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comparison snpEff_databases.xml @ 7:aaa749ea91a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e
author iuc
date Tue, 07 Jun 2016 09:40:10 -0400
parents 92b80578fa22
children 1501e66908de
comparison
equal deleted inserted replaced
6:9ec1cb6f760d 7:aaa749ea91a2
3 <macros> 3 <macros>
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 <command> 9 <command>
9 <![CDATA[ 10 <![CDATA[
10 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"
11 ]]> 12 ]]>
12 </command> 13 </command>
13 <inputs> 14 <inputs>
14 </inputs> 15 </inputs>
15 <outputs> 16 <outputs>
16 <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" />
17 </outputs> 18 </outputs>
18 <help> 19 <tests>
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