updated to set up baseline of cell type mapping

perfEval/data-sim/call-deconv-on-sim.cwl

@@ -15,6 +15,7 @@ inputs:
      type: File
    permutation:
      type: string
+     default: '1'
    prot-alg:
      type: string
    sampleType:
@@ -23,6 +24,9 @@ inputs:
    dataType:
      type: string
      default: 'prot'
+   simType:
+     type: string
+     default: 'prot'
 
 outputs:
   pat-cor-file:
@@ -46,6 +50,7 @@ steps:
      run: ../../simulatedData/sim-data-tool.cwl
      in:
        repNumber: permutation
+       simType: simType
      out:
        [matrix,cellType]
   deconv-prot:

perfEval/data-sim/sim-test.yml

@@ -3,6 +3,7 @@ prot-algorithms:
   - epic
   - xcell
   - cibersort
+  - bayesdebulk
 reps:
   - "1"
   - "2"

perfEval/mrna-prot/alg-test.yml

@@ -1,5 +1,5 @@
 cancerTypes:
-  - endometrial
+  - luad
   - ccrcc
 prot-algorithms:
   - mcpcounter

simulatedData/Dockerfile

@@ -3,7 +3,9 @@ FROM rocker/tidyverse
 
 COPY *rda /bin/
 COPY getSimDataMatrices.R /bin/
+COPY mapSimDataMatrices.R /bin/
 
 RUN chmod 777 /bin/getSimDataMatrices.R
+RUN chmod 777 /bin/mapSimDataMatrices.R
 
 VOLUME ['/tmp']

simulatedData/map-sig-tool.cwl

@@ -9,7 +9,7 @@ arguments:
 
 requirements:
    - class: DockerRequirement
-     dockerPull: tumodeconv/sim-data
+     dockerPull: tumordeconv/sim-data
 
 
 inputs:
@@ -25,3 +25,9 @@ inputs:
      type: File
      inputBinding:
         position: 3
+
+outputs:
+  updated-deconv:
+     type: File
+     outputBinding:
+        glob: "*.tsv"

simulatedData/mapSimDataMatrices.R

@@ -0,0 +1,11 @@
+main <- function(){
+    argv <- commandArgs(trailingOnly = TRUE)
+    deconv.mat <- read.table(argv[1],header=T,row.names=1,sep='\t') #matrix to be fixed
+    sig.mat <- argv[2] #signature used to deconvolve matrix
+    sim.type <- argv[3] #type of simulation performed
+
+    if(sig.mat=='LM9.txt')
+    write.table(deconv.mat,file='fixed.tsv',sep='\t')
+}
+
+main()