diff picard_AddOrReplaceReadGroups.xml @ 0:5166ed57b1c4 draft

Uploaded version 1.135

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_AddOrReplaceReadGroups.xml	Mon Jul 06 14:46:32 2015 -0400
@@ -0,0 +1,125 @@
+<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.135-gx-1">
+  <description>add or replaces read group information</description>
+  <macros>
+    <import>picard_macros.xml</import>
+    <import>read_group_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>
+    @define_read_group_helpers@
+    #set $rg_auto_name = $read_group_name_default($inputFile)
+    @set_read_group_vars@
+    @java_options@
+    java -jar \$JAVA_JAR_PATH/picard.jar
+      AddOrReplaceReadGroups
+      INPUT="${inputFile}"
+      $format_read_group("RGLB=", $rg_lb, '"')
+      $format_read_group("RGPL=", $rg_pl, '"')
+      $format_read_group("RGPU=", $rg_pu, '"')
+      $format_read_group("RGSM=", $rg_sm, '"')
+      $format_read_group("RGID=", $rg_id, '"')
+      $format_read_group("RGDS=", $rg_ds, '"')
+      $format_read_group("RGPI=", $rg_pi, '"')
+      $format_read_group("RGDT=", $rg_dt, '"')
+      VALIDATION_STRINGENCY="${validation_stringency}"
+      QUIET=true
+      VERBOSITY=ERROR
+      OUTPUT="${outFile}"
+      
+  </command>
+  
+  <inputs>
+    <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
+    <expand macro="read_group_inputs_picard" />
+    <expand macro="VS" />
+    
+  </inputs>
+  
+  <outputs>
+    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
+  </outputs>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <tests>
+    <test>
+      <param name="inputFile" value="picard_ARRG.bam" />
+      <param name="LB" value="tumor-a" />
+      <param name="PL" value="ILLUMINA" />
+      <param name="PU" value="run-1" />
+      <param name="SM" value="sample-a" />
+      <param name="ID" value="id-1" />
+      <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Add or Replace Read Groups in an input BAM or SAM file.
+
+@dataset_collections@
+
+@RG@
+
+@description@
+
+  INPUT=File
+  I=File                  Input file (bam or sam).  Required. 
+
+  OUTPUT=File
+  O=File                  Output file (bam or sam).  Required. 
+
+  SORT_ORDER=SortOrder
+  SO=SortOrder            Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.  
+                          Default value: null. Possible values: {unsorted, queryname, coordinate} 
+
+  RGID=String
+  ID=String               Read Group ID  Default value: 1. This option can be set to 'null' to clear the default 
+                          value. 
+
+  RGLB=String
+  LB=String               Read Group Library  Required. 
+  
+  RGPL=String
+  PL=String               Read Group platform (e.g. illumina, solid)  Required. 
+
+  RGPU=String
+  PU=String               Read Group platform unit (eg. run barcode)  Required. 
+
+  RGSM=String
+  SM=String               Read Group sample name  Required. 
+
+  RGCN=String
+  CN=String               Read Group sequencing center name  Default value: null. 
+
+  RGDS=String
+  DS=String               Read Group description  Default value: null. 
+
+  RGDT=Iso8601Date
+  DT=Iso8601Date          Read Group run date  Default value: null. 
+
+  RGPI=Integer
+  PI=Integer              Read Group predicted insert size  Default value: null. 
+
+@more_info@
+  </help>
+</tool>
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