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comparison snpSift_macros.xml @ 2:9ba6e2c298ab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
author iuc
date Mon, 19 Sep 2016 14:43:55 -0400
parents 0af41de4eda1
children 847db7b39bdc
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1:0af41de4eda1 2:9ba6e2c298ab
8 <stdio> 8 <stdio>
9 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 9 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
10 <exit_code range="1:" level="fatal" description="Error" /> 10 <exit_code range="1:" level="fatal" description="Error" />
11 </stdio> 11 </stdio>
12 </xml> 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>
13 <xml name="version_command"> 14 <xml name="version_command">
14 <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command> 15 <version_command><![CDATA[
16 if [ -z "$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>
15 </xml> 20 </xml>
16 <token name="@WRAPPER_VERSION@">4.1</token> 21 <token name="@WRAPPER_VERSION@">4.1</token>
17 <token name="@EXTERNAL_DOCUMENTATION@"> 22 <token name="@EXTERNAL_DOCUMENTATION@">
18 23
19 For details about this tool, please go to: 24 For details about this tool, please go to: