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comparison snpEff_databases.xml @ 5:92b80578fa22 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:37:25 -0400
parents 114f423f99c0
children aaa749ea91a2
comparison
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4:b86c907031ad 5:92b80578fa22
1 <tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0">
2 <description></description> 2 <description></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" />
7 <command> 8 <command>
8 <![CDATA[ 9 <![CDATA[
9 java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > $snpeff_dbs 10 java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > $snpeff_dbs
10 ]]> 11 ]]>
11 </command> 12 </command>
12 <inputs> 13 <inputs>
13 </inputs> 14 </inputs>
14 <outputs> 15 <outputs>
15 <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" /> 16 <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" />
16 </outputs> 17 </outputs>
17 <expand macro="stdio" />
18 <help> 18 <help>
19 19
20 @EXTERNAL_DOCUMENTATION@ 20 @EXTERNAL_DOCUMENTATION@
21 21
22 @CITATION_SECTION@ 22 @CITATION_SECTION@