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comparison gemini_query.xml @ 17:65f742e605ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:46:38 -0400
parents 53a5647e5271
children ce61d4876838
comparison
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16:ae03de7a9fee 17:65f742e605ec
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Querying the GEMINI database</description> 2 <description>Querying the GEMINI database</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros> 3 <macros>
6 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">query</token> 5 <token name="@BINARY@">query</token>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
9 <command> 10 <command>
10 <![CDATA[ 11 <![CDATA[
11 gemini @BINARY@ 12 gemini @BINARY@
12 13
13 --in "${in}" 14 --in "${in}"
45 <!-- 46 <!--
46 ##TODO: 47 ##TODO:
47 - -carrier-summary-by-phenotype CARRIER_SUMMARY 48 - -carrier-summary-by-phenotype CARRIER_SUMMARY
48 Output columns of counts of carriers and non-carriers 49 Output columns of counts of carriers and non-carriers
49 stratified by the given sample phenotype column--> 50 stratified by the given sample phenotype column-->
50 <expand macro="stdio" />
51 <inputs> 51 <inputs>
52 <expand macro="infile" /> 52 <expand macro="infile" />
53 53
54 <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)"> 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" /> 55 <expand macro="sanitize_query" />
59 </param> 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)"> 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" /> 61 <expand macro="sanitize_query" />
62 </param> 62 </param>
63 63
64 <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False" 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)"/> 65 label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>
66 66
67 <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False" 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)"/> 68 label="Add a column listing all of the families with a variant to each variant" help="(--show-families)"/>
69 69
70 <param name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False" 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)"/> 71 label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/>
72 72
73 <expand macro="add_header_column" /> 73 <expand macro="add_header_column" />
74 74
75 <!-- TODO: is there any default values set? --> 75 <!-- TODO: is there any default values set? -->
76 <param name="min_kindreds" size="4" type="integer" value="-1" label="Minimum number of families for a variant passing a family-wise filter to be in" help="-1 means default values (--min-kindreds)" /> 76 <param name="min_kindreds" size="4" type="integer" value="-1" label="Minimum number of families for a variant passing a family-wise filter to be in" help="-1 means default values (--min-kindreds)" />
77 77
78 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False" 78 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False"
79 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/> 79 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/>
80 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)"> 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> 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> 83 <option value="none">Return a variant if the variant does not appear in any of the matching samples. (none)</option>
97 </test> 97 </test>
98 </tests> 98 </tests>
99 <help> 99 <help>
100 **What it does** 100 **What it does**
101 101
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. 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! 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!
104 104
105 http://gemini.readthedocs.org/en/latest/content/querying.html 105 http://gemini.readthedocs.org/en/latest/content/querying.html
106 106
107 @CITATION@ 107 @CITATION@