Mercurial > repos > yokofakun > jvarkit
comparison jvarkit/vcftrio.xml @ 8:98106098dcd1 draft
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author | yokofakun |
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date | Fri, 27 Feb 2015 09:52:06 -0500 |
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7:e5723e64ea43 | 8:98106098dcd1 |
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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 && 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> |