Mercurial > repos > iuc > snpsift_genesets

comparison snpSift_macros.xml @ 3:847db7b39bdc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:06:09 -0500
parents 9ba6e2c298ab
children d12a810c837e
comparison
equal deleted inserted replaced
2:9ba6e2c298ab 3:847db7b39bdc
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_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token> 13 <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token>
14 <xml name="version_command"> 14 <xml name="version_command">
15 <version_command><![CDATA[ 15 <version_command><![CDATA[
16 if [ -z "$SNPEFF_JAR_PATH" ]; then 16 if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi &&
17 export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff))); 17 java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1
18 fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
19 ]]></version_command> 18 ]]></version_command>
20 </xml> 19 </xml>
21 <token name="@WRAPPER_VERSION@">4.1</token> 20 <token name="@WRAPPER_VERSION@">4.1</token>
22 <token name="@EXTERNAL_DOCUMENTATION@"> 21 <token name="@EXTERNAL_DOCUMENTATION@">
23 22
24 For details about this tool, please go to: 23 For details about this tool, please go to:
25 http://snpeff.sourceforge.net/SnpEff_manual.html 24 http://snpeff.sourceforge.net/SnpEff_manual.html
26 25
27 </token> 26 </token>
28 <token name="@CITATION_SECTION@">------
29
30 **Citation**
31
32 For the underlying tool, please cite the following two publications:
33
34 SnpSift citation:
35 "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.
36
37 </token>
38 <xml name="citations"> 27 <xml name="citations">
39 <citations> 28 <citations>
40 <citation type="doi">10.3389/fgene.2012.00035</citation> 29 <citation type="doi">10.3389/fgene.2012.00035</citation>
41 <yield /> 30 <yield />
42 </citations> 31 </citations>