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view samtools_split.xml @ 2:51390195d350 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_split commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author | devteam |
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date | Fri, 18 Dec 2015 19:46:52 -0500 |
parents | 76449db9ee44 |
children | ac469d103b51 |
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<tool id="samtools_split" name="Split" version="1.1"> <description>BAM dataset on readgroups</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"></expand> <expand macro="stdio"></expand> <expand macro="version_command"></expand> <command><![CDATA[ samtools split -f 'Read_Group_%!.bam' #if $header: -u "${output}":"${header}" #else: -u "${output}" #end if "${input_bam}" ]]></command> <inputs> <param name="input_bam" type="data" format="bam" label="BAM file" /> <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" /> </inputs> <outputs> <data format="bam" name="output" label="${tool.name} on ${on_string}"> <discover_datasets pattern="Read_Group_(?P<designation>.+)\.bam" ext="bam" visible="true" directory="" /> </data> </outputs> <tests> <test> <param name="input_bam" value="phiX.bam" ftype="bam" /> <output name="output" file="samtools_split_out.bam"> <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" /> <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" /> <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" /> </output> </test> </tests> <help> **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"></expand> </tool>