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comparison 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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-1:000000000000 0:0369de831b32
1 <tool id="query" name="Query" version="@TOOL_VERSION@">
2 <macros>
3 <token name="@TOOL_VERSION@">0.1</token>
4 <xml name="formats">
5 <option value="csv">csv</option>
6 <option value="tsv">tsv</option>
7 <option value="h5">h5</option>
8 <option value="feather">feather</option>
9 <option value="parquet">parquet</option>
10 <option value="sqlite">sqlite</option>
11 </xml>
12 <xml name="internal_name" token_format="">
13 <when value="@FORMAT@">
14 <param name="name" type="text" help="Specify the format's internal name of the table."/>
15 </when>
16 </xml>
17 </macros>
18
19 <requirements>
20 <requirement type="package">click</requirement>
21 <requirement type="package">pyarrow</requirement>
22 <requirement type="package">pytables</requirement>
23 <requirement type="package">pandas</requirement>
24 <requirement type="package">pandasql</requirement>
25 <requirement type="package" version="3.7">python</requirement>
26 </requirements>
27
28 <command><![CDATA[
29 python '$__tool_directory__/query.py'
30 $config
31 ]]></command>
32
33 <configfiles>
34 <configfile name="config"><![CDATA[
35 #def filetype(data):
36 #if $data.is_of_type('h5')
37 #return 'hdf'
38 #elif $data.is_of_type('csv')
39 #return 'csv'
40 #elif $data.is_of_type('tsv', 'tabular')
41 #return 'tsv'
42 #elif $data.is_of_type('feather', 'arrow')
43 #return 'feather'
44 #elif $data.is_of_type('parquet')
45 #return 'parquet'
46 #elif $data.is_of_type('sqlite')
47 #return 'sqlite'
48 #end if
49 #end def
50
51 #set $config = {
52 'tables': [
53 {
54 'path': str($table.file),
55 'name': str($table.name) if $table.name else 't{}'.format(str($index)),
56 'format': str($table.format) if $table.format else $filetype($table.file)
57 }
58 for $index, $table in enumerate($tables)
59 ],
60 'query': str($query),
61 'result': {
62 'path': str($output),
63 'name': str($result.name) if str($result.format) in ('h5', 'hdf', 'sqlite') and $result.name else None,
64 'format': str($result.format)
65 }
66 }
67
68 #import json
69 #echo $json.dumps($config)
70 ]]></configfile>
71 </configfiles>
72
73 <inputs>
74 <repeat name="tables" title="Table">
75 <param name="file" type="data" format="csv,tsv,h5,feather,parquet,sqlite" label="File"/>
76 <param name="format" type="select" optional="true">
77 <label>Force the file format</label>
78 <help>Force a particular file format to get around formats unknown to Galaxy, ie. Parquet.</help>
79 <expand macro="formats"/>
80 </param>
81 <param name="name" type="text" optional="true">
82 <label>Table name</label>
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>
84 </param>
85 </repeat>
86 <param name="query" type="text" area="true">
87 <label>SQL Query</label>
88 <help>
89 Type an arbitrary SQL SELECT to perform on the input tables. The input tables may be referred by their given names.
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.
91 </help>
92 </param>
93 <conditional name="result">
94 <param name="format" type="select">
95 <label>SQL Query</label>
96 <help>Specify the file format of the query result.</help>
97 <expand macro="formats"/>
98 </param>
99 <expand macro="internal_name" format="h5"/>
100 <expand macro="internal_name" format="sqlite"/>
101 </conditional>
102 </inputs>
103
104 <outputs>
105 <data name="output">
106 <change_format>
107 <when input="result.format" value="h5" format="h5"/>
108 <when input="result.format" value="csv" format="csv"/>
109 <when input="result.format" value="tsv" format="tsv"/>
110 <when input="result.format" value="feather" format="feather"/>
111 <when input="result.format" value="parquet" format="parquet"/>
112 <when input="result.format" value="sqlite" format="sqlite"/>
113 </change_format>
114 </data>
115 </outputs>
116
117 <tests>
118 <test>
119 <repeat name="tables">
120 <param name="file" value="a.csv" ftype="csv"/>
121 <param name="name" value="a"/>
122 </repeat>
123 <repeat name="tables">
124 <param name="file" value="b.csv" ftype="csv"/>
125 <param name="name" value="b"/>
126 </repeat>
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"/>
128 <conditional name="result">
129 <param name="format" value="csv"/>
130 </conditional>
131 <output name="output" file="ab.csv" ftype="csv"/>
132 </test>
133 </tests>
134 </tool>