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comparison gemini_region.xml @ 0:720cbfb4190d draft

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Imported from capsule None
author iuc
date Mon, 25 Aug 2014 17:15:54 -0400
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children 93bb0cfacefb
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-1:000000000000 0:720cbfb4190d
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Extracting variants from specific regions or genes</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros>
6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">region</token>
8 </macros>
9 <command>
10 <![CDATA[
11 gemini @BINARY@
12
13 #if $region.region_selector == '--reg':
14 #if str(${region.region}) != '':
15 --reg "${region.region}"
16 #end if
17 #else:
18 #if str(${region.gene}) != '':
19 --gene "${region.gene}"
20 #end if
21 #end if
22
23 #if $report.report_selector != 'all':
24 --columns "${report.columns}"
25 #end if
26
27 #if $filter.filter_selector == 'yes':
28 --filter "${filter.filter}"
29 #end if
30
31 $header
32 "${ infile }"
33 > "${ outfile }"
34 ]]>
35 </command>
36 <expand macro="stdio" />
37 <inputs>
38 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
39
40 <conditional name="region">
41 <param name="region_selector" type="select" label="Select by ...?" help="">
42 <option value="--reg">genomic coordinates</option>
43 <option value="--gene">gene name</option>
44 </param>
45 <when value="--reg">
46 <param name="region" type="text" label="Specify genomic region" help="e.g. chr1:100-200 (--reg)"/>
47 </when>
48 <when value="--gene">
49 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (--gene)" />
50 </when>
51 </conditional>
52
53 <expand macro="column_filter" />
54 <expand macro="filter" />
55
56
57 <expand macro="add_header_column" />
58
59 </inputs>
60 <outputs>
61 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
62 </outputs>
63 <tests>
64 <test>
65 </test>
66 </tests>
67 <help>
68 **What it does**
69
70 One often is concerned with variants found solely in a particular gene or genomic region.
71
72 @CITATION@
73 </help>
74 <expand macro="citations"/>
75 </tool>