Mercurial > repos > iuc > gemini_query

annotate gemini_query.xml @ 4:7ca6716748c2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:51:59 -0500
parents 666f60a9331a
children cd00221d67cb
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
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2 <description>Querying the GEMINI database</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">query</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 gemini @BINARY@
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14 --in "${in}"
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15
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16 #set $multiline_sql_expr = $gt_filter
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17 #set $cmdln_param = "--gt-filter"
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18 @MULTILN_SQL_EXPR_TO_CMDLN@
0
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19
3
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20 #set $multiline_sql_expr = $sample_filter
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21 #set $cmdln_param = "--sample-filter"
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22 @MULTILN_SQL_EXPR_TO_CMDLN@
0
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23
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24 $show_samples
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25 $show_families
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26 $family_wise
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27 $header
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28 $dgidb
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29 #if $region.strip():
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30 --region "${region}"
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31 #end if
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32 #if int($min_kindreds) > 0:
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33 --min-kindreds $min_kindreds
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34 #end if
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35 ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being
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36 ## --sample-delim STRING The delimiter to be used with the --show-samples option.
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37
3
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38 #set $multiline_sql_expr = $q
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39 #set $cmdln_param = "-q"
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40 @MULTILN_SQL_EXPR_TO_CMDLN@
0
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41
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42 "${ infile }"
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43 > "${ outfile }"
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44 ]]>
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45 </command>
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46 <!--
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47 ##TODO:
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48 - -carrier-summary-by-phenotype CARRIER_SUMMARY
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49 Output columns of counts of carriers and non-carriers
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50 stratified by the given sample phenotype column-->
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51 <inputs>
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52 <expand macro="infile" />
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53
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54 <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)">
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55 <expand macro="sanitize_query" />
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56 </param>
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57 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)">
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58 <expand macro="sanitize_query" />
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59 </param>
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60 <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)">
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61 <expand macro="sanitize_query" />
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62 </param>
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63
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64 <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False"
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65 label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>
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66
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67 <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False"
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68 label="Add a column listing all of the families with a variant to each variant" help="(--show-families)"/>
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69
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70 <param name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False"
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71 label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/>
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72
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73 <expand macro="add_header_column" />
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74 <expand macro="min_kindreds" />
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75
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76 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False"
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77 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/>
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78
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79 <param name="in" type="select" label="A variant must be in either all, none or any samples passing the sample-query filter" help="(--in)">
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80 <option value="all">Return a variant if all samples matching the query have the variant. (all)</option>
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81 <option value="none">Return a variant if the variant does not appear in any of the matching samples. (none)</option>
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82 <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>
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83 <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>
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84 </param>
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85
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86 <param name="region" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/>
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87
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88
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89 </inputs>
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90 <outputs>
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91 <data name="outfile" format="tabular" />
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92 </outputs>
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93 <tests>
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94 <test>
4
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95 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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96 <param name="q" value="select chrom,start from variants limit 10" />
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97 <param name="header" value="True" />
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98 <output name="outfile">
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99 <assert_contents>
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100 <has_line_matching expression="chrom&#009;start" />
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101 </assert_contents>
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102 </output>
0
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103 </test>
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104 </tests>
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105 <help>
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106 <![CDATA[
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107 **What it does**
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108
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109 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.
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110 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!
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111
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112 http://gemini.readthedocs.org/en/latest/content/querying.html
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113 ]]>
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114 </help>
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115 <expand macro="citations"/>
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116 </tool>