Mercurial > repos > erasmus-medical-center > dr_disco
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dr-disco_bam_extract.xml Wed Jan 25 08:06:06 2017 -0500 @@ -0,0 +1,51 @@ +<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>