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comparison snpSift_macros.xml @ 280:2c41c1631d1c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:24:50 -0400
parents 02f54bf45aaf
children
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279:3ebd796c90e0 280:2c41c1631d1c
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.1">snpsift</requirement> 4 <requirement type="package" version="4.3.1p">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 <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 "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi && 16 SnpSift dbnsfp 2>&1|head -n 1
17 java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1 17 ]]></version_command>
18 ]]></version_command> 18 </xml>
19 </xml> 19 <token name="@WRAPPER_VERSION@">4.3</token>
20 <token name="@WRAPPER_VERSION@">4.1</token> 20 <token name="@EXTERNAL_DOCUMENTATION@">
21 <token name="@EXTERNAL_DOCUMENTATION@"> 21 For details about this tool, please go to:
22 22
23 For details about this tool, please go to: 23 - http://snpeff.sourceforge.net/SnpEff_manual.html
24 http://snpeff.sourceforge.net/SnpEff_manual.html 24 </token>
25 25 <xml name="citations">
26 </token> 26 <citations>
27 <xml name="citations"> 27 <citation type="doi">10.3389/fgene.2012.00035</citation>
28 <citations> 28 <yield />
29 <citation type="doi">10.3389/fgene.2012.00035</citation> 29 </citations>
30 <yield /> 30 </xml>
31 </citations>
32 </xml>
33 </macros> 31 </macros>