Mercurial > repos > iuc > bamtools_split_tag
view bamtools_split_tag.xml @ 0:c9fbbe6f5fc8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
author | iuc |
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date | Sat, 27 Nov 2021 10:02:45 +0000 |
parents | |
children | e30af4e78cd3 |
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<tool id="bamtools_split_tag" name="Split BAM by Tag" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>into dataset list collection</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command> <![CDATA[ #import re #set $name = 'split_bam' + $re.sub('\W','_',$re.sub('\.bam$','',$input_bam.name)) ln -s '${input_bam}' 'localbam.bam' && ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' && bamtools split -tag $tag_name -in 'localbam.bam' -stub '$name' ]]> </command> <inputs> <param name="input_bam" type="data" format="bam" label="BAM dataset to split by tag value"/> <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> </inputs> <outputs> <collection name="output_bams" type="list" label="${input_bam.name} Split List"> <discover_datasets pattern="split_bam(?P<designation>.+)\.bam" ext="bam" visible="false"/> </collection> </outputs> <tests> <test> <param name="input_bam" ftype="bam" value="bamtools-input-tags.bam"/> <param name="tag_name" value="XG"/> <output_collection name="output_bams" type="list"> <element name="bamtools_input_tags.TAG_XG_V" file="bamtools_input_tags.TAG_XG_V.bam" compare="sim_size" delta="500" /> </output_collection> </test> </tests> <help> **What is does** BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). ----- .. class:: warningmark **DANGER: Multiple Outputs** As described below, splitting a BAM dataset(s) on tag value can produce very large numbers of outputs. Read below and know what you are doing. ----- **How it works** Split alignments by tag name into a dataset list collection. This can generate a huge number of output datasets depending on the number of distinct values of the TAG. ----- .. class:: infomark **More information** Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki </help> <citations> <citation type="doi">10.1093/bioinformatics/btr174</citation> </citations> </tool>