Mercurial > repos > yokofakun > jvarkit

comparison jvarkit/vcftrio.xml @ 8:98106098dcd1 draft

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author yokofakun
date Fri, 27 Feb 2015 09:52:06 -0500
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7:e5723e64ea43 8:98106098dcd1
1 <?xml version="1.0"?>
2 <tool xmlns:date="http://exslt.org/dates-and-times" hidden="false" id="com.github.lindenb.jvarkit.tools.vcftrios.VCFTrios" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcftrio">
3 <!--Date: 2015-02-27T15:54:05+01:00-->
4 <description>Check for mendelian incompatibilities in a VCF</description>
5 <requirements>
6 <requirement type="binary">java</requirement>
7 </requirements>
8 <command>(gunzip -c ${input} || cat ${input}) | java -cp $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.128.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcftrio.jar com.github.lindenb.jvarkit.tools.vcftrios.VCFTrios $filter -p $ped -o ${output}.vcf.gz &amp;&amp; mv ${output}.vcf.gz ${output}</command>
9 <inputs>
10 <param format="vcf" name="input" type="data" label="VCF input"/>
11 <param name="filter" type="boolean" checked="false" label="Create a FILTER in the FILTER column" truevalue="-f" falsevalue=""/>
12 <param name="ped" type="data" format="tabular" label="Pedigree file (Family/name/father/mother/sex)"/>
13 </inputs>
14 <outputs>
15 <data format="vcf" name="output"/>
16 </outputs>
17 <stdio>
18 <exit_code range="1:"/>
19 <exit_code range=":-1"/>
20 </stdio>
21 <help>
22
23 **Inputs**
24
25
26 - **VCF input** : VCF input
27
28 - **Create a FILTER in the FILTER column** : Create a FILTER in the FILTER column
29
30 - **Pedigree file (Family/name/father/mother/sex)** : Pedigree file (Family/name/father/mother/sex)
31
32
33 **Outputs**
34
35
36 - **output** : output
37
38
39 **Wiki**
40
41 https://github.com/lindenb/jvarkit/wiki/VCFTrio
42
43 -----
44
45
46 **Author**
47
48 Pierre Lindenbaum PhD @yokofakun
49
50 **Citation**
51
52 If you use this Galaxy tool in work leading to a scientific publication please
53 cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit
54
55 **Contribute**
56
57 - Issue Tracker: http://github.com/lindenb/jvarkit/issues`
58 - Source Code: http://github.com/lindenb/jvarkit
59
60 **License**
61
62 The project is licensed under the MIT license.
63
64 **Compilation**
65
66 Date: 2015-02-27T15:54:05+01:00
67 Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9
68 </help>
69 </tool>