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comparison gemini_interactions.xml @ 0:720cbfb4190d draft

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Imported from capsule None
author iuc
date Mon, 25 Aug 2014 17:15:54 -0400
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children 93bb0cfacefb
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-1:000000000000 0:720cbfb4190d
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Find genes among variants that are interacting partners</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros>
6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">interactions</token>
8 </macros>
9 <command>
10 <![CDATA[
11 gemini
12 --annotation-dir ${annotation_databases.fields.path}
13 #if $gene.gene_selector == 'lof':
14 ## lof interactions is a separate program
15 lof_interactions
16 #else:
17 ## use normal gemini interactions program
18 @BINARY@
19 -g "${gene.gene}"
20 #end if
21
22 -r "${radius}"
23 $variant_mode
24 "${ infile }"
25 > "${ outfile }"
26 ]]>
27 </command>
28 <expand macro="stdio" />
29 <inputs>
30 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
31
32 <conditional name="gene">
33 <param name="gene_selector" type="select" label="Studying" help="">
34 <option value="gene">Interesting gene</option>
35 <option value="lof">All loss-of-function variants</option>
36 </param>
37 <when value="gene">
38 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" />
39 </when>
40 <when value="lof"/>
41 </conditional>
42 <expand macro="annotation_dir" />
43 <expand macro="radius" />
44 <expand macro="variant_mode" />
45 </inputs>
46 <outputs>
47 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
48 </outputs>
49 <tests>
50 <test>
51 </test>
52 </tests>
53 <help>
54 **What it does**
55
56 Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data.
57 Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the
58 protein itself. We have used the HPRD_ binary interaction data to build a p-p network graph which can be explored by GEMINI.
59
60 .. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627
61
62
63 @CITATION@
64 </help>
65 <expand macro="citations">
66 <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation -->
67 </expand>
68 </tool>