Mercurial > repos > iuc > gemini_query

annotate gemini_query.xml @ 3:87e5559c248e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:32:48 -0500
parents 9dc6c42486a1
children ff3597f6e01b
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
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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[
3
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12 @PROVIDE_ANNO_DATA@
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13
0
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14 gemini @BINARY@
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16 --in "${in}"
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18 #set $multiline_sql_expr = $gt_filter
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19 #set $cmdln_param = "--gt-filter"
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20 @MULTILN_SQL_EXPR_TO_CMDLN@
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21
3
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22 #set $multiline_sql_expr = $sample_filter
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23 #set $cmdln_param = "--sample-filter"
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24 @MULTILN_SQL_EXPR_TO_CMDLN@
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26 $show_samples
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27 $show_families
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28 $family_wise
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29 $header
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30 $dgidb
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31 #if $region.strip():
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32 --region "${region}"
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33 #end if
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34 #if int($min_kindreds) > 0:
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35 --min-kindreds $min_kindreds
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36 #end if
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37 ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being
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38 ## --sample-delim STRING The delimiter to be used with the --show-samples option.
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39
3
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40 #set $multiline_sql_expr = $q
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41 #set $cmdln_param = "-q"
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42 @MULTILN_SQL_EXPR_TO_CMDLN@
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43
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44 "${ infile }"
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45 > "${ outfile }"
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46 ]]>
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47 </command>
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48 <!--
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49 ##TODO:
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50 - -carrier-summary-by-phenotype CARRIER_SUMMARY
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51 Output columns of counts of carriers and non-carriers
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52 stratified by the given sample phenotype column-->
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53 <inputs>
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54 <expand macro="infile" />
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55
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56 <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)">
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57 <expand macro="sanitize_query" />
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58 </param>
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59 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)">
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60 <expand macro="sanitize_query" />
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61 </param>
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62 <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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63 <expand macro="sanitize_query" />
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64 </param>
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65
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66 <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False"
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67 label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>
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68
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69 <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False"
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70 label="Add a column listing all of the families with a variant to each variant" help="(--show-families)"/>
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71
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72 <param name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False"
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73 label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/>
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74
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75 <expand macro="add_header_column" />
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76 <expand macro="min_kindreds" />
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77
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78 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False"
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79 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/>
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80
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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)">
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82 <option value="all">Return a variant if all samples matching the query have the variant. (all)</option>
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83 <option value="none">Return a variant if the variant does not appear in any of the matching samples. (none)</option>
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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>
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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>
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86 </param>
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87
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88 <param name="region" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/>
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90
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91 </inputs>
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92 <outputs>
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93 <data name="outfile" format="tabular" />
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94 </outputs>
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95 <tests>
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96 <test>
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97 <param name="infile" value="gemini_load_result.db" ftype="gemini.sqlite" />
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98 <param name="q" value="select start from variants limit 10" />
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99 <output name="outfile" file="gemini_query_result.tabular" />
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100 </test>
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101 </tests>
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102 <help>
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103 <![CDATA[
0
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104 **What it does**
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105
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106 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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107 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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108
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109 http://gemini.readthedocs.org/en/latest/content/querying.html
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110 ]]>
0
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111 </help>
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112 <expand macro="citations"/>
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113 </tool>