Mercurial > repos > hepcat72 > extractsplitreads_bwamem
diff extractSplitReads_BwaMem.xml @ 0:839c219ab0aa draft
planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
author | hepcat72 |
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date | Fri, 10 Aug 2018 11:46:23 -0400 |
parents | |
children | a20ac5d90c16 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extractSplitReads_BwaMem.xml Fri Aug 10 11:46:23 2018 -0400 @@ -0,0 +1,109 @@ +<tool id="extractsplitreads_bwamem" + name="Extract Split Reads" + version="0.1.0"> + + <description>from bwaMEM (part of lumpy-sv)</description> + + <requirements> + <requirement type="package" version="0.2.14a">lumpy-sv</requirement> + </requirements> + + <!-- Not sure yet how to call the command if the lumpy-sv package in bioconda doesn't put the script in an executable location on PATH --> + + <version_command>extractSplitReads_BwaMem | grep ^extractSplitReads_BwaMem | cut -d v -f 2</version_command> + + <command detect_errors="aggressive"> + <![CDATA[ + extractSplitReads_BwaMem + -i '$input' + -n $numSplits + $includeDups + -m $minNonOverlap + > '$output' + ]]> + </command> + + <inputs> + + <param format="sam" name="input" type="data" label="Sam alignment file" argument="--infile"/> + + <param name="numSplits" + label="numSplits" + argument="--numSplits" + + type="integer" + value="2" + + help="The maximum number of split-read mappings to allow per read. Reads with more are excluded." /> + + <param name="includeDups" + label="includeDups" + argument="--includeDups" + + type="boolean" + truevalue="--includeDups" + falsevalue="" + checked="no" + value="false" + + help="Include alignments marked as duplicates." /> + + <param name="minNonOverlap" + label="minNonOverlap" + argument="--minNonOverlap" + + type="integer" + value="20" + + help="Minimum non-overlap between split alignments on the query." /> + + </inputs> + <outputs> + <data format="sam" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="JS01-BWA-MEM.splitters.sam"/> + <output name="output" file="JS01-BWA-MEM.splitters.out.sam"/> + </test> + <test> + <param name="input" value="pe.pos_sorted.sam"/> + <output name="output" file="pe.pos_sorted.out.sam"/> + </test> + </tests> + + <help> + <![CDATA[ + +Usage: `extractSplitReads_BwaMem -i <file>` + +extractSplitReads_BwaMem v0.1.0 + +Author: Ira Hall + +Description: Get split-read alignments from bwa-mem in lumpy compatible format. Ignores reads marked as duplicates. + +Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405. + + +Options: + -h, --help show this help message and exit + -i FILE, --inFile=FILE + A SAM file or standard input (-i stdin). + -n INT, --numSplits=INT + The maximum number of split-read mappings to allow per + read. Reads with more are excluded. Default=2 + -d, --includeDups Include alignments marked as duplicates. Default=False + -m INT, --minNonOverlap=INT + minimum non-overlap between split alignments on the + query (default=20) + + ]]> + </help> + + <citations> + <citation type="doi">doi:10.1186/gb-2014-15-6-r84</citation> + </citations> + +</tool>