Mercurial > repos > iuc > gatk4_mutect2

comparison macros.xml @ 1:fd2d6e035c3f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"
author iuc
date Mon, 18 Nov 2019 13:45:47 -0500
parents f41a1e03538b
children 3be27a9a7313
comparison
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0:f41a1e03538b 1:fd2d6e035c3f
20 <!--Command token, java options should not be hard coded here.--> 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> 21 <token name="@CMD_BEGIN@">[[ -z \$_JAVA_OPTIONS ]] &amp;&amp; export JAVA_OPTS=\$_JAVA_OPTIONS &amp;&amp; gatk</token>
22 22
23 <!--Define sections that parameters could exist within.--> 23 <!--Define sections that parameters could exist within.-->
24 <template name="set_sections"> 24 <template name="set_sections">
25 #set global $sections = ['', 'optional.', 'advanced.', 'common.', 'deprecated.'] 25 #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.']
26 </template> 26 </template>
27 27
28 <!--Reference genome handling--> 28 <!--Reference genome handling-->
29 <!--One template each for the different reference genome parameter names.--> 29 <!--One template each for the different reference genome parameter names.-->
30 <!--TODO: Can the reference parameters all be the same?--> 30 <!--TODO: Can the reference parameters all be the same?-->
669 </data> 669 </data>
670 </xml> 670 </xml>
671 671
672 672
673 <!--<template name="ref_opts">--> 673 <!--<template name="ref_opts">-->
674 <!--#set $sections = ['optional','advanced','common','deprecated','']--> 674 <!--#set $sections = ['optional','advanced','deprecated','']-->
675 <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: '${sections}'\n")--> 675 <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: '${sections}'\n")-->
676 <!--#for $sect in $sections--> 676 <!--#for $sect in $sections-->
677 <!--#if $varExists('$sect.reference_source.reference_source_selector')--> 677 <!--#if $varExists('$sect.reference_source.reference_source_selector')-->
678 <!--#if $sect.reference_source.reference_source_selector != "no_ref"--> 678 <!--#if $sect.reference_source.reference_source_selector != "no_ref"-->
679 <!--#if $sect.reference_source.reference_source_selector != "history"--> 679 <!--#if $sect.reference_source.reference_source_selector != "history"-->