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comparison jvarkit/vcffilterso.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.misc.VcfFilterSequenceOntology" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcffilterso">
3 <!--Date: 2015-02-27T15:54:06+01:00-->
4 <description>Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology</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__/vcffilterso.jar com.github.lindenb.jvarkit.tools.misc.VcfFilterSequenceOntology
9 #for s in $accessions
10 -A '$s'
11 #end for
12 $inverse $noreason -o ${output}.vcf.gz &amp;&amp; mv ${output}.vcf.gz ${output} </command>
13 <inputs>
14 <param format="vcf" name="input" type="data" label="VCF input"/>
15 <repeat name="accessions" title="accessions">
16 <param name="acn" type="text" label="SO Accession Number">
17 <validator type="regex" message="must match with SO:(number)">SO\:[0-9]+</validator>
18 </param>
19 </repeat>
20 <param name="inverse" type="boolean" checked="false" label="inverse selection" truevalue="-v" falsevalue=""/>
21 <param name="noreason" type="boolean" checked="false" label="disable reasoning" truevalue="-d" falsevalue=""/>
22 </inputs>
23 <outputs>
24 <data format="vcf" name="output"/>
25 </outputs>
26 <stdio>
27 <exit_code range="1:"/>
28 <exit_code range=":-1"/>
29 </stdio>
30 <help>
31
32
33 **Examples**
34
35
36
37
38 **Inputs**
39
40
41 - **VCF input** : VCF input
42
43 - **inverse selection** : inverse selection
44
45 - **disable reasoning** : disable reasoning
46
47
48 **Outputs**
49
50
51 - **output** : output
52
53
54 **Wiki**
55
56 https://github.com/lindenb/jvarkit/wiki/VcfFilterSequenceOntology
57
58 -----
59
60
61 **Author**
62
63 Pierre Lindenbaum PhD @yokofakun
64
65 **Citation**
66
67 If you use this Galaxy tool in work leading to a scientific publication please
68 cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit
69
70 **Contribute**
71
72 - Issue Tracker: http://github.com/lindenb/jvarkit/issues`
73 - Source Code: http://github.com/lindenb/jvarkit
74
75 **License**
76
77 The project is licensed under the MIT license.
78
79 **Compilation**
80
81 Date: 2015-02-27T15:54:06+01:00
82 Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9
83 </help>
84 </tool>