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comparison data_manager/snpEff_macros.xml @ 2:c54b7693456f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
author iuc
date Mon, 31 Oct 2016 08:11:53 -0400
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1:c33041cee35a 2:c54b7693456f
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="4.1">snpEff</requirement>
5 </requirements>
6 </xml>
7 <xml name="stdio">
8 <stdio>
9 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
10 <exit_code range="1:" level="fatal" description="Error" />
11 </stdio>
12 </xml>
13 <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
14 <xml name="version_command">
15 <version_command><![CDATA[
16 if [ -z "$SNPEFF_JAR_PATH" ]; then
17 export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
18 fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
19 ]]></version_command>
20 </xml>
21 <token name="@WRAPPER_VERSION@">4.1</token>
22 <xml name="citations">
23 <citations>
24 <citation type="doi">10.4161/fly.19695</citation>
25 <yield />
26 </citations>
27 </xml>
28 </macros>