Mercurial > repos > devteam > samtools_split
view samtools_split.xml @ 5:3570a794565c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author | iuc |
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date | Tue, 28 Sep 2021 16:07:39 +0000 |
parents | 229681b8c662 |
children | eda9f7aa1d54 |
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<tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>BAM dataset on readgroups</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @ADDTHREADS@ samtools split -f 'Read_Group_%!.bam' #if $header: -u '${output}:${header}' #else: -u '${output}' #end if -@ \$addthreads '$input_bam' ]]></command> <inputs> <param name="input_bam" type="data" format="bam" label="BAM file" /> <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" /> </inputs> <outputs> <data name="output" format="bam" label="${tool.name} on ${on_string}"> <discover_datasets pattern="Read_Group_(?P<designation>.+)\.bam" ext="bam" visible="true" directory="" assign_primary_output="false"/> </data> </outputs> <tests> <test> <param name="input_bam" value="phiX.bam" ftype="bam" /> <output name="output"> <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" lines_diff="4" /> <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" lines_diff="4" /> <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" lines_diff="4" /> </output> </test> </tests> <help><![CDATA[ **What it does** Splits BAM files on readgroups. This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. ]]></help> <expand macro="citations"/> </tool>