_one_plot.cwl
rename to pipeline/tango_one_plot.cwl
index 2de3440..135d9aa 100644
--- a/tango_one_plot.cwl
+++ b/pipeline/tango_one_plot.cwl
@@ -30,7 +30,7 @@ inputs:
configuration
default:
class: Directory
- location: ./data
+ location: ../data
figure:
doc: |-
@@ -57,7 +57,7 @@ inputs:
Scripts for predefined figures
default:
class: Directory
- location: ./scripts
+ location: ../scripts
baseCommand:
- python
diff --git a/tango_optimization_wf.cwl b/pipeline/tango_optimization_wf.cwl
similarity index 100%
rename from tango_optimization_wf.cwl
rename to pipeline/tango_optimization_wf.cwl
diff --git a/tango_plots.cwl b/pipeline/tango_plots.cwl
similarity index 92%
rename from tango_plots.cwl
rename to pipeline/tango_plots.cwl
index c3f2911..2bdd2d4 100644
--- a/tango_plots.cwl
+++ b/pipeline/tango_plots.cwl
@@ -26,7 +26,7 @@ steps:
name:
valueFrom: "results"
out: [out_dir]
- run: pipeline/mkdir_files.cwl
+ run: mkdir_files.cwl
plot_figures:
scatter: [figure]
@@ -45,4 +45,4 @@ steps:
nested:
source: plot_figures/plots
out: [flattened]
- run: pipeline/flatten_array.cwl
+ run: flatten_array.cwl
diff --git a/tango_experiments+types_job.yml b/tango_experiments+types_job.yml
deleted file mode 100644
index bb64016..0000000
--- a/tango_experiments+types_job.yml
+++ /dev/null
@@ -1,46 +0,0 @@
-pure_culture:
- - models:
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- freud_sim: "metabolites"
- - models:
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- freud_sim: "growth"
- - models:
- - class: File
- path: "metabolic_models/lactis.sbml"
- format: http://edamontology.org/format_2585
- freud_sim: "growth"
- - models:
- - class: File
- path: "metabolic_models/plantarum.sbml"
- format: http://edamontology.org/format_2585
- freud_sim: "growth"
-
-community:
- - models:
- - class: File
- path: "metabolic_models/freudenreichii.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/lactis.sbml"
- format: http://edamontology.org/format_2585
- - class: File
- path: "metabolic_models/plantarum.sbml"
- format: http://edamontology.org/format_2585
-
-dynamics:
- class: File
- location: "pipeline/config_file/config_dynamic.yml"
- format: http://edamontology.org/format_3750
-culture:
- class: File
- location: "pipeline/config_file/config_culture.yml"
- format: http://edamontology.org/format_3750
-solver:
- class: File
- location: "pipeline/config_file/config_optim.yml"
- format: http://edamontology.org/format_3750
diff --git a/tango_plots_job.yml b/tango_plots_job.yml
deleted file mode 100644
index bcbb122..0000000
--- a/tango_plots_job.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-results:
- - class: File
- path: "results/result_community_model_whole.pkz"
- - class: File
- path: "results/result_dfba_com_without_optim.csv"
- - class: File
- path: "results/result_pure_culture_model_freudenreichii_growth.pkz"
- - class: File
- path: "results/result_pure_culture_model_freudenreichii_metabolites.pkz"
- - class: File
- path: "results/result_pure_culture_model_lactis.pkz"
- - class: File
- path: "results/result_pure_culture_model_plantarum.pkz"
-
-models:
- class: Directory
- location: ./metabolic_models
-which_figures:
- - com
- - flux
- - indiv
- - goodness_of_fit
- - switch_pathways
- - transcripts
diff --git a/tango_workflow.cwl b/tango_workflow.cwl
index d82f655..5c6d864 100644
--- a/tango_workflow.cwl
+++ b/tango_workflow.cwl
@@ -46,7 +46,7 @@ steps:
pure_culture:
source: pure_culture
out: [result_optimization]
- run: tango_optimization_wf.cwl
+ run: pipeline/tango_optimization_wf.cwl
dynamics:
in:
@@ -57,7 +57,7 @@ steps:
community:
source: community
out: [results, time_series]
- run: tango_dynamics_wf.cwl
+ run: pipeline/tango_dynamics_wf.cwl
mkdir_results:
in:
@@ -78,7 +78,7 @@ steps:
models:
source: models_dir
out: [figures]
- run: tango_plots.cwl
+ run: pipeline/tango_plots.cwl
mkdir_figures:
in:
--
GitLab
From 04e9ab8511370946e2f183bf094422b857203b54 Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Tue, 23 Apr 2024 16:11:08 +0200
Subject: [PATCH 13/14] Also record time series from community simulation
---
pipeline/tango_dynamics_wf.cwl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/pipeline/tango_dynamics_wf.cwl b/pipeline/tango_dynamics_wf.cwl
index 0b7a050..ff10800 100644
--- a/pipeline/tango_dynamics_wf.cwl
+++ b/pipeline/tango_dynamics_wf.cwl
@@ -82,7 +82,7 @@ steps:
solver:
source: community
valueFrom: $(self.solver || null)
- out: [results]
+ out: [results, time_series]
combine:
run: flatten_array.cwl
@@ -96,6 +96,6 @@ steps:
run: flatten_array.cwl
in:
nested:
- source: [individual_each/time_series]
+ source: [individual_each/time_series, community_together/time_series]
linkMerge: merge_flattened
out: [flattened]
--
GitLab
From 1956c35ed5c2247f8d086299d79ea345ed4eb57d Mon Sep 17 00:00:00 2001
From: David James Sherman <david.sherman@inria.fr>
Date: Wed, 24 Apr 2024 08:50:40 +0200
Subject: [PATCH 14/14] Cleanup and improve documentation
---
mock/data | 1 -
mock/pipeline | 1 -
mock/tango_models.cwl | 280 -----------------------------
mock/tango_models_mock.py | 84 ---------
pipeline/combine_files.cwl | 22 ---
pipeline/combine_res_optim.cwl | 21 ---
pipeline/flatten_array.cwl | 9 +-
pipeline/tango_dynamics_wf.cwl | 4 +-
pipeline/tango_models.cwl | 9 +-
pipeline/tango_one_plot.cwl | 2 +-
pipeline/tango_optimization_wf.cwl | 3 +-
pipeline/tango_plots.cwl | 4 +
tango_workflow.cwl | 44 +++++
13 files changed, 68 insertions(+), 416 deletions(-)
delete mode 120000 mock/data
delete mode 120000 mock/pipeline
delete mode 100644 mock/tango_models.cwl
delete mode 100755 mock/tango_models_mock.py
delete mode 100644 pipeline/combine_files.cwl
delete mode 100644 pipeline/combine_res_optim.cwl
diff --git a/mock/data b/mock/data
deleted file mode 120000
index eed2d0b..0000000
--- a/mock/data
+++ /dev/null
@@ -1 +0,0 @@
-../data/
\ No newline at end of file
diff --git a/mock/pipeline b/mock/pipeline
deleted file mode 120000
index 32aee15..0000000
--- a/mock/pipeline
+++ /dev/null
@@ -1 +0,0 @@
-../pipeline
\ No newline at end of file
diff --git a/mock/tango_models.cwl b/mock/tango_models.cwl
deleted file mode 100644
index b40b82c..0000000
--- a/mock/tango_models.cwl
+++ /dev/null
@@ -1,280 +0,0 @@
-cwlVersion: v1.2
-class: CommandLineTool
-
-label: Numerical reconciliation of bacterial fermentation in cheese production
-doc: |-
- TANGO uses a numerical strategy to reconcile multi-omics data and
- metabolic networks for characterising bacterial fermentation in
- cheese production composed of 3 species:
- *P. freudenreichii*, *L. lactis* and *L. plantarum*
-
-requirements:
- ShellCommandRequirement: {}
- InlineJavascriptRequirement: {}
- InitialWorkDirRequirement:
- listing:
- - $(inputs.data)
- - $(inputs.initial_res_optim)
- - basename: "results"
- class: Directory
- listing: []
- - basename: "pipeline"
- class: Directory
- listing: []
- NetworkAccess:
- class: NetworkAccess
- networkAccess: true
-
-hints:
- DockerRequirement:
- dockerImageId: tango_models
- dockerFile: |-
- FROM continuumio/miniconda
- WORKDIR /usr/src/app
- COPY ./ ./
- RUN conda env create -f env-minimal.yml
-
-inputs:
- cobra_solver:
- doc: |-
- solver used for FBA computation by Cobra
- {glpk,glpk_exact,cplex,scipy}
- type:
- # - "null"
- - type: enum
- symbols:
- - "glpk"
- - "glpk_exact"
- - "cplex"
- - "scipy"
- default: "glpk"
- inputBinding:
- position: 5
- prefix: "-CobraSolver"
-
- community_scale:
- doc: |-
- dFBA at the community scale {True,False}
- type:
- # - "null"
- - type: enum
- symbols:
- - "True"
- - "False"
- default: "False"
- inputBinding:
- position: 5
- prefix: "-com"
-
- culture:
- type: File
- format: edam:format_3750
- doc: |-
- specific media and/or specif modification applied to the FBA
- models
- default:
- class: File
- location: "pipeline/config_file/config_culture.yml"
- format: http://edamontology.org/format_3750
- inputBinding:
- position: 2
- prefix: "-cp"
-
- data:
- type: Directory
- doc: |-
- Directory containing experimental data, referenced in optimize
- configuration
- default:
- class: Directory
- location: ./data
-
- dynamics:
- type: File
- format: edam:format_3750
- doc: |-
- specific paramters for your dFBA analysis
- default:
- class: File
- location: "pipeline/config_file/config_dynamic.yml"
- format: http://edamontology.org/format_3750
- inputBinding:
- position: 3
- prefix: "-dp"
-
- freud_sim:
- doc: |-
- different initial conditions for lactate where defined in the
- experiments for growth and metabolite dosage => this parameter
- allows to switch between both situations {growth,metabolites}
- type:
- # - "null"
- - type: enum
- symbols:
- - "growth"
- - "metabolites"
- default: "growth"
- inputBinding:
- position: 5
- prefix: "-fsim"
-
- lactic_acid_model:
- doc: |-
- lactic acid model use total if lactate represents total lactic
- acid concentration, or dissociated if lactate represents the
- dissociated lactic acid {total,dissociated}
- type:
- # - "null"
- - type: enum
- symbols:
- - "total"
- - "dissociated"
- default: "total"
- inputBinding:
- position: 5
- prefix: "-lam"
-
- model:
- type:
- type: array
- items: File
- format: edam:format_2585
- doc: |-
- SBML model
- inputBinding:
- position: 1
- prefix: "-mp"
-
- optimize:
- doc: |-
- activatee or not the optimization on parameters {True,False}
- type:
- # - "null"
- - type: enum
- symbols:
- - "True"
- - "False"
- default: "False"
- inputBinding:
- position: 5
- prefix: "-optim"
-
- recovery:
- doc: |-
- activate or not recovery of the optimization on parameters
- {True,False}
- type:
- # - "null"
- - type: enum
- symbols:
- - "True"
- - "False"
- default: "False"
- inputBinding:
- position: 6
- prefix: "-r"
-
- initial_res_optim:
- type: File?
- doc: |-
- Per-species optimization results
- # default:
- # class: File
- # location: ./res_optim.txt
-
- solver:
- type: File
- format: edam:format_3750
- doc: |-
- configuration file for optimization
- default:
- class: File
- location: "pipeline/config_file/config_optim.yml"
- format: http://edamontology.org/format_3750
- inputBinding:
- position: 4
- prefix: "-sp"
-
- verbose:
- doc: |-
- active or not verbose reporting {True,False}
- type:
- # - "null"
- - type: enum
- symbols:
- - "True"
- - "False"
- default: "False"
- inputBinding:
- position: 6
- prefix: "-v"
-
-baseCommand:
- - ./tango_models_mock
- - sim
-
-outputs:
- results:
- type: File[]
- outputBinding:
- glob: "results/*.pkz"
- outputEval: |
- ${
- return self.filter(function(i) { return -1 == i.basename.indexOf("_t_") })
- }
- doc: |
- Pickled Pandas data frames containing simulation results
- format: edam:format_2333
- recovery_optimisation:
- type: File?
- outputBinding:
- glob: "recover_optim*yml"
- doc: |-
- Pickle file of recovery optimization
- format: edam:format_2333
- result_optimization:
- type: File
- outputBinding:
- glob: "res_optim.txt"
- doc: |-
- optimization results
- format: edam:format_3475
- standard_output:
- type: stdout
- format: edam:format_1964
- standard_error:
- type: stderr
- format: edam:format_1964
-
-stdout: stdout.txt
-stderr: stderr.txt
-
-s:author:
- - class: s:Person
- s:name: Simon Labarthe
- s:identifier: https://orcid.org/0000-0003-2114-0697
- - class: s:Person
- s:name: Clémence Frioux
- s:identifier: https://orcid.org/0000-0003-2114-0697
- - class: s:Person
- s:name: David James Sherman
- s:identifier: https://orcid.org/0000-0002-2316-1005
- - class: s:Person
- s:name: Maxime Lecomte
- s:identifier: https://orcid.org/0000-0002-4558-6151
- - class: s:Person
- s:name: Hélène Falentin
- s:identifier: https://orcid.org/0000-0001-6254-5303
- - class: s:Person
- s:name: Julie Aubert
- s:identifier: https://orcid.org/0000-0001-5203-5748
-
-s:dateCreated: "2024-03-02"
-s:license: https://spdx.org/licenses/LGPL-3.0-or-later
-
-$namespaces:
- s: https://schema.org/
- edam: http://edamontology.org/
-$schemas:
- - https://schema.org/version/latest/schemaorg-current-http.rdf
- - http://edamontology.org/EDAM_1.23.owl
diff --git a/mock/tango_models_mock.py b/mock/tango_models_mock.py
deleted file mode 100755
index 282f4d1..0000000
--- a/mock/tango_models_mock.py
+++ /dev/null
@@ -1,84 +0,0 @@
-#!/usr/bin/env python3
-
-import click
-import sys
-from pathlib import Path
-
-
-@click.command()
-@click.option(
- "--cobra_solver", help="solver used for FBA computation by Cobra", default="glpk"
-)
-@click.option("--community_scale", help="dFBA at the community scale", default="False")
-@click.option(
- "--freud_sim", help="different initial conditions for lactate", default="growth"
-)
-@click.option("--lactic_acid_model", help="lactic acid model", default="total")
-@click.option("--optimize", help="type: array", default="False")
-@click.option(
- "--recovery", help="activate or not recovery of the optimization", default="False"
-)
-@click.option(
- "--verbose", help="active or not verbose reporting {True,False}", default="False"
-)
-@click.argument(
- "culture",
- # help="specific media and/or specif modification",
- type=click.File("rb"),
- default="pipeline/config_file/config_culture.yml",
-)
-@click.argument(
- "dynamics",
- # help="specific paramters for your dFBA analysis",
- type=click.File("rb"),
- default="pipeline/config_file/config_dynamic.yml",
-)
-@click.argument(
- "solver",
- # help="configuration file for optimization",
- type=click.File("rb"),
- default="pipeline/config_file/config_optim.yml",
-)
-@click.argument(
- "data",
- # help="experimental data",
- type=click.Path("rb"),
- default="./data",
-)
-@click.argument(
- "initial_res_optim",
- # help="Per-species optimization results",
- type=click.Path(exists=False),
- default="./res_optim.txt",
-)
-@click.argument(
- "model",
- # help="SBML model",
- nargs=-1,
-)
-def tango_models(
- cobra_solver,
- community_scale,
- freud_sim,
- lactic_acid_model,
- optimize,
- recovery,
- verbose,
- culture,
- dynamics,
- solver,
- data,
- initial_res_optim,
- model,
-):
- """Mock TANGO models."""
- click.echo(f"TANGO")
-
- results = Path("results/")
- results.mkdir(parents=True, exist_ok=True)
-
- click.echo(f'Models { ", ".join(model) }')
-
-
-if __name__ == "__main__":
- tango_models()
diff --git a/pipeline/combine_files.cwl b/pipeline/combine_files.cwl
deleted file mode 100644
index b1dc9aa..0000000
--- a/pipeline/combine_files.cwl
+++ /dev/null
@@ -1,22 +0,0 @@
-cwlVersion: v1.2
-class: CommandLineTool
-requirements:
- InlineJavascriptRequirement: {}
- InitialWorkDirRequirement:
- listing:
- - entryname: $(inputs.name)
- entry: ${ return inputs.file_list.map(function(f) {return f.contents}).join("") }
-inputs:
- name: string
- file_list:
- type:
- type: array
- items: File
- inputBinding:
- loadContents: true
-outputs:
- concat:
- type: File
- outputBinding:
- glob: $(inputs.name)
-baseCommand: ["true"]
diff --git a/pipeline/combine_res_optim.cwl b/pipeline/combine_res_optim.cwl
deleted file mode 100644
index d0f479b..0000000
--- a/pipeline/combine_res_optim.cwl
+++ /dev/null
@@ -1,21 +0,0 @@
-cwlVersion: v1.2
-class: CommandLineTool
-requirements:
- InlineJavascriptRequirement: {}
- InitialWorkDirRequirement:
- listing:
- - entryname: res_optim.txt
- entry: ${ return inputs.file_list.map(function(f) {return f.contents}).join("") }
-inputs:
- file_list:
- type:
- type: array
- items: File
- inputBinding:
- loadContents: true
-outputs:
- concat:
- type: File
- outputBinding:
- glob: "res_optim.txt"
-baseCommand: ["true"]
diff --git a/pipeline/flatten_array.cwl b/pipeline/flatten_array.cwl
index 9b701a9..b70bf55 100644
--- a/pipeline/flatten_array.cwl
+++ b/pipeline/flatten_array.cwl
@@ -1,8 +1,13 @@
+---
cwlVersion: v1.2
class: ExpressionTool
-doc: "Flatten a nested array of 'Any' type into an array."
+
+doc: |
+ Flatten a nested array of 'Any' type into an array.
+
requirements:
InlineJavascriptRequirement: {}
+
inputs:
nested:
type:
@@ -10,11 +15,13 @@ inputs:
items:
type: array
items: ["null", Any]
+
outputs:
flattened:
type:
type: array
items: Any
+
expression: |
${
var flattened = [];
diff --git a/pipeline/tango_dynamics_wf.cwl b/pipeline/tango_dynamics_wf.cwl
index ff10800..c1694f4 100644
--- a/pipeline/tango_dynamics_wf.cwl
+++ b/pipeline/tango_dynamics_wf.cwl
@@ -36,7 +36,9 @@ outputs:
doc: |-
For each model file in the input model_list, run an individual
- simulation.
+ simulation. For each collection of models into a community, run
+ a community simulation. Return both summary and time series
+ simulation results.
steps:
diff --git a/pipeline/tango_models.cwl b/pipeline/tango_models.cwl
index 20be795..1fdaf43 100644
--- a/pipeline/tango_models.cwl
+++ b/pipeline/tango_models.cwl
@@ -6,7 +6,7 @@ doc: |-
TANGO uses a numerical strategy to reconcile multi-omics data and
metabolic networks for characterising bacterial fermentation in
cheese production composed of 3 species:
- *P. freudenreichii*, *L. lactis* and *L. plantarum*
+ *P. freudenreichii*, *L. lactis* and *L. plantarum*.
requirements:
ShellCommandRequirement: {}
@@ -282,9 +282,12 @@ s:author:
- class: s:Person
s:name: Julie Aubert
s:identifier: https://orcid.org/0000-0001-5203-5748
-
-s:dateCreated: "2024-03-02"
+
+s:citation: https://doi.org/10.1016/j.ymben.2024.02.014
+s:codeRepository: https://forgemia.inra.fr/tango/tango_models.git
s:license: https://spdx.org/licenses/LGPL-3.0-or-later
+s:programmingLanguage: Python
+s:dateCreated: "2024-03-02"
$namespaces:
s: https://schema.org/
diff --git a/pipeline/tango_one_plot.cwl b/pipeline/tango_one_plot.cwl
index 135d9aa..7a77c21 100644
--- a/pipeline/tango_one_plot.cwl
+++ b/pipeline/tango_one_plot.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
label: Plot TANGO results
doc: |-
- Use plot_* scripts to make figures from TANGO results
+ Use plot_* scripts to make figures from TANGO results.
requirements:
ShellCommandRequirement: {}
diff --git a/pipeline/tango_optimization_wf.cwl b/pipeline/tango_optimization_wf.cwl
index 3af2e68..d2e2856 100644
--- a/pipeline/tango_optimization_wf.cwl
+++ b/pipeline/tango_optimization_wf.cwl
@@ -25,7 +25,8 @@ outputs:
doc: |-
For each model file in the input model_list, run an individual
- optimization. Return combined result_optimization.
+ optimization to obtain lambda, k_lactate, vmax_lactose parameters
+ as each model requires. Return a combined result_optimization.
steps:
diff --git a/pipeline/tango_plots.cwl b/pipeline/tango_plots.cwl
index 2bdd2d4..3208be1 100644
--- a/pipeline/tango_plots.cwl
+++ b/pipeline/tango_plots.cwl
@@ -1,6 +1,10 @@
cwlVersion: v1.2
class: Workflow
+label: Plot TANGO results
+doc: |-
+ Assemble all figures requested by which_figures.
+
requirements:
MultipleInputFeatureRequirement: {}
StepInputExpressionRequirement: {}
diff --git a/tango_workflow.cwl b/tango_workflow.cwl
index 5c6d864..fc5527b 100644
--- a/tango_workflow.cwl
+++ b/tango_workflow.cwl
@@ -1,6 +1,17 @@
cwlVersion: v1.2
class: Workflow
+label: Numerical reconciliation of bacterial fermentation in cheese production
+doc: |-
+ Complete workflow for TANGO as reported in Lecomte et al (2024),
+ "Revealing the dynamics and mechanisms of bacterial interactions in
+ cheese production with metabolic modelling", Metabolic Eng. 83:24-38
+ https://doi.org/10.1016/j.ymben.2024.02.014
+
+ 1. Parameters for individual models are obtained by optimization
+ 2. Individual dynamics and community dynamics are simulated
+ 3. Figures for the manuscript are assembled from the results.
+
requirements:
MultipleInputFeatureRequirement: {}
StepInputExpressionRequirement: {}
@@ -88,3 +99,36 @@ steps:
valueFrom: "figures"
out: [out_dir]
run: pipeline/mkdir_files.cwl
+
+s:author:
+ - class: s:Person
+ s:name: Simon Labarthe
+ s:identifier: https://orcid.org/0000-0003-2114-0697
+ - class: s:Person
+ s:name: Clémence Frioux
+ s:identifier: https://orcid.org/0000-0003-2114-0697
+ - class: s:Person
+ s:name: David James Sherman
+ s:identifier: https://orcid.org/0000-0002-2316-1005
+ - class: s:Person
+ s:name: Maxime Lecomte
+ s:identifier: https://orcid.org/0000-0002-4558-6151
+ - class: s:Person
+ s:name: Hélène Falentin
+ s:identifier: https://orcid.org/0000-0001-6254-5303
+ - class: s:Person
+ s:name: Julie Aubert
+ s:identifier: https://orcid.org/0000-0001-5203-5748
+
+s:citation: https://doi.org/10.1016/j.ymben.2024.02.014
+s:codeRepository: https://forgemia.inra.fr/tango/tango_models.git
+s:license: https://spdx.org/licenses/LGPL-3.0-or-later
+s:programmingLanguage: Python
+s:dateCreated: "2024-03-02"
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-http.rdf
+ - http://edamontology.org/EDAM_1.23.owl
--
GitLab