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comparison snpSift_macros.xml @ 2:bf8c1526871b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:11:18 -0500
parents 98708b88af9f
children 20c7d583fec1
comparison
equal deleted inserted replaced
1:98708b88af9f 2:bf8c1526871b
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="4.1">snpsift</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_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token>
13 <xml name="version_command"> 14 <xml name="version_command">
14 <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command> 15 <version_command><![CDATA[
16 if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi &&
17 java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1
18 ]]></version_command>
15 </xml> 19 </xml>
16 <token name="@WRAPPER_VERSION@">4.1</token> 20 <token name="@WRAPPER_VERSION@">4.1</token>
17 <token name="@EXTERNAL_DOCUMENTATION@"> 21 <token name="@EXTERNAL_DOCUMENTATION@">
18 22
19 For details about this tool, please go to: 23 For details about this tool, please go to:
20 http://snpeff.sourceforge.net/SnpEff_manual.html 24 http://snpeff.sourceforge.net/SnpEff_manual.html
21
22 </token>
23 <token name="@CITATION_SECTION@">------
24
25 **Citation**
26
27 For the underlying tool, please cite the following two publications:
28
29 SnpSift citation:
30 "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012.
31 25
32 </token> 26 </token>
33 <xml name="citations"> 27 <xml name="citations">
34 <citations> 28 <citations>
35 <citation type="doi">10.3389/fgene.2012.00035</citation> 29 <citation type="doi">10.3389/fgene.2012.00035</citation>