comparison gemini_query.xml @ 0:720cbfb4190d draft

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>Querying the GEMINI database</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros>
6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">query</token>
8 </macros>
9 <command>
10 <![CDATA[
11 gemini @BINARY@
12
13 --in "${in}"
14
15 #if $gt_filter.strip():
16 --gt-filter "${gt_filter}"
17 #end if
18
19 #if $sample_filter.strip():
20 --sample-filter "${sample_filter}"
21 #end if
22
23 $show_samples
24 $show_families
25 $family_wise
26 $header
27 $dgidb
28 #if $region.strip():
29 --region "${region}"
30 #end if
31 #if int($min_kindreds) > 0:
32 --min-kindreds $min_kindreds
33 #end if
34 ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being
35 ## --sample-delim STRING The delimiter to be used with the --show-samples option.
36
37 #if $q.strip():
38 -q "${q}"
39 #end if
40
41 "${ infile }"
42 > "${ outfile }"
43 ]]>
44 </command>
45 <!--
46 ##TODO:
47 - -carrier-summary-by-phenotype CARRIER_SUMMARY
48 Output columns of counts of carriers and non-carriers
49 stratified by the given sample phenotype column-->
50 <expand macro="stdio" />
51 <inputs>
52 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
53
54 <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)">
55 <expand macro="sanitize_query" />
56 </param>
57 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)">
58 <expand macro="sanitize_query" />
59 </param>
60 <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)">
61 <expand macro="sanitize_query" />
62 </param>
63
64 <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False"
65 label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>
66
67 <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False"
68 label="Add a column listing all of the families with a variant to each variant" help="(--show-families)"/>
69
70 <param name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False"
71 label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/>
72
73 <expand macro="add_header_column" />
74
75 <!-- TODO: is there any default values set? -->
76 <param name="min_kindreds" size="4" type="integer" value="-1" lebel="Minimum number of families for a variant passing a family-wise filter to be in" help="-1 means default values (--min-kindreds)" />
77
78 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False"
79 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/>
80
81 <param name="in" type="select" label="A variant must be in either all, none or any samples passing the sample-query filter" help="(--in)">
82 <option value="all">Return a variant if all samples matching the query have the variant. (all)</option>
83 <option value="none">Return a variant if the variant does not appear in any of the matching samples. (none)</option>
84 <option value="any">Return all of the variant which are in all of the matching samples and not in any of the non-matching samples. (any)</option>
85 <option value="only">Return a variant if the variant is only in the matching samples and not in any of the non-matching samples. (only)</option>
86 </param>
87
88 <param name="region" size="30" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/>
89
90
91 </inputs>
92 <outputs>
93 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
94 </outputs>
95 <tests>
96 <test>
97 </test>
98 </tests>
99 <help>
100 **What it does**
101
102 The real power in the GEMINI framework lies in the fact that all of your genetic variants have been stored in a convenient database in the context of a wealth of genome annotations that facilitate variant interpretation.
103 The expressive power of SQL allows one to pose intricate questions of one’s variation data. This tool offers you an easy way to query your variants!
104
105 http://gemini.readthedocs.org/en/latest/content/querying.html
106
107 @CITATION@
108 </help>
109 <expand macro="citations"/>
110 </tool>