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annotate query.xml @ 0:0369de831b32 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/query commit e781279d988f26eff9ccfff898a7d8cc4f0ceafb"
author recetox
date Wed, 09 Dec 2020 02:04:20 +0000
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children 55ca5d902f62
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1 <tool id="query" name="Query" version="@TOOL_VERSION@">
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2 <macros>
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3 <token name="@TOOL_VERSION@">0.1</token>
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4 <xml name="formats">
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5 <option value="csv">csv</option>
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6 <option value="tsv">tsv</option>
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7 <option value="h5">h5</option>
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8 <option value="feather">feather</option>
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9 <option value="parquet">parquet</option>
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10 <option value="sqlite">sqlite</option>
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11 </xml>
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12 <xml name="internal_name" token_format="">
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13 <when value="@FORMAT@">
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14 <param name="name" type="text" help="Specify the format's internal name of the table."/>
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15 </when>
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16 </xml>
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17 </macros>
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18
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19 <requirements>
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20 <requirement type="package">click</requirement>
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21 <requirement type="package">pyarrow</requirement>
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22 <requirement type="package">pytables</requirement>
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23 <requirement type="package">pandas</requirement>
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24 <requirement type="package">pandasql</requirement>
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25 <requirement type="package" version="3.7">python</requirement>
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26 </requirements>
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27
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28 <command><![CDATA[
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29 python '$__tool_directory__/query.py'
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30 $config
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31 ]]></command>
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32
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33 <configfiles>
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34 <configfile name="config"><![CDATA[
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35 #def filetype(data):
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36 #if $data.is_of_type('h5')
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37 #return 'hdf'
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38 #elif $data.is_of_type('csv')
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39 #return 'csv'
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40 #elif $data.is_of_type('tsv', 'tabular')
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41 #return 'tsv'
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42 #elif $data.is_of_type('feather', 'arrow')
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43 #return 'feather'
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44 #elif $data.is_of_type('parquet')
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45 #return 'parquet'
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46 #elif $data.is_of_type('sqlite')
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47 #return 'sqlite'
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48 #end if
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49 #end def
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50
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51 #set $config = {
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52 'tables': [
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53 {
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54 'path': str($table.file),
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55 'name': str($table.name) if $table.name else 't{}'.format(str($index)),
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56 'format': str($table.format) if $table.format else $filetype($table.file)
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57 }
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58 for $index, $table in enumerate($tables)
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59 ],
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60 'query': str($query),
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61 'result': {
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62 'path': str($output),
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63 'name': str($result.name) if str($result.format) in ('h5', 'hdf', 'sqlite') and $result.name else None,
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64 'format': str($result.format)
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65 }
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66 }
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67
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68 #import json
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69 #echo $json.dumps($config)
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70 ]]></configfile>
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71 </configfiles>
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72
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73 <inputs>
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74 <repeat name="tables" title="Table">
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75 <param name="file" type="data" format="csv,tsv,h5,feather,parquet,sqlite" label="File"/>
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76 <param name="format" type="select" optional="true">
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77 <label>Force the file format</label>
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78 <help>Force a particular file format to get around formats unknown to Galaxy, ie. Parquet.</help>
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79 <expand macro="formats"/>
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80 </param>
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81 <param name="name" type="text" optional="true">
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82 <label>Table name</label>
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83 <help>Choose an unique name for the table which then you may use in the SQL Query. By default tables will be named as: t0, t1, ...</help>
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84 </param>
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85 </repeat>
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86 <param name="query" type="text" area="true">
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87 <label>SQL Query</label>
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88 <help>
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89 Type an arbitrary SQL SELECT to perform on the input tables. The input tables may be referred by their given names.
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90 An example query is SELECT employees.name AS employee, emails.value AS email FROM one JOIN b ON employees.id = emails.employee, provided that the input tables are named employees and emails.
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91 </help>
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92 </param>
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93 <conditional name="result">
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94 <param name="format" type="select">
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95 <label>SQL Query</label>
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96 <help>Specify the file format of the query result.</help>
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97 <expand macro="formats"/>
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98 </param>
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99 <expand macro="internal_name" format="h5"/>
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100 <expand macro="internal_name" format="sqlite"/>
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101 </conditional>
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102 </inputs>
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103
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104 <outputs>
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105 <data name="output">
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106 <change_format>
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107 <when input="result.format" value="h5" format="h5"/>
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108 <when input="result.format" value="csv" format="csv"/>
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109 <when input="result.format" value="tsv" format="tsv"/>
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110 <when input="result.format" value="feather" format="feather"/>
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111 <when input="result.format" value="parquet" format="parquet"/>
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112 <when input="result.format" value="sqlite" format="sqlite"/>
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113 </change_format>
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114 </data>
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115 </outputs>
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116
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117 <tests>
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118 <test>
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119 <repeat name="tables">
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120 <param name="file" value="a.csv" ftype="csv"/>
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121 <param name="name" value="a"/>
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122 </repeat>
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123 <repeat name="tables">
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124 <param name="file" value="b.csv" ftype="csv"/>
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125 <param name="name" value="b"/>
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126 </repeat>
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127 <param name="query" value="SELECT a.x AS ax, a.y AS ay, a.z AS az, b.x AS bx, b.y AS by, b.z AS bz FROM a JOIN b ON a.x = b.x"/>
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128 <conditional name="result">
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129 <param name="format" value="csv"/>
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130 </conditional>
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131 <output name="output" file="ab.csv" ftype="csv"/>
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132 </test>
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133 </tests>
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134 </tool>