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comparison gemini_pathways.xml @ 17:65f742e605ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:46:38 -0400
parents 53a5647e5271
children ce61d4876838
comparison
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16:ae03de7a9fee 17:65f742e605ec
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Map genes and variants to KEGG pathways</description> 2 <description>Map genes and variants to KEGG pathways</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros> 3 <macros>
6 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">pathways</token> 5 <token name="@BINARY@">pathways</token>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
9 <command> 10 <command>
10 <![CDATA[ 11 <![CDATA[
11 gemini 12 gemini
12 --annotation-dir ${annotation_databases.fields.path} 13 --annotation-dir ${annotation_databases.fields.path}
13 @BINARY@ 14 @BINARY@
14 -v $ensembl 15 -v $ensembl
15 $lof 16 $lof
16 "${ infile }" 17 "${ infile }"
17 > "${ outfile }" 18 > "${ outfile }"
18 ]]> 19 ]]>
19 </command> 20 </command>
20 <expand macro="stdio" />
21 <inputs> 21 <inputs>
22 <expand macro="infile" /> 22 <expand macro="infile" />
23 23
24 <param name="ensembl" type="integer" value="68" size="5" label="Version of ensembl genes to use" 24 <param name="ensembl" type="integer" value="68" size="5" label="Version of ensembl genes to use"
25 help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)"> 25 help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)">
26 <validator type="in_range" min="66" max="71"/> 26 <validator type="in_range" min="66" max="71"/>
27 </param> 27 </param>
28 28
29 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" 29 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
30 label="Report only pathways with loss-of-function variants" help="(--lof)"/> 30 label="Report only pathways with loss-of-function variants" help="(--lof)"/>
31 <expand macro="annotation_dir" /> 31 <expand macro="annotation_dir" />
32 </inputs> 32 </inputs>
33 <outputs> 33 <outputs>
34 <data name="outfile" format="tabular" /> 34 <data name="outfile" format="tabular" />
38 </test> 38 </test>
39 </tests> 39 </tests>
40 <help> 40 <help>
41 **What it does** 41 **What it does**
42 42
43 Mapping genes to biological pathways is useful in understanding the function/role played by a gene. 43 Mapping genes to biological pathways is useful in understanding the function/role played by a gene.
44 Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases. 44 Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases.
45 We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation. 45 We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation.
46 46
47 This requires your VCF be annotated with either snpEff/VEP. 47 This requires your VCF be annotated with either snpEff/VEP.
48 48
49 @CITATION@ 49 @CITATION@
50 </help> 50 </help>