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comparison snpEff_macros.xml @ 11:81fba81425a4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
author iuc
date Tue, 18 Apr 2017 09:33:43 -0400
parents 1501e66908de
children bbbab2d84e3b
comparison
equal deleted inserted replaced
10:3efa0848f013 11:81fba81425a4
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.1">snpEff</requirement> 4 <requirement type="package" version="4.3k">snpeff</requirement>
5 </requirements> 5 </requirements>
6 </xml> 6 </xml>
7 <xml name="stdio"> 7 <xml name="stdio">
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>
14 <xml name="version_command"> 13 <xml name="version_command">
15 <version_command><![CDATA[ 14 <version_command><![CDATA[
16 if [ -z "$SNPEFF_JAR_PATH" ]; then 15 snpEff -version
17 export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
18 fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
19 ]]></version_command> 16 ]]></version_command>
20 </xml> 17 </xml>
21 <token name="@WRAPPER_VERSION@">4.1</token> 18 <token name="@WRAPPER_VERSION@">4.3k</token>
22 <token name="@SNPEFF_VERSION@">SnpEff4.1</token> 19 <token name="@SNPEFF_VERSION@">SnpEff4.3</token>
23 <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token> 20 <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
24 <token name="@EXTERNAL_DOCUMENTATION@"> 21 <token name="@EXTERNAL_DOCUMENTATION@">
25 22 For details about this tool, please go to: http://snpeff.sourceforge.net/SnpEff_manual.html
26 For details about this tool, please go to:
27 http://snpeff.sourceforge.net/SnpEff_manual.html
28
29 </token> 23 </token>
30 <xml name="citations"> 24 <xml name="citations">
31 <citations> 25 <citations>
32 <citation type="doi">10.4161/fly.19695</citation> 26 <citation type="doi">10.4161/fly.19695</citation>
33 <yield /> 27 <yield />