From 369db8ab7b9e85a6bcbaabcef4250b31de87df89 Mon Sep 17 00:00:00 2001
From: Sara Gosline <sara.gosline@pnnl.gov>
Date: Wed, 21 Apr 2021 13:37:50 -0700
Subject: [PATCH] updated to set up baseline of cell type mapping

---
 perfEval/data-sim/call-deconv-on-sim.cwl |  5 +++++
 perfEval/data-sim/sim-test.yml           |  1 +
 perfEval/mrna-prot/alg-test.yml          |  2 +-
 simulatedData/Dockerfile                 |  2 ++
 simulatedData/map-sig-tool.cwl           |  8 +++++++-
 simulatedData/mapSimDataMatrices.R       | 11 +++++++++++
 6 files changed, 27 insertions(+), 2 deletions(-)
 create mode 100644 simulatedData/mapSimDataMatrices.R

diff --git a/perfEval/data-sim/call-deconv-on-sim.cwl b/perfEval/data-sim/call-deconv-on-sim.cwl
index 2707ee1..3ce7808 100644
--- a/perfEval/data-sim/call-deconv-on-sim.cwl
+++ b/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:
diff --git a/perfEval/data-sim/sim-test.yml b/perfEval/data-sim/sim-test.yml
index e987e08..0629935 100644
--- a/perfEval/data-sim/sim-test.yml
+++ b/perfEval/data-sim/sim-test.yml
@@ -3,6 +3,7 @@ prot-algorithms:
   - epic
   - xcell
   - cibersort
+  - bayesdebulk
 reps:
   - "1"
   - "2"
diff --git a/perfEval/mrna-prot/alg-test.yml b/perfEval/mrna-prot/alg-test.yml
index 38770bd..3203396 100644
--- a/perfEval/mrna-prot/alg-test.yml
+++ b/perfEval/mrna-prot/alg-test.yml
@@ -1,5 +1,5 @@
 cancerTypes:
-  - endometrial
+  - luad
   - ccrcc
 prot-algorithms:
   - mcpcounter
diff --git a/simulatedData/Dockerfile b/simulatedData/Dockerfile
index 3f34736..a725f85 100644
--- a/simulatedData/Dockerfile
+++ b/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']
diff --git a/simulatedData/map-sig-tool.cwl b/simulatedData/map-sig-tool.cwl
index 3f35818..ba30ed8 100644
--- a/simulatedData/map-sig-tool.cwl
+++ b/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"
diff --git a/simulatedData/mapSimDataMatrices.R b/simulatedData/mapSimDataMatrices.R
new file mode 100644
index 0000000..b344971
--- /dev/null
+++ b/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()