Mercurial > repos > iuc > gemini_mendel_errors

comparison gemini_macros.xml @ 1:453eb01e00e7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:48:15 -0500
parents 886fdfe90b01
children 083ddae3ec8b
comparison
equal deleted inserted replaced
0:886fdfe90b01 1:453eb01e00e7
1 <macros> 1 <macros>
2 <!-- gemini version to be used -->
3 <token name="@VERSION@">0.18.1</token>
4 <!-- minimal annotation files version required by this version of gemini -->
5 <token name="@DB_VERSION@">181</token>
6
2 <xml name="requirements"> 7 <xml name="requirements">
3 <requirements> 8 <requirements>
4 <requirement type="package" version="0.18.1">gemini</requirement> 9 <requirement type="package" version="@VERSION@">gemini</requirement>
10 <requirement type="package" version="0.2.6">tabix</requirement>
11 <!-- for conda useage -->
12 <!--requirement type="package" version="1.3.1">htslib</requirement-->
5 <yield /> 13 <yield />
6 </requirements> 14 </requirements>
7 </xml> 15 </xml>
8 16
9 <xml name="version_command"> 17 <xml name="version_command">
18 <regex match="Exception:" /> 26 <regex match="Exception:" />
19 </stdio> 27 </stdio>
20 </xml> 28 </xml>
21 29
22 <xml name="annotation_dir"> 30 <xml name="annotation_dir">
23 <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database"> 31 <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
24 <options from_data_table="gemini_databases"> 32 <options from_data_table="gemini_versioned_databases">
25 <filter type="sort_by" column="0" /> 33 <filter type="sort_by" column="0" />
34 <filter type="static_value" column="2" value="@DB_VERSION@" />
26 </options> 35 </options>
27 </param> 36 </param>
28 </xml> 37 </xml>
29 38
30 <xml name="add_header_column"> 39 <xml name="add_header_column">
60 <option value="alt">alt</option> 69 <option value="alt">alt</option>
61 <option value="impact">impact</option> 70 <option value="impact">impact</option>
62 <option value="impact_severity">impact_severity</option> 71 <option value="impact_severity">impact_severity</option>
63 <option value="max_aaf_all">alternative allele frequency</option> 72 <option value="max_aaf_all">alternative allele frequency</option>
64 </param> 73 </param>
74 <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/>
65 </when> 75 </when>
66 </conditional> 76 </conditional>
67 </xml> 77 </xml>
68 78
69 <xml name="filter"> 79 <xml name="filter">
82 </conditional> 92 </conditional>
83 </xml> 93 </xml>
84 94
85 <xml name="sanitize_query"> 95 <xml name="sanitize_query">
86 <sanitizer invalid_char=""> 96 <sanitizer invalid_char="">
87 <valid initial="string.printable"/> 97 <valid initial="string.printable">
98 <remove value="&apos;" />
99 </valid>
100 <mapping initial="none">
101 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
102 </mapping>
88 </sanitizer> 103 </sanitizer>
89 </xml> 104 </xml>
90 105
106 <token name="@PROVIDE_ANNO_DATA@"><![CDATA[
107 mkdir gemini &&
108 ln -s "${annotation_databases.fields.path}/gemini/data" gemini/data &&
109 export GEMINI_CONFIG="${annotation_databases.fields.path}" &&
110 ]]></token>
111
112 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
113 #set $sql_expr = str($multiline_sql_expr).strip()
114 #if str($sql_expr):
115 #set $sql_expr = $sql_expr.replace('\r\n', '\n')
116 #set $sql_expr = $sql_expr.replace('\r', '\n')
117 #set $sql_expr = $sql_expr.replace('\\\n', ' ')
118 $cmdln_param '$sql_expr'
119 #end if
120 </token>
121
91 <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@"> 122 <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
92 #if str($filter.filter_selector) == 'yes' and $filter.filter: 123 #if str($filter.filter_selector) == 'yes' and $filter.filter:
93 #import pipes 124 --filter '${ str( $filter.filter ) }'
94 --filter ${ pipes.quote( str( $filter.filter ) ) or "''" } 125 #end if
126 </token>
127
128 <token name="@COLUMN_SELECT@">
129 #if $report.report_selector != 'all':
130 --columns "${report.columns}
131 #if str($report.extra_cols).strip()
132 #echo ','+','.join(str($report.extra_cols).split())
133 #end if
134 "
95 #end if 135 #end if
96 </token> 136 </token>
97 137
98 <xml name="family"> 138 <xml name="family">
99 <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/> 139 <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>
123 </xml> 163 </xml>
124 164
125 <xml name="gt_pl_max"> 165 <xml name="gt_pl_max">
126 <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" /> 166 <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" />
127 </xml> 167 </xml>
128 <token name="@VERSION@">0.18.1</token>
129 168
130 <xml name="citations"> 169 <xml name="citations">
131 <citations> 170 <citations>
132 <citation type="doi">10.1371/journal.pcbi.1003153</citation> 171 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
133 <yield /> 172 <yield />