Mercurial > repos > iuc > gemini_interactions

comparison gemini_interactions.xml @ 4:a6d326ffbb72 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:50:32 -0500
parents 527c8e4a356f
children 7028ca3cac1c
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3:184aa4e686e2 4:a6d326ffbb72
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
2 <description>Find genes among variants that are interacting partners</description> 2 <description>Find genes among variants that are interacting partners</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">interactions</token> 5 <token name="@BINARY@">interactions</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 @PROVIDE_ANNO_DATA@
13
12 gemini 14 gemini
13 #if $annotation_databases:
14 --annotation-dir "${annotation_databases.fields.path}"
15 #end if
16
17 #if $gene.gene_selector == 'lof': 15 #if $gene.gene_selector == 'lof':
18 ## lof interactions is a separate program 16 ## lof interactions is a separate program
19 lof_interactions 17 lof_interactions
20 #else: 18 #else:
21 ## use normal gemini interactions program 19 ## use normal gemini interactions program
49 <outputs> 47 <outputs>
50 <data name="outfile" format="tabular" /> 48 <data name="outfile" format="tabular" />
51 </outputs> 49 </outputs>
52 <tests> 50 <tests>
53 <test> 51 <test>
54 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" /> 52 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
55 <param name="gene" value="CTBP2" /> 53 <param name="gene" value="BCL6" />
56 <param name="radius" value="5" /> 54 <param name="radius" value="5" />
57 <output name="outfile" file="gemini_interactions_result.tabular" /> 55 <output name="outfile">
56 <assert_contents>
57 <has_line_matching expression="sample&#009;gene&#009;order_of_interaction&#009;interacting_gene.*" />
58 </assert_contents>
59 </output>
58 </test> 60 </test>
59 </tests> 61 </tests>
60 <help><![CDATA[ 62 <help><![CDATA[
61 **What it does** 63 **What it does**
62 64