Mercurial > repos > erasmus-medical-center > dr_disco

comparison dr-disco_bam-extract.xml @ 1:9495360713d4 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
author erasmus-medical-center
date Thu, 16 Mar 2017 04:24:23 -0400
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children 173ca9768e22
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0:fca9c1ace23c 1:9495360713d4
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>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements" />
8 <expand macro="version_command"/>
9
10 <command detect_errors="exit_code"><![CDATA[
11 dr-disco bam-extract
12 '$region1'
13 '$region2'
14 '$output'
15 '$input_alignment'
16 ]]></command>
17 <inputs>
18 <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" />
20 <param name="region2" type="text" value="chr21:42834478-42882085" label="Genomic region 2" />
21 </inputs>
22 <outputs>
23 <data name="output" format="bam" label="${tool.name} on ${input_alignment.name}" />
24 </outputs>
25
26 <tests>
27 <test>
28 <param name="input_alignment" value="bam_extract.bam" />
29 <param name="region1" value="chr21:39737183-40035618" />
30 <param name="region2" value="chr21:42834478-42882085" />
31
32 <output name="output" file="bam_extract.bam" />
33 </test>
34 <test>
35 <param name="input_alignment" value="bam_extract.bam" />
36 <param name="region1" value="chr22:39737183-40035618" />
37 <param name="region2" value="chr11:42834478-42882085" />
38
39 <output name="output" file="bam_extract.empty.bam" />
40 </test>
41 </tests>
42
43 <help>
44 Extract reads from two chromosomal positions (and also takes mates with the same name)
45
46 Regions are in the format:
47 chr1:123-546
48 </help>
49
50 <expand macro="citations"/>
51 </tool>