Mercurial > repos > erasmus-medical-center > dr_disco

comparison dr-disco_bam-extract.xml @ 3:5348cfd3ba5c draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
author erasmus-medical-center
date Thu, 10 Aug 2017 05:38:27 -0400
parents 173ca9768e22
children 922b52cf9b35
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2:173ca9768e22 3:5348cfd3ba5c
1 <tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@-g0"> 1 <tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@-g0">
2 <description>Extracts reads from two targeted regions</description> 2 <description>Extracts reads from two targeted regions</description>
3
3 <macros> 4 <macros>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 7
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 10
10 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
11 dr-disco bam-extract 12 dr-disco bam-extract
12 '$region1' 13 '$region1'
13 '$region2' 14 '$region2'
15 '$input_alignment'
14 '$output' 16 '$output'
15 '$input_alignment'
16 ]]></command> 17 ]]></command>
18
17 <inputs> 19 <inputs>
18 <param name="input_alignment" type="data" format="bam" label="Discordant alignment file of STAR)" /> 20 <param name="input_alignment" type="data" format="bam" label="Discordant alignment file of STAR)" />
19 <param name="region1" type="text" value="chr21:39737183-40035618" label="Genomic region 1" /> 21 <param name="region1" type="text" value="chr21:39737183-40035618" label="Genomic region 1" />
20 <param name="region2" type="text" value="chr21:42834478-42882085" label="Genomic region 2" /> 22 <param name="region2" type="text" value="chr21:42834478-42882085" label="Genomic region 2" />
21 </inputs> 23 </inputs>
24
22 <outputs> 25 <outputs>
23 <data name="output" format="bam" label="${tool.name} on ${input_alignment.name}" /> 26 <data name="output" format="bam" label="${tool.name} on ${input_alignment.name}" />
24 </outputs> 27 </outputs>
25 28
26 <tests> 29 <tests>