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comparison snpEff_databases.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_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" />
8 <expand macro="version_command" />
7 <command> 9 <command>
8 <![CDATA[ 10 <![CDATA[
9 java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > $snpeff_dbs 11 java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > "$snpeff_dbs"
10 ]]> 12 ]]>
11 </command> 13 </command>
12 <inputs> 14 <inputs>
13 </inputs> 15 </inputs>
14 <outputs> 16 <outputs>
15 <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" /> 17 <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" />
16 </outputs> 18 </outputs>
17 <expand macro="stdio" /> 19 <tests>
18 <help> 20 <test>
21 <output name="snpeff_dbs">
22 <assert_contents>
23 <has_text text="ebola_zaire" />
24 </assert_contents>
25 </output>
26 </test>
27 </tests>
28 <help><![CDATA[
19 29
20 @EXTERNAL_DOCUMENTATION@ 30 @EXTERNAL_DOCUMENTATION@
21 31
22 @CITATION_SECTION@ 32 ]]>
23
24 </help> 33 </help>
34 <expand macro="citations" />
25 </tool> 35 </tool>
26 36