Mercurial > repos > devteam > picard_122_up
diff picard_AddOrReplaceReadGroups.xml @ 0:b76a4f17bbbb draft
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author | devteam |
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date | Thu, 23 Oct 2014 11:31:30 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_AddOrReplaceReadGroups.xml Thu Oct 23 11:31:30 2014 -0400 @@ -0,0 +1,147 @@ +<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.122.0"> + <description>add or replaces read group information</description> + <requirements> + <requirement type="package" version="1.122.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + java -jar \$JAVA_JAR_PATH/AddOrReplaceReadGroups.jar + INPUT="${inputFile}" + RGLB="${rglb}" + RGPL="${rgpl}" + RGPU="${rgpu}" + RGSM="${rgsm}" + RGID="${rgid}" + + #if str( $rgcn): + RGCN="${rgcn}" + #end if + + #if str( $rgds): + RGDS="${rgds}" + #end if + + #if str( $rgpi): + RGPI="${rgpi}" + #end if + + #if str( $rgdt): + RGDT="${rgdt}" + #end if + + 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" /> + <param name="rgid" value="A" type="text" label="Read Group ID" help="RGID; Required" /> + <param name="rgsm" value="sample-a" type="text" label="Read Group Sample name" help="RGSM; Required" /> + <param name="rglb" value="tumor-a" type="text" label="Read Group library" help="RGLB; Required" /> + <param name="rgpl" value="Illumina" type="text" label="Read Group Platform" help="RGPL; Required; e.g., Illumina, 454, IonTorrent, etc" /> + <param name="rgpu" value="run-1" type="text" label="Read Group Platform Unit" help="RGPU; Required; e.g., run, barcode, etc" /> + <!-- optional params --> + <param name="rgcn" value="" optional="True" type="text" label="Read Group sequencing center name" help="RGCN; Optional" /> + <param name="rgds" value="" optional="True" type="text" label="Read Group description" help="RGDS; Optional" /> + <param name="rgpi" value="" optional="True" type="integer" label="Read Group predicted insert size" help="RGPI; Optional" /> + <param name="rgdt" value="" optional="True" type="text" label="Read Group run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/> + + <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="rglb" value="tumor-a" /> + <param name="rgpl" value="Illumina" /> + <param name="rgpu" value="run-1" /> + <param name="rgsm" value="sample-a" /> + <param name="rgid" 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> + + + + + + + + + + + + +