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comparison gemini_query.xml @ 2:e6512af21622 draft

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author iuc
date Sun, 24 Aug 2014 17:49:00 -0400
parents 14caa57eca63
children 71dc82354595
comparison
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1:5fec0c2b77c7 2:e6512af21622
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description></description> 2 <description>Querying the GEMINI database</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <expand macro="version_command" /> 4 <expand macro="version_command" />
5 <macros> 5 <macros>
6 <import>gemini_macros.xml</import> 6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">query</token> 7 <token name="@BINARY@">query</token>
8 </macros> 8 </macros>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 gemini @BINARY@ 11 gemini @BINARY@
12 12
13 #if $q.strip(): 13 --in "${in}"
14 -q "${q}"
15 #end if
16 14
17 #if $gt_filter.strip(): 15 #if $gt_filter.strip():
18 --gt-filter "${gt_filter}" 16 --gt-filter "${gt_filter}"
19 #end if 17 #end if
20 18
25 $show_samples 23 $show_samples
26 $show_families 24 $show_families
27 $family_wise 25 $family_wise
28 $header 26 $header
29 $dgidb 27 $dgidb
30 --in $in
31 #if $region.strip(): 28 #if $region.strip():
32 --region "${region}" 29 --region "${region}"
33 #end if 30 #end if
34 #if int($min_kindreds) > 0: 31 #if int($min_kindreds) > 0:
35 --min-kindreds $min_kindreds 32 --min-kindreds $min_kindreds
36 #end if 33 #end if
37 ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being 34 ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being
38 ## --sample-delim STRING The delimiter to be used with the --show-samples option. 35 ## --sample-delim STRING The delimiter to be used with the --show-samples option.
39 36
40 37 #if $q.strip():
41 38 -q "${q}"
39 #end if
42 40
43 "${ infile }" 41 "${ infile }"
44 > "${ outfile }" 42 > "${ outfile }"
45 ]]> 43 ]]>
46 </command> 44 </command>
51 stratified by the given sample phenotype column--> 49 stratified by the given sample phenotype column-->
52 <expand macro="stdio" /> 50 <expand macro="stdio" />
53 <inputs> 51 <inputs>
54 <param name="infile" type="data" format="sqlite" label="GEMINI database" /> 52 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
55 53
56 <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database"/> 54 <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)"/>
57 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values"/> 55 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)"/>
58 <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table"/> 56 <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)"/>
59 <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table"/>
60 57
61 <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False" 58 <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False"
62 label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/> 59 label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>
63 60
64 <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False" 61 <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False"
74 71
75 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False" 72 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False"
76 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/> 73 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/>
77 74
78 <param name="in" type="select" label="A variant must be in either all, none or any samples passing the sample-query filter" help="(--in)"> 75 <param name="in" type="select" label="A variant must be in either all, none or any samples passing the sample-query filter" help="(--in)">
79 <option value="all">all</option> 76 <option value="all">Return a variant if all samples matching the query have the variant. (all)</option>
80 <option value="none">none</option> 77 <option value="none">Return a variant if the variant does not appear in any of the matching samples. (none)</option>
81 <option value="any">any</option> 78 <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>
82 <option value="only">only</option> 79 <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>
83 </param> 80 </param>
84 81
85 <param name="region" size="30" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/> 82 <param name="region" size="30" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/>
86 83
87 84