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view dr-disco_bam_extract.xml @ 0:fca9c1ace23c draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
author | erasmus-medical-center |
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date | Wed, 25 Jan 2017 08:06:06 -0500 |
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<tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@-g0"> <description>Extracts reads from two targeted regions</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command"/> <command><![CDATA[ dr-disco bam-extract '$region1' '$region2' '$output' '$input_alignment' ]]></command> <inputs> <param name="input_alignment" type="data" format="bam" label="Discordant alignment file of STAR)" /> <param name="region1" type="text" value="chr21:39737183-40035618" label="Genomic region 1" /> <param name="region2" type="text" value="chr21:42834478-42882085" label="Genomic region 2" /> </inputs> <outputs> <data name="output" format="bam" label="${tool.name} on ${input_alignment.name}" /> </outputs> <tests> <test> <param name="input_alignment" value="bam_extract.bam" /> <param name="region1" value="chr21:39737183-40035618" /> <param name="region2" value="chr21:42834478-42882085" /> <output name="output" file="bam_extract.bam" /> </test> <test> <param name="input_alignment" value="bam_extract.bam" /> <param name="region1" value="chr22:39737183-40035618" /> <param name="region2" value="chr11:42834478-42882085" /> <output name="output" file="bam_extract.empty.bam" /> </test> </tests> <help> Extract reads from two chromosomal positions (and also takes mates with the same name) Regions are in the format: chr1:123-546 </help> <expand macro="citations"/> </tool>