Mercurial > repos > iuc > gatk4_mutect2

comparison macros.xml @ 2:5f71f3690b95 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 093a027ca9e7d34e7d12cd14ca0d0dacadfcb78b"
author iuc
date Fri, 10 Apr 2020 18:10:33 +0000
parents 09393225f90f
children d2c0c2698f58
comparison
equal deleted inserted replaced
1:09393225f90f 2:5f71f3690b95
14 14
15 <!--Hacky way to determine GATK version, for display in tool info--> 15 <!--Hacky way to determine GATK version, for display in tool info-->
16 <xml name="version_cmd"> 16 <xml name="version_cmd">
17 <version_command>gatk SortSam --version 2>&amp;1 | grep Version | cut -d ':' -f 2</version_command> 17 <version_command>gatk SortSam --version 2>&amp;1 | grep Version | cut -d ':' -f 2</version_command>
18 </xml> 18 </xml>
19
20 <!--Command token, java options should not be hard coded here.-->
21 <token name="@CMD_BEGIN@">[[ -z \$_JAVA_OPTIONS ]] &amp;&amp; export JAVA_OPTS=\$_JAVA_OPTIONS &amp;&amp; gatk</token>
22 19
23 <!--Define sections that parameters could exist within.--> 20 <!--Define sections that parameters could exist within.-->
24 <template name="set_sections"> 21 <template name="set_sections">
25 #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.'] 22 #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.']
26 </template> 23 </template>