Mercurial > repos > iuc > gemini_actionable_mutations

comparison gemini_macros.xml @ 2:a0379503290f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 13:19:15 -0500
parents 9f0f5e984ae3
children 3630a6e624d4
comparison
equal deleted inserted replaced
1:9f0f5e984ae3 2:a0379503290f
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.18.1">gemini</requirement> 4 <requirement type="package" version="0.18.1">gemini</requirement>
5 <requirement type="package" version="0.2.6">tabix</requirement> 5 <requirement type="package" version="0.2.6">tabix</requirement>
6 <!-- for conda useage -->
7 <!--requirement type="package" version="1.3.1">htslib</requirement-->
6 <yield /> 8 <yield />
7 </requirements> 9 </requirements>
8 </xml> 10 </xml>
9 11
10 <xml name="version_command"> 12 <xml name="version_command">
61 <option value="alt">alt</option> 63 <option value="alt">alt</option>
62 <option value="impact">impact</option> 64 <option value="impact">impact</option>
63 <option value="impact_severity">impact_severity</option> 65 <option value="impact_severity">impact_severity</option>
64 <option value="max_aaf_all">alternative allele frequency</option> 66 <option value="max_aaf_all">alternative allele frequency</option>
65 </param> 67 </param>
68 <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/>
66 </when> 69 </when>
67 </conditional> 70 </conditional>
68 </xml> 71 </xml>
69 72
70 <xml name="filter"> 73 <xml name="filter">
91 94
92 <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@"> 95 <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
93 #if str($filter.filter_selector) == 'yes' and $filter.filter: 96 #if str($filter.filter_selector) == 'yes' and $filter.filter:
94 #import pipes 97 #import pipes
95 --filter ${ pipes.quote( str( $filter.filter ) ) or "''" } 98 --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
99 #end if
100 </token>
101
102 <token name="@COLUMN_SELECT@">
103 #if $report.report_selector != 'all':
104 --columns "${report.columns}
105 #if str($report.extra_cols).strip()
106 #echo ','+','.join(str($report.extra_cols).split())
107 #end if
108 "
96 #end if 109 #end if
97 </token> 110 </token>
98 111
99 <xml name="family"> 112 <xml name="family">
100 <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/> 113 <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>