Mercurial > repos > yokofakun > jvarkit
comparison jvarkit/vcffilterjs.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.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 && 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> |