Mercurial > repos > devteam > picard
view picard_AddOrReplaceReadGroups.xml @ 9:5eaa8a968300 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
author | devteam |
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date | Fri, 09 Oct 2015 17:43:13 -0400 |
parents | 3a3234d7a2e8 |
children | 05087b27692a |
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<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.0"> <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>