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comparison snpEff_download.xml @ 7:7adfd0589f49 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
author iuc
date Tue, 18 Apr 2017 09:33:56 -0400
parents 698ef30638a8
children 68693743661e
comparison
equal deleted inserted replaced
6:20f0429a4bfe 7:7adfd0589f49
4 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command><![CDATA[
10 <![CDATA[ 10 snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version'
11 @CONDA_SNPEFF_JAR_PATH@ && 11 ]]></command>
12 java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version"
13 ]]>
14 </command>
15 <inputs> 12 <inputs>
16 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> 13 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh38.86, GRCh37.75, hg38, or GRCm38.86)">
17 <help>@SNPEFF_DATABASE_URL@</help> 14 <help>@SNPEFF_DATABASE_URL@</help>
18 <validator type="regex" message="A genome version name is required">\S+</validator> 15 <validator type="regex" message="A genome version name is required">\S+</validator>
19 </param> 16 </param>
20 </inputs> 17 </inputs>
21 <outputs> 18 <outputs>
30 </assert_contents> 27 </assert_contents>
31 </output> 28 </output>
32 </test> 29 </test>
33 </tests> 30 </tests>
34 <help><![CDATA[ 31 <help><![CDATA[
35
36 @EXTERNAL_DOCUMENTATION@ 32 @EXTERNAL_DOCUMENTATION@
37 33 ]]></help>
38 ]]>
39 </help>
40 <expand macro="citations" /> 34 <expand macro="citations" />
41 </tool> 35 </tool>
42