updated simulation and tests to not use toy data at alll

metrics/correlations/getBestCor.py

@@ -12,7 +12,7 @@
 matrix = ""
 alg = ""
 for file in filelist:
-    [data,disease,mrna,to,prot,mat,cor] = os.path.basename(file).split('-')
+    [data,disease,mrna,to,prot,mat,frac,sample,rep,cor] = os.path.basename(file).split('-')
     if mrna == prot:
         tab = pandas.read_csv(file, sep='\t', header=None)
         meanVal = tab[1].mean()

metrics/data-sim/run-best-alg-by-sim.cwl

@@ -38,7 +38,7 @@ steps:
        out:
          [value]
    get-mat:
-       run: https://raw.githubusercontent.com/PNNL-CompBio/proteomicsTumorDeconv/main/signature_matrices/get-signature-matrix.cwl
+       run: ../../signature_matrices/get-signature-matrix.cwl
        in:
           sigMatrixName: get-best-sim-mat/value
        out:
@@ -52,7 +52,7 @@ steps:
       out:
         [value]
    run-best-algs-by-sig:
-      run: https://raw.githubusercontent.com/PNNL-CompBio/proteomicsTumorDeconv/main/tumorDeconvAlgs/run-deconv.cwl
+      run: ../../tumorDeconvAlgs/run-deconv.cwl
       in:
         signature: get-mat/sigMatrix
         alg: get-best-sim-alg/value

metrics/data-sim/simul-data-comparison.cwl

@@ -52,11 +52,11 @@ steps:
    run-all-algs-by-mrna:
      run: call-deconv-on-sim.cwl
      when: $(inputs.simType.trim() == 'mrna')
-     scatter: [protAlg,simulation,signature]
+     scatter: [protAlg,repNumber,signature]
      scatterMethod: flat_crossproduct
      in:
         protAlg: prot-algorithms
-        simulation: mrna-perms
+        repNumber: mrna-perms
         signature: rna-sigs
         sample: sample
         sampleType:

metrics/data-sim/simul-data-files.cwl

@@ -0,0 +1,97 @@
+#!/usr/bin/env cwltool
+class: Workflow
+label: simul-data-sampling
+id: simul-data-sampling
+cwlVersion: v1.2
+
+requirements:
+   - class: SubworkflowFeatureRequirement
+   - class: MultipleInputFeatureRequirement
+   - class: ScatterFeatureRequirement
+   - class: StepInputExpressionRequirement
+   - class: InlineJavascriptRequirement
+
+inputs:
+   num-reps:
+      type: int
+      default: 1
+   samples:
+      type: int[]
+      default: [20,40,60,80,100]
+   mrna-perms:
+      type: string[]
+      default: ['1','2','3','4','5','6','7','8','9','10','pbmc']
+   prot-perms:
+      type: string[]
+      default: ['1','2','3','4','5']
+   prot-algorithms:
+      type: string[]
+      default:
+      - mcpcounter
+      - xcell
+      - epic
+      - cibersort
+   rna-sigs: 
+      type: string[]
+      default: ['LM22','PBMC']
+   prot-sigs:
+      type: string[]
+      default: ['LM7c','LM9']
+   simType: 
+      type: string
+
+outputs:
+   cell-cor-file:
+      type: File[]
+      outputSource: run-all-algs-by-prot
+   deconv:
+      type: File[]
+      outputSource: run-all-algs-by-prot
+   cellPred:
+      type: File[]
+      outputSource: run-all-algs-by-prot
+   deconvoluted:
+      type: File[]
+      outputSource: run-all-algs-by-prot
+   matrix:
+      type: File[]
+      outputSource: run-all-algs-by-prot
+
+
+steps:
+   run-all-algs-by-mrna:
+     run: call-deconv-on-sim.cwl
+     when: $(inputs.simType.trim() == 'mrna')
+     scatter: [protAlg,permutation,signature,samples]
+     scatterMethod: flat_crossproduct
+     in:
+        protAlg: prot-algorithms
+        permutation: mrna-perms
+        signature: rna-sigs
+        sample: samples
+        num-reps: num-reps
+        sampleType:
+          valueFrom: 'normal'
+        dataType:
+          valueFrom: 'prot'
+        simType: simType
+     out:
+        [cell-cor-file, deconv, cellPred, deconvoluted, matrix]
+   run-all-algs-by-prot:
+     run: call-deconv-on-sim.cwl
+     when: $(inputs.simType.trim() == 'prot')
+     scatter: [protAlg,permutation,signature,samples]
+     scatterMethod: flat_crossproduct
+     in:
+        protAlg: prot-algorithms
+        permutation: prot-perms
+        sample: samples
+        num-reps: num-reps
+        signature: prot-sigs
+        sampleType:
+          valueFrom: 'normal'
+        dataType:
+          valueFrom: 'prot'
+        simType: simType
+     out:
+        [cell-cor-file,deconv, cellPred, deconvoluted, matrix]   

metrics/mrna-prot/best-test.yml

@@ -10,10 +10,10 @@ prot-algorithms:
 
 protFile:
   class: File
-  path: ../../toy_data/TOY_log2ratio_protein_abundance_withNA.tsv
+  path: ../../toy_data/ov-all-prot-reduced.tsv
 
 rnaFile:
   class: File
-  path: ../../toy_data/TOY_rna_expression_imputed.tsv
+  path: ../../toy_data/ov-all-mrna-reduced.tsv
 cancerType: test
 tissueType: test