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comparison jvarkit/groupbygene.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.groupbygene.GroupByGene" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="groupbygene">
3 <!--Date: 2015-02-27T15:54:07+01:00-->
4 <description>Group VCF (+ VEP + SnpEff) data by gene/transcript</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__/groupbygene.jar com.github.lindenb.jvarkit.tools.groupbygene.GroupByGene -o ${output}.tsv &amp;&amp; mv ${output}.tsv ${output}</command>
9 <inputs>
10 <param format="vcf" name="input" type="data" label="VCF input"/>
11 </inputs>
12 <outputs>
13 <data format="vcf" name="output"/>
14 </outputs>
15 <stdio>
16 <exit_code range="1:"/>
17 <exit_code range=":-1"/>
18 </stdio>
19 <help>
20
21 **Inputs**
22
23
24 - **VCF input** : VCF input
25
26
27 **Outputs**
28
29
30 - **output** : output
31
32
33 **Wiki**
34
35 https://github.com/lindenb/jvarkit/wiki/GroupByGene
36
37 -----
38
39
40 **Author**
41
42 Pierre Lindenbaum PhD @yokofakun
43
44 **Citation**
45
46 If you use this Galaxy tool in work leading to a scientific publication please
47 cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit
48
49 **Contribute**
50
51 - Issue Tracker: http://github.com/lindenb/jvarkit/issues`
52 - Source Code: http://github.com/lindenb/jvarkit
53
54 **License**
55
56 The project is licensed under the MIT license.
57
58 **Compilation**
59
60 Date: 2015-02-27T15:54:07+01:00
61 Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9
62 </help>
63 </tool>