Mercurial > repos > iuc > gemini
comparison gemini_query.xml @ 0:720cbfb4190d draft
Imported from capsule None
author | iuc |
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date | Mon, 25 Aug 2014 17:15:54 -0400 |
parents | |
children | 93bb0cfacefb |
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-1:000000000000 | 0:720cbfb4190d |
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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> |