Mercurial > repos > iuc > gemini_set_somatic

comparison gemini_macros.xml @ 4:7b031989ea12 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:53:10 -0500
parents ef9991a4a9a7
children 991049484627
comparison
equal deleted inserted replaced
3:ef9991a4a9a7 4:7b031989ea12
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>
5 <requirement type="package" version="0.2.6">tabix</requirement> 10 <requirement type="package" version="0.2.6">tabix</requirement>
6 <!-- for conda useage --> 11 <!-- for conda useage -->
7 <!--requirement type="package" version="1.3.1">htslib</requirement--> 12 <!--requirement type="package" version="1.3.1">htslib</requirement-->
8 <yield /> 13 <yield />
9 </requirements> 14 </requirements>
21 <regex match="Exception:" /> 26 <regex match="Exception:" />
22 </stdio> 27 </stdio>
23 </xml> 28 </xml>
24 29
25 <xml name="annotation_dir"> 30 <xml name="annotation_dir">
26 <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 source">
27 <options from_data_table="gemini_databases"> 32 <options from_data_table="gemini_versioned_databases">
28 <filter type="sort_by" column="0" /> 33 <filter type="sort_by" column="0" />
34 <filter type="static_value" column="2" value="@DB_VERSION@" />
29 </options> 35 </options>
30 </param> 36 </param>
31 </xml> 37 </xml>
32 38
33 <xml name="add_header_column"> 39 <xml name="add_header_column">
95 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" /> 101 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
96 </mapping> 102 </mapping>
97 </sanitizer> 103 </sanitizer>
98 </xml> 104 </xml>
99 105
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
100 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@"> 112 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
101 #set $sql_expr = str($multiline_sql_expr).strip() 113 #set $sql_expr = str($multiline_sql_expr).strip()
102 #if str($sql_expr): 114 #if str($sql_expr):
103 #set $sql_expr = $sql_expr.replace('\r\n', '\n') 115 #set $sql_expr = $sql_expr.replace('\r\n', '\n')
104 #set $sql_expr = $sql_expr.replace('\r', '\n') 116 #set $sql_expr = $sql_expr.replace('\r', '\n')
151 </xml> 163 </xml>
152 164
153 <xml name="gt_pl_max"> 165 <xml name="gt_pl_max">
154 <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)" />
155 </xml> 167 </xml>
156 <token name="@VERSION@">0.18.1</token>
157 168
158 <xml name="citations"> 169 <xml name="citations">
159 <citations> 170 <citations>
160 <citation type="doi">10.1371/journal.pcbi.1003153</citation> 171 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
161 <yield /> 172 <yield />