Mercurial > repos > iuc > gemini_actionable_mutations

comparison gemini_actionable_mutations.xml @ 0:b6fb24500a86 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:54:38 -0500
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children 712aa8283200
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-1:000000000000 0:b6fb24500a86
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Retrieve genes with actionable somatic mutations via COSMIC and DGIdb</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">actionable_mutations</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini @BINARY@
13 "${ infile }" | tr -s ' ' '\t'
14 > "${ outfile }"
15 ]]>
16 </command>
17 <inputs>
18 <expand macro="infile" />
19 </inputs>
20 <outputs>
21 <data name="outfile" format="tabular" />
22 </outputs>
23 <tests>
24 <test>
25 <!-- Like in set_somatic this example is nonsensical because otherwise
26 the testdata would be too big.-->
27 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
28 <output name="outfile" file="gemini_actionable_mutations_result.tabular" />
29 </test>
30 </tests>
31 <help><![CDATA[
32 **What it does**
33
34 Retrieve genes with actionable somatic mutations via COSMIC and DGIdb. It checks for variants that have the somatic flag set (which can be done with GEMINI set_somatic) with high or medium impact severity. The results are then compared to entries in COSMIC and DGIdb
35
36 ]]></help>
37 <expand macro="citations"/>
38 </tool>