Commit 96253754 authored by Kersten Breuer's avatar Kersten Breuer

Merge branch 'development' into 'cwl-workflow'

# Conflicts:
#   CWL/tools/01_validate_data.cwl
#   CWL/tools/04_filter_features.cwl
#   CWL/tools/06_normalize_features.cwl
#   CWL/tools/07_add_metadata_as_predictor.cwl
#   CWL/tools/08_split_data.cwl
#   CWL/tools/09_train_models.cwl
#   CWL/tools/10_make_predictions.cwl
#   CWL/tools/11_evaluate_predictions.cwl
#   CWL/tools/12_interprete_model.cwl
#   CWL/workflows/siamcat_workflow.cwl
#   Rscript_flavor/00_setup.r
parents c6f9095b f0cf540b
......@@ -31,10 +31,11 @@ arguments:
prefix: '--label_out'
valueFrom: $(inputs.label_in.nameroot)_valid.tsv
- position: 2
prefix: '--metadata_out'
valueFrom: |
${
if (inputs.metadata_in){
return [ "--metadata_out", inputs.metadata_in.nameroot + "_valid.tsv" ];
return inputs.metadata_in.nameroot + "_valid.tsv";
} else {
return null;
}
......
......@@ -23,17 +23,17 @@ inputs:
prefix: --cutoff
position: 2
rm_unmapped:
type: boolean?
doc: TRUE or FALSE is allowed
type: string?
inputBinding:
prefix: --rm_unmapped
position: 2
valueFrom: $(self.toString())
recomp_prop:
type: boolean?
doc: TRUE or FALSE is allowed
type: string?
inputBinding:
prefix: --recomp_prop
position: 2
valueFrom: $(self.toString())
arguments:
- prefix: --feat_out
......
......@@ -28,28 +28,28 @@ inputs:
prefix: --sd_min_quantile
position: 2
norm_sample:
type: boolean?
doc: TRUE or FALSE is allowed
type: string?
inputBinding:
prefix: --norm_sample
position: 2
valueFrom: $(self.toString())
norm_global:
type: boolean?
doc: TRUE or FALSE is allowed
type: string?
inputBinding:
prefix: --norm_global
position: 2
valueFrom: $(self.toString())
vector_norm:
type: int?
inputBinding:
prefix: --vector_norm
position: 2
norm_feature:
type: boolean?
doc: TRUE or FALSE is allowed
type: string?
inputBinding:
prefix: --norm_feature
position: 2
valueFrom: $(self.toString())
arguments:
- position: 3
......@@ -64,7 +64,7 @@ outputs:
type: File
outputBinding:
glob: $(inputs.feat_in.nameroot)_norm.tsv
normalization_parameters_out:
type: File
normalization_parameters:
type: File?
outputBinding:
glob: $(inputs.feat_in.nameroot)_normParam.txt
......@@ -23,11 +23,11 @@ inputs:
prefix: --pred_names
position: 2
std_meta:
type: boolean?
doc: TRUE or FALSE is allowed
type: string?
inputBinding:
prefix: --std_meta
position: 3
valueFrom: $(self.toString())
arguments:
- prefix: --feat_out
......
......@@ -24,15 +24,16 @@ inputs:
position: 2
resample:
type: int?
default: 0
inputBinding:
prefix: --resample
position: 2
stratify:
type: boolean?
doc: TRUE or FALSE is allowed
type: string?
inputBinding:
position: 2
prefix: --stratify
valueFrom: $(self.toString())
inseparable:
type: string?
inputBinding:
......@@ -42,17 +43,17 @@ inputs:
arguments:
- position: 3
prefix: --train_sets
valueFrom: $(inputs.feat_in.nameroot)_trainSets.tsv
valueFrom: $(inputs.label_in.nameroot)_trainSets.tsv
- position: 3
prefix: --test_sets
valueFrom: $(inputs.feat_in.nameroot)_testSets.tsv
valueFrom: $(inputs.label_in.nameroot)_testSets.tsv
outputs:
train_sets_out:
type: File
outputBinding:
glob: $(inputs.feat_in.nameroot)_trainSets.tsv
glob: $(inputs.label_in.nameroot)_trainSets.tsv
test_sets_out:
type: File
outputBinding:
glob: $(inputs.feat_in.nameroot)_testSets.tsv
glob: $(inputs.label_in.nameroot)_testSets.tsv
......@@ -28,10 +28,10 @@ inputs:
prefix: --method
position: 2
stratify:
type: boolean?
doc: TRUE or FALSE is allowed
type: string?
inputBinding:
prefix: --stratify
valueFrom: $(self.toString())
position: 2
sel_criterion:
type: string?
......@@ -45,26 +45,12 @@ inputs:
position: 2
arguments:
- position: 3
prefix: --model
valueFrom: $(inputs.feat_in.nameroot)_model.tsv
- position: 3
prefix: --mlr_models_list
valueFrom: $(inputs.feat_in.nameroot)_model.RData
- position: 3
prefix: --model_matrix
valueFrom: $(inputs.feat_in.nameroot)_modelMatrix.txt
outputs:
model_tsv:
type: File
outputBinding:
glob: $(inputs.feat_in.nameroot)_model.tsv
model_rdata:
model:
type: File
outputBinding:
glob: $(inputs.feat_in.nameroot)_model.RData
model_matrix:
type: File
outputBinding:
glob: $(inputs.feat_in.nameroot)_modelMatrix.txt
......@@ -13,7 +13,7 @@ inputs:
prefix: --feat_in
position: 1
label_in:
type: File?
type: File
inputBinding:
prefix: --label_in
position: 1
......@@ -22,16 +22,11 @@ inputs:
inputBinding:
prefix: --test_sets
position: 1
model_rdata:
model:
type: File
inputBinding:
prefix: --mlr_models_list
position: 1
model_matrix:
type: File
inputBinding:
prefix: --model_matrix
position: 1
arguments:
- position: 2
......
......@@ -10,7 +10,7 @@ inputs:
label_in:
type: File
inputBinding:
prefix: --label
prefix: --label_in
position: 1
predictions:
type: File
......@@ -18,26 +18,26 @@ inputs:
prefix: --pred
position: 1
write_eval_results:
type: boolean?
doc: TRUE or FALSE is allowed
type: string?
inputBinding:
prefix: --write_eval_results
valueFrom: $(self.toString())
position: 2
arguments:
- position: 3
prefix: --plot
valueFrom: $(inputs.feat_in.nameroot)_evalPlots.pdf
valueFrom: $(inputs.label_in.nameroot)_evalPlots.pdf
- position: 3
prefix: --output_results
valueFrom: $(inputs.feat_in.nameroot)_evalResults.txt
valueFrom: $(inputs.label_in.nameroot)_evalResults.txt
outputs:
evaluation_plot:
type: File
outputBinding:
glob: $(inputs.feat_in.nameroot)_evalPlot.pdf
glob: $(inputs.label_in.nameroot)_evalPlots.pdf
evaluation_results:
type: File?
outputBinding:
glob: $(inputs.feat_in.nameroot)_evalResults.txt
glob: $(inputs.label_in.nameroot)_evalResults.txt
......@@ -11,51 +11,51 @@ inputs:
type: File
inputBinding:
position: 1
prefix: '--feat'
prefix: --feat_in
original_feat:
type: File
inputBinding:
position: 1
prefix: '--origin_feat'
prefix: --origin_feat
label_in:
type: File
inputBinding:
position: 1
prefix: '--label'
prefix: --label_in
metadata_in:
type: File?
inputBinding:
position: 1
prefix: '--meta'
model_tsv:
prefix: --metadata_in
model:
type: File
inputBinding:
position: 1
prefix: '--model'
prefix: --mlr_models_list
predictions:
type: File
inputBinding:
position: 1
prefix: '--pred'
prefix: --pred
color_scheme:
type: string?
inputBinding:
position: 2
prefix: '--col_scheme'
prefix: --col_scheme
consensus_threshold:
type: float?
inputBinding:
position: 2
prefix: '--consens_thres'
prefix: --consens_thres
heatmap_type:
type: string?
inputBinding:
position: 2
prefix: '--heatmap_type'
prefix: --heatmap_type
arguments:
- position: 3
prefix: '--plot'
prefix: --plot
valueFrom: $(inputs.feat_in.nameroot)_model_plots.pdf
outputs:
......
class: Workflow
cwlVersion: v1.0
requirements:
MultipleInputFeatureRequirement: {}
id: siamcat_workflow
label: siamcat_workflow
inputs:
......@@ -26,10 +22,10 @@ outputs:
type: File
'sbg:x': 1952.6685911746124
'sbg:y': 725.331343086159
- id: normalization_parameters_out
- id: normalization_parameters
outputSource:
- normalize_features/normalization_parameters_out
type: File
- normalize_features/normalization_parameters
type: File?
'sbg:x': 1170.382378133225
'sbg:y': 588.6885709128314
- id: evaluation_results
......@@ -56,9 +52,9 @@ outputs:
type: File
'sbg:x': 1941.2224255879937
'sbg:y': -322.2702631625083
- id: model_tsv
- id: model
outputSource:
- train_models/model_tsv
- train_models/model
type: File
'sbg:x': 1183.3419863384065
'sbg:y': -202.1716046648809
......@@ -111,7 +107,7 @@ steps:
- filter_features/filtered_feat
out:
- id: feat_out
- id: normalization_parameters_out
- id: normalization_parameters
run: ../tools/06_normalize_features.cwl
'sbg:x': 657.0314061482312
'sbg:y': 465.6464459739973
......@@ -137,12 +133,9 @@ steps:
- id: label_in
source:
- validate_data/validated_label
- id: model_matrix
- id: model
source:
- train_models/model_matrix
- id: model_rdata
source:
- train_models/model_rdata
- train_models/model
- id: test_sets
source:
- split_data/test_sets_out
......@@ -163,9 +156,7 @@ steps:
source:
- split_data/train_sets_out
out:
- id: model_matrix
- id: model_rdata
- id: model_tsv
- id: model
run: ../tools/09_train_models.cwl
'sbg:x': 951.9482287088812
'sbg:y': 176.0787371317328
......@@ -177,8 +168,6 @@ steps:
- id: predictions
source:
- make_predictions/predictions
- id: write_eval_results
default: true
out:
- id: evaluation_plot
- id: evaluation_results
......@@ -196,9 +185,9 @@ steps:
- id: metadata_in
source:
- validate_data/validated_metadata
- id: model_tsv
- id: model
source:
- train_models/model_tsv
- train_models/model
- id: original_feat
source:
- validate_data/validated_feat
......@@ -223,3 +212,5 @@ steps:
run: ../tools/03_check_for_confounders.cwl
'sbg:x': 648.4335802713812
'sbg:y': -322.994492847952
requirements:
MultipleInputFeatureRequirement: {}
This diff is collapsed.
class: Workflow
cwlVersion: v1.0
id: siamcat_workflow
label: siamcat_workflow
inputs:
- id: label_in
type: File
'sbg:x': -211.46906743520267
'sbg:y': 215.17076736908456
- id: feat_in
type: File
'sbg:x': -213.1508026123047
'sbg:y': 354.48820821737314
- id: metadata_in
type: File?
'sbg:x': -213.43544332479505
'sbg:y': 65.19374084472656
outputs:
- id: association_plots_out
outputSource:
- check_associations/association_plots_out
type: File
'sbg:x': 1920.3959628117993
'sbg:y': -265.89943341310783
- id: normalization_parameters_out
outputSource:
- normalize_features/normalization_parameters_out
type: File
'sbg:x': 1104.0839124465738
'sbg:y': -203.8899465928698
- id: evaluation_results
outputSource:
- evaluate_predictions/evaluation_results
type: File?
'sbg:x': 1931.515819217699
'sbg:y': 423.6074051792846
- id: evaluation_plot
outputSource:
- evaluate_predictions/evaluation_plot
type: File
'sbg:x': 1936.9710693359375
'sbg:y': 560.4991510912977
- id: model_plots
outputSource:
- interprete_model/model_plots
type: File
'sbg:x': 1924.0077850204946
'sbg:y': -32.05451321281125
- id: confounders_plot
outputSource:
- check_for_confounders/confounders_plot
type: File
'sbg:x': 1939.0229602762402
'sbg:y': 771.1966557660979
- id: model_tsv
outputSource:
- train_models/model_tsv
type: File
'sbg:x': 1105.4731946731363
'sbg:y': -87.36692340320536
steps:
- id: validate_data
in:
- id: feat_in
source:
- feat_in
- id: label_in
source:
- label_in
- id: metadata_in
source:
- metadata_in
out:
- id: validated_feat
- id: validated_label
- id: validated_metadata
run: >-
/media/sf_Dokumente/MicrobiomeEMBL/siamcat_cwl/CWL/tools/01_validate_data.cwl
'sbg:x': 15.152003171656446
'sbg:y': 213.78602506789176
- id: filter_features
in:
- id: feat_in
source:
- select_samples/selected_feat
- validate_data/validated_feat
out:
- id: filtered_feat
run: >-
/media/sf_Dokumente/MicrobiomeEMBL/siamcat_cwl/CWL/tools/04_filter_features.cwl
'sbg:x': 249.00100933052406
'sbg:y': 12.314643731955186
- id: check_associations
in:
- id: feat_in
source:
- filter_features/filtered_feat
- id: label_in
source:
- select_samples/selected_label
- validate_data/validated_label
out:
- id: association_plots_out
run: >-
/media/sf_Dokumente/MicrobiomeEMBL/siamcat_cwl/CWL/tools/05_check_associations.cwl
'sbg:x': 758.5679099044457
'sbg:y': -262.3459206756455
- id: normalize_features
in:
- id: feat_in
source:
- filter_features/filtered_feat
out:
- id: feat_out
- id: normalization_parameters_out
run: >-
/media/sf_Dokumente/MicrobiomeEMBL/siamcat_cwl/CWL/tools/06_normalize_features.cwl
'sbg:x': 546.7723766116638
'sbg:y': 2.6954385965526964
- id: split_data
in:
- id: label_in
source:
- validate_data/validated_label
- id: metadata_in
source:
- validate_data/validated_metadata
out:
- id: test_sets_out
- id: train_sets_out
run: /media/sf_Dokumente/MicrobiomeEMBL/siamcat_cwl/CWL/tools/08_split_data.cwl
'sbg:x': 617.3671975721693
'sbg:y': 497.5342735119465
- id: make_predictions
in:
- id: feat_in
source:
- normalize_features/feat_out
- id: label_in
source:
- validate_data/validated_label
- id: model_matrix
source:
- train_models/model_matrix
- id: model_rdata
source:
- train_models/model_rdata
- id: test_sets
source:
- split_data/test_sets_out
out:
- id: predictions
run: >-
/media/sf_Dokumente/MicrobiomeEMBL/siamcat_cwl/CWL/tools/10_make_predictions.cwl
'sbg:x': 1480.8948640695066
'sbg:y': 239.193603515625
- id: train_models
in:
- id: feat_in
source:
- normalize_features/feat_out
- id: label_in
source:
- validate_data/validated_label
- id: train_sets
source:
- split_data/train_sets_out
out:
- id: model_matrix
- id: model_rdata
- id: model_tsv
run: >-
/media/sf_Dokumente/MicrobiomeEMBL/siamcat_cwl/CWL/tools/09_train_models.cwl
'sbg:x': 885.5039230004554
'sbg:y': 187.50314745710568
- id: evaluate_predictions
in:
- id: label_in
source:
- validate_data/validated_label
- id: predictions
source:
- make_predictions/predictions
- id: write_eval_results
default: true
out:
- id: evaluation_plot
- id: evaluation_results
run: >-
/media/sf_Dokumente/MicrobiomeEMBL/siamcat_cwl/CWL/tools/11_evaluate_predictions.cwl
'sbg:x': 1742.0773034613228
'sbg:y': 478.7590748329334
- id: interprete_model
in:
- id: feat_in
source:
- normalize_features/feat_out
- id: label_in
source:
- validate_data/validated_label
- id: metadata_in
source:
- validate_data/validated_metadata
- id: model_tsv
source:
- train_models/model_tsv
- id: original_feat
source:
- validate_data/validated_feat
- id: predictions
source:
- make_predictions/predictions
out:
- id: model_plots
run: >-
/media/sf_Dokumente/MicrobiomeEMBL/siamcat_cwl/CWL/tools/12_interprete_model.cwl
'sbg:x': 1741.5103701741173
'sbg:y': -29.675089878030956
- id: check_for_confounders
in:
- id: label_in
source:
- validate_data/validated_label
- id: metadata_in
source:
- validate_data/validated_metadata
out:
- id: confounders_plot
run: >-
/media/sf_Dokumente/MicrobiomeEMBL/siamcat_cwl/CWL/tools/03_check_for_confounders.cwl
'sbg:x': 490.946993293249
'sbg:y': 753.4881214090526
This diff is collapsed.
Package: SIAMCAT
Type: Package
Title: Statistical Inference of Associations between Microbial Communities And host phenoTypes
Version: 0.2.0