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comparison snpEff_macros.xml @ 4:698ef30638a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
author iuc
date Fri, 16 Sep 2016 13:06:42 -0400
parents b24873564cf6
children 7adfd0589f49
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equal deleted inserted replaced
3:b24873564cf6 4:698ef30638a8
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="@SNPEFF_VERSION@">SnpEff4.1</token> 22 <token name="@SNPEFF_VERSION@">SnpEff4.1</token>
18 <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token> 23 <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token>
19 <token name="@EXTERNAL_DOCUMENTATION@"> 24 <token name="@EXTERNAL_DOCUMENTATION@">
20 25
21 For details about this tool, please go to: 26 For details about this tool, please go to:
22 http://snpeff.sourceforge.net/SnpEff_manual.html 27 http://snpeff.sourceforge.net/SnpEff_manual.html
23 28
24 </token> 29 </token>
25 <token name="@CITATION_SECTION@">------
26
27 **Citation**
28
29 For the underlying tool, please cite the following two publications:
30
31 SnpEff citation:
32 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly 6(2):80-92, 2012
33
34 </token>
35 <xml name="citations"> 30 <xml name="citations">
36 <citations> 31 <citations>
37 <citation type="doi">10.4161/fly.19695</citation> 32 <citation type="doi">10.4161/fly.19695</citation>
38 <yield /> 33 <yield />
39 </citations> 34 </citations>