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comparison gemini_pathways.xml @ 4:ca4449689d61 draft

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author iuc
date Mon, 25 Aug 2014 03:19:30 -0400
parents e6512af21622
children 6ab82d8ca805
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3:2ebcf5c69c5e 4:ca4449689d61
6 <import>gemini_macros.xml</import> 6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">pathways</token> 7 <token name="@BINARY@">pathways</token>
8 </macros> 8 </macros>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 gemini @BINARY@ 11 gemini
12 --annotation-dir ${annotation_databases}
13 @BINARY@
12 -v $ensembl 14 -v $ensembl
13 $lof 15 $lof
14 "${ infile }" 16 "${ infile }"
15 > "${ outfile }" 17 > "${ outfile }"
16 ]]> 18 ]]>
24 <validator type="in_range" min="66" max="71"/> 26 <validator type="in_range" min="66" max="71"/>
25 </param> 27 </param>
26 28
27 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" 29 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
28 label="Report only pathways with loss-of-function variants" help="(--lof)"/> 30 label="Report only pathways with loss-of-function variants" help="(--lof)"/>
29 31 <expand macro="annotation_dir" />
30 </inputs> 32 </inputs>
31 <outputs> 33 <outputs>
32 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> 34 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
33 </outputs> 35 </outputs>
34 <tests> 36 <tests>