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comparison snpEff_download.xml @ 23:924af057bbca draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Sat, 09 Apr 2016 11:51:40 -0400
parents bb0797deab78
children
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22:bb0797deab78 23:924af057bbca
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>
10 <![CDATA[ 10 <![CDATA[
11 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 "$genome_version"
12 ]]> 12 ]]>
13 </command> 13 </command>
14 <inputs> 14 <inputs>
15 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> 15 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
16 <help>@SNPEFF_DATABASE_URL@</help> 16 <help>@SNPEFF_DATABASE_URL@</help>
18 </param> 18 </param>
19 </inputs> 19 </inputs>
20 <outputs> 20 <outputs>
21 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> 21 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
22 </outputs> 22 </outputs>
23 <tests>
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>
23 <help><![CDATA[ 33 <help><![CDATA[
24 34
25 @EXTERNAL_DOCUMENTATION@ 35 @EXTERNAL_DOCUMENTATION@
26
27 @CITATION_SECTION@
28 36
29 ]]> 37 ]]>
30 </help> 38 </help>
31 <expand macro="citations" /> 39 <expand macro="citations" />
32 </tool> 40 </tool>