Merge pull request #14 from FarahZKhan/patch-4

Create realignTargetCreator.cwl

Author: portah

tools/realignTargetCreator.cwl

@@ -0,0 +1,86 @@
+#!/usr/bin/env cwl-runner
+#
+# To use it as stand alone tool - example: "cwltool realignerTargerCreator.cwl realignerTargerCreator.json"
+# Still testing to make it work as a part of the workflow
+#
+# Authors: [email protected] and [email protected] UNIVERSITY OF MELBOURNE
+# Developed for CWL consortium http://commonwl.org/
+
+class: CommandLineTool
+
+description: |
+  This is a tool wrapper for GATK tool called realignerTargetCreator. It accepts 3 input files and produces a file containing list of target intervals to pass to the IndelRealigner.
+  Usage: java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I inout.bam --known indels.vcf -o forIndelRealigner.intervals 
+  Options: 
+    -T tool Tool name to be executed
+    -R File Reference sequence in fasta format
+    -I File  bam file produced from sam to bam conversion step
+    --known File set of known indels   
+    
+requirements:
+  - import: node-engine.cwl
+  - import: envvar-global.cwl
+
+inputs:
+  - id: "#java_arg"
+    type: string
+    default: "-Xmx4g"
+    inputBinding: 
+      position: 1
+
+  - id: "#jar_file"
+    type: File
+    inputBinding: { position: 2, prefix: "-jar" }
+    description: GATK jar file
+     
+  - id: "#RealignerTarget"
+    type: string
+    default: "RealignerTargetCreator"
+    inputBinding: { position: 3, prefix: "-T" }
+    description: tool used for this step from GATK jar
+     
+  - id: "#reference"
+    type: File
+    inputBinding:
+      position: 4
+      prefix: "-R"
+      secondaryFiles:
+        - ".amb"
+        - ".ann"
+        - ".bwt"
+        - ".pac"
+        - ".rbwt"
+        - ".rpac"
+        - ".rsa"
+        - ".sa"
+
+  - id: "#inputBam_realign"
+    type: File
+    description: bam file produced after mark-duplicates execution
+    inputBinding:
+      position: 5 
+      prefix: "-I"
+      
+  - id: "#known"  
+    type:
+      type: array
+      items: File
+      inputBinding: { prefix: "--known" }
+    inputBinding:  position: 6
+
+  - id: "#outputfile_realignTarget"
+    type: string
+    description: name of the output file from realignTargetCreator
+    inputBinding:
+      position: 9
+      prefix: "-o"
+        
+outputs:
+  - id: "#output_realignTarget"
+    type: File
+    outputBinding: 
+      glob:
+        engine: cwl:JsonPointer
+        script: /job/outputfile_realignTarget
+
+baseCommand: ["java"]