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comparison snpEff_download.xml @ 3:b24873564cf6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author iuc
date Tue, 07 Jun 2016 10:03:17 -0400
parents 500832f27cbc
children 698ef30638a8
comparison
equal deleted inserted replaced
2:e09ce114d240 3:b24873564cf6
1 <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0">
2 <description>Download a new database</description> 2 <description>Download a new database</description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" />
7 <command> 9 <command>
8 <![CDATA[ 10 <![CDATA[
9 java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version 11 java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version"
10 ]]> 12 ]]>
11 </command> 13 </command>
12 <inputs> 14 <inputs>
13 <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> 15 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
14 <help>@SNPEFF_DATABASE_URL@</help> 16 <help>@SNPEFF_DATABASE_URL@</help>
15 <validator type="regex" message="A genome version name is required">\S+</validator> 17 <validator type="regex" message="A genome version name is required">\S+</validator>
16 </param> 18 </param>
17 </inputs> 19 </inputs>
18 <outputs> 20 <outputs>
19 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> 21 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
20 </outputs> 22 </outputs>
21 <expand macro="stdio" /> 23 <tests>
22 <help> 24 <test>
25 <param name="genome_version" value="ebola_zaire"/>
26 <output name="snpeff_db">
27 <assert_contents>
28 <has_text text="ebola_zaire" />
29 </assert_contents>
30 </output>
31 </test>
32 </tests>
33 <help><![CDATA[
23 34
24 @EXTERNAL_DOCUMENTATION@ 35 @EXTERNAL_DOCUMENTATION@
25 36
26 @CITATION_SECTION@ 37 ]]>
27
28 </help> 38 </help>
29 <expand macro="citations" /> 39 <expand macro="citations" />
30 </tool> 40 </tool>
31 41