Mercurial > repos > iuc > gemini_db_info

annotate gemini_db_info.xml @ 7:7d75673f4d6f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
author iuc
date Tue, 10 Mar 2020 06:20:59 -0400
parents bc8b01d1b496
children c2a413e47fe9
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1 <tool id="gemini_db_info" name="GEMINI database info" version="@VERSION@">
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2 <description>Retrieve information about tables, columns and annotation data stored in a GEMINI database</description>
0
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11 #if str($select.info_type) == 'scheme':
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12 gemini db_info '$infile' | tr -s ' ' '\t'
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13 #elif str($select.info_type) == 'resources':
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14 gemini query --header -q "SELECT name as data_source, resource as resource_file from resources" '$infile'
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15 #elif str($select.info_type) == 'gene_detailed':
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16 gemini query --header -q "SELECT gene, synonym as synonyms, transcript FROM gene_detailed WHERE gene is not NULL GROUP BY transcript ORDER BY gene" '$infile'
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17 #else:
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18 gemini query --header -q "SELECT * FROM samples" "$infile" | cut -f 2-${select.format}
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19 #end if
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21 > '$outfile'
0
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22 ]]>
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23 </command>
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24 <inputs>
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25 <expand macro="infile" />
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26 <conditional name="select">
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27 <param name="info_type" type="select"
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28 label="Information to retrieve from the database">
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29 <option value="scheme">Names of database tables and their columns</option>
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30 <option value="resources">List of annotation data sources</option>
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31 <option value="gene_detailed">List of genes and their transcripts</option>
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32 <option value="samples">Write out sample information in PED format</option>
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33 </param>
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34 <when value="scheme" />
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35 <when value="resources" />
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36 <when value="gene_detailed" />
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37 <when value="samples">
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38 <param name="format" type="select" display="radio"
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39 label="Format of the pedigree file">
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40 <option value="">Allow extra columns to accomodate custom sample info</option>
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41 <option value="7">Restrict to 6 PED standard columns and drop additional info</option>
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42 </param>
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43 </when>
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44 </conditional>
0
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45 </inputs>
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46 <outputs>
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47 <data name="outfile" format="tabular" />
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48 </outputs>
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49 <tests>
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50 <test>
4
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51 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
5
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52 <conditional name="select">
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53 <param name="info_type" value="scheme" />
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54 </conditional>
4
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55 <output name="outfile">
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56 <assert_contents>
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57 <has_line_matching expression="table_name&#009;column_name&#009;type.*" />
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58 </assert_contents>
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59 </output>
0
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60 </test>
5
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61 <test>
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62 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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63 <conditional name="select">
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64 <param name="info_type" value="resources" />
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65 </conditional>
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66 <output name="outfile">
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67 <assert_contents>
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68 <has_line line="data_source&#009;resource_file" />
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69 <has_n_columns n="2" />
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70 </assert_contents>
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71 </output>
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72 </test>
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73 <test>
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74 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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75 <conditional name="select">
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76 <param name="info_type" value="gene_detailed" />
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77 </conditional>
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78 <output name="outfile">
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79 <assert_contents>
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80 <has_line line="gene&#009;synonyms&#009;transcript" />
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81 <has_n_columns n="3" />
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82 </assert_contents>
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83 </output>
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84 </test>
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85 <test>
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86 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
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87 <conditional name="select">
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88 <param name="info_type" value="samples" />
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89 </conditional>
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90 <output name="outfile">
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91 <assert_contents>
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92 <has_line_matching expression="family_id&#009;name&#009;paternal_id&#009;maternal_id&#009;sex&#009;phenotype&#009;.+" />
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93 </assert_contents>
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94 </output>
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95 </test>
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96 <test>
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97 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
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98 <conditional name="select">
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99 <param name="info_type" value="samples" />
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100 <param name="format" value="7" />
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101 </conditional>
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102 <output name="outfile">
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103 <assert_contents>
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104 <has_line line="family_id&#009;name&#009;paternal_id&#009;maternal_id&#009;sex&#009;phenotype" />
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105 <has_n_columns n="6" />
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106 </assert_contents>
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107 </output>
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108 </test>
0
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109 </tests>
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110 <help><![CDATA[
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111 **What it does**
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112
5
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113 Because of the sheer number of annotations that are stored in gemini, it is easy to lose the overview of what is actually available through database queries.
0
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114
5
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115 This tool offers a simple way to inspect the structure, the origin of the
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116 annotations and some of the actual annotation content quickly.
0
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117 ]]></help>
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118 <expand macro="citations"/>
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119 </tool>