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comparison gemini_region.xml @ 0:bb4a5f979906 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:51:44 -0500
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-1:000000000000 0:bb4a5f979906
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Extracting variants from specific regions or genes</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">region</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 gemini @BINARY@
13
14 #if $region.region_selector == '--reg':
15 #if str($region.region).strip():
16 --reg "${region.region}"
17 #end if
18 #else:
19 #if str($region.gene).strip():
20 --gene "${region.gene}"
21 #end if
22 #end if
23
24 #if $report.report_selector != 'all':
25 --columns "${report.columns}"
26 #end if
27
28 @CMDLN_SQL_FILTER_FILTER_OPTION@
29
30 $show_samples
31
32
33 $header
34 "${ infile }"
35 > "${ outfile }"
36 ]]>
37 </command>
38 <inputs>
39 <expand macro="infile" />
40
41 <conditional name="region">
42 <param name="region_selector" type="select" label="Select by ...?" help="">
43 <option value="--reg">genomic coordinates</option>
44 <option value="--gene">gene name</option>
45 </param>
46 <when value="--reg">
47 <param name="region" type="text" label="Specify genomic region" help="e.g. chr1:100-200 (--reg)"/>
48 </when>
49 <when value="--gene">
50 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (--gene)" />
51 </when>
52 </conditional>
53
54 <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False" label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>
55
56 <expand macro="column_filter" />
57 <expand macro="filter" />
58 <expand macro="add_header_column" />
59
60 </inputs>
61 <outputs>
62 <data name="outfile" format="tabular" />
63 </outputs>
64 <tests>
65 <test>
66 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
67 <param name="region_selector" value="--reg" />
68 <param name="region" value="chr10:48000000-49000000" />
69 <param name="columns" value="chrom,start,gene" />
70 <output name="outfile" file="gemini_region_result.tabular" />
71 </test>
72 </tests>
73 <help>
74 **What it does**
75
76 One often is concerned with variants found solely in a particular gene or genomic region.
77
78 </help>
79 <expand macro="citations"/>
80 </tool>