|
8
|
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>
|
