Mercurial > repos > devteam > picard
diff picard_AddOrReplaceReadGroups.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | f9242e01365a |
| children |
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--- a/picard_AddOrReplaceReadGroups.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_AddOrReplaceReadGroups.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,59 +1,53 @@ -<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>add or replaces read group information</description> - <macros> - <import>picard_macros.xml</import> - <import>read_group_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ +<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> + <description>add or replaces read group information</description> + <macros> + <import>picard_macros.xml</import> + <import>read_group_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ @define_read_group_helpers@ #set $rg_auto_name = $read_group_name_default($inputFile) @set_read_group_vars@ @java_options@ @symlink_element_identifier@ - picard - AddOrReplaceReadGroups - INPUT='$escaped_element_identifier' - $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="${outFile}" + picard AddOrReplaceReadGroups + --INPUT '$escaped_element_identifier' + $format_read_group("", $rg_lb, quote='"', arg=" --RGLB ") + $format_read_group("", $rg_pl, quote='"', arg=" --RGPL ") + $format_read_group("", $rg_pu, quote='"', arg=" --RGPU ") + $format_read_group("", $rg_sm, quote='"', arg=" --RGSM ") + $format_read_group("", $rg_id, quote='"', arg=" --RGID ") + $format_read_group("", $rg_ds, quote='"', arg=" --RGDS ") + $format_read_group("", $rg_pi, quote='"', arg=" --RGPI ") + $format_read_group("", $rg_dt, quote='"', arg=" --RGDT ") + --OUTPUT '${outFile}' + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]></command> - - <inputs> - <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> - <expand macro="read_group_inputs_picard" /> - <expand macro="VS" /> - - </inputs> - - <outputs> - <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/> - </outputs> - - - <tests> - <test> - <param name="inputFile" value="picard_ARRG.bam" /> - <param name="LB" value="tumor-a" /> - <param name="PL" value="ILLUMINA" /> - <param name="PU" value="run-1" /> - <param name="SM" value="sample-a" /> - <param name="ID" value="id-1" /> - <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" /> - </test> - </tests> - <help> + <inputs> + <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <expand macro="read_group_inputs_picard"/> + <expand macro="VS"/> + </inputs> + <outputs> + <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/> + </outputs> + <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 @@ -107,5 +101,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>