Mercurial > repos > iuc > gemini_pathways

comparison gemini_pathways.xml @ 3:1e10a153192d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:38:41 -0500
parents 71c51883304f
children 1e736aee3c8c
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2:71c51883304f 3:1e10a153192d
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
2 <description>Map genes and variants to KEGG pathways</description> 2 <description>Map genes and variants to KEGG pathways</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">pathways</token> 5 <token name="@BINARY@">pathways</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 @BINARY@ 15 @BINARY@
17 -v $ensembl 16 -v $ensembl
18 $lof 17 $lof
19 "${ infile }" 18 "${ infile }"
20 > "${ outfile }" 19 > "${ outfile }"