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comparison jvarkit/vcffilterjs.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.vcffilterjs.VCFFilterJS" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcffilterjs">
3 <!--Date: 2015-02-27T15:54:02+01:00-->
4 <description>Filters a VCF with Javascript</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:$__tool_directory__/vcffilterjs.jar com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e '${expression}' -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="expression" type="text" label="javascript expression">
12 <sanitizer>
13 <valid initial="string.printable">
14 <add source="'" target="\'"/>
15 </valid>
16 </sanitizer>
17 </param>
18 </inputs>
19 <outputs>
20 <data format="vcf" name="output"/>
21 </outputs>
22 <stdio>
23 <exit_code range="1:"/>
24 <exit_code range=":-1"/>
25 </stdio>
26 <help>
27
28 **Inputs**
29
30
31 - **VCF input** : VCF input
32
33 - **javascript expression** : javascript expression
34
35
36 **Outputs**
37
38
39 - **output** : output
40
41
42 **Wiki**
43
44 https://github.com/lindenb/jvarkit/wiki/VCFFilterJS
45
46 -----
47
48
49 **Author**
50
51 Pierre Lindenbaum PhD @yokofakun
52
53 **Citation**
54
55 If you use this Galaxy tool in work leading to a scientific publication please
56 cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit
57
58 **Contribute**
59
60 - Issue Tracker: http://github.com/lindenb/jvarkit/issues`
61 - Source Code: http://github.com/lindenb/jvarkit
62
63 **License**
64
65 The project is licensed under the MIT license.
66
67 **Compilation**
68
69 Date: 2015-02-27T15:54:02+01:00
70 Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9
71 </help>
72 </tool>