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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
author iuc
date Wed, 09 Aug 2017 17:44:54 -0400
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1 <tool id="join_files_by_id" name="Join datasets by identifier column" version="1.0">
2 <requirements>
3 <requirement type="package" version="1.10.4">r-data.table</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 Rscript '$__tool_directory__/join_files.R'
7 --out='$out_file1'
8 --he='$header'
9 --jc='$field'
10 --sep='$delimiter'
11 --nc='$null_str'
12 --in='$input1'
13 #for $q in $queries
14 --in='${q.input}'
15 #end for
16 ]]></command>
17 <inputs>
18 <param name="header" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Header" help="If header is true, the column name used for joining need to be the same in all datasets"/>
19 <param name="delimiter" type="select" label="Delimited by">
20 <option value="ta">Tab</option>
21 <option value="do">Dot</option>
22 <option value="co">Comma</option>
23 <option value="un">Underscore</option>
24 <option value="da">Dash</option>
25 <option value="sp">Space</option>
26 </param>
27 <param name="null_str" type="select" label="Select mismatch character">
28 <option value="0">0</option>
29 <option value="-">-</option>
30 <option value="">"empty"</option>
31 <option value="NA">NA</option>
32 </param>
33 <param name="input1" type="data" format="tabular" label="Select table" help="Single dataset selection only to preserve the order"/>
34 <repeat name="queries" min="1" title="Select table">
35 <param name="input" type="data" format="tabular" label="Select table" help="Single dataset selection only to preserve the order"/>
36 </repeat>
37 <param name="field" type="data_column" data_ref="input1" label="Column used for joining" />
38 </inputs>
39 <outputs>
40 <data name="out_file1" format="tabular" />
41 </outputs>
42 <tests>
43 <test>
44 <param name="header" value="1"/>
45 <param name="null_str" value="0"/>
46 <param name="delimiter" value="ta"/>
47 <param name="input1" value="df1.txt"/>
48 <repeat name="queries">
49 <param name="input" value="df2.txt"/>
50 </repeat>
51 <repeat name="queries">
52 <param name="input" value="df3.txt"/>
53 </repeat>
54 <param name="field" value="1"/>
55 <output name="out_file1" file="df.txt"/>
56 </test>
57 </tests>
58 <help><![CDATA[
59 **What it does**
60
61 Joins datasets by identifier column
62
63 -----
64
65 '''Example'''
66
67 Dataset 1:
68
69 +--------+--------+---------+
70 | name | counts | percent |
71 +========+========+=========+
72 | gene 1 | 10 | 0.3 |
73 +--------+--------+---------+
74 | gene 2 | 20 | 0.2 |
75 +--------+--------+---------+
76 | gene 3 | 20 | 0.2 |
77 +--------+--------+---------+
78
79
80 and Dataset 2:
81
82 +--------+--------+---------+
83 | name | counts | percent |
84 +========+========+=========+
85 | gene 1 | 13 | 0.5 |
86 +--------+--------+---------+
87 | gene 4 | 4 | 0.4 |
88 +--------+--------+---------+
89
90
91 and Dataset 3:
92
93 +--------+--------+---------+
94 | name | counts | percent |
95 +========+========+=========+
96 | gene 1 | 10 | 0.3 |
97 +--------+--------+---------+
98 | gene 3 | 12 | 0.2 |
99 +--------+--------+---------+
100 | gene 4 | 4 | 0.4 |
101 +--------+--------+---------+
102 | gene 5 | 19 | 0.6 |
103 +--------+--------+---------+
104
105
106 will result in the following:
107
108 +--------+--------+---------+--------+---------+--------+---------+
109 | name | counts | percent | counts | percent | counts | percent |
110 +========+========+=========+========+=========+========+=========+
111 | gene 1 | 10 | 0.3 | 13 | 0.5 | 10 | 0.3 |
112 +--------+--------+---------+--------+---------+--------+---------+
113 | gene 2 | 20 | 0.2 | 0 | 0 | 0 | 0 |
114 +--------+--------+---------+--------+---------+--------+---------+
115 | gene 3 | 12 | 0.2 | 0 | 0 | 12 | 0.2 |
116 +--------+--------+---------+--------+---------+--------+---------+
117 | gene 4 | 0 | 0 | 4 | 0.4 | 4 | 0.4 |
118 +--------+--------+---------+--------+---------+--------+---------+
119 | gene 5 | 0 | 0 | 0 | 0 | 19 | 0.6 |
120 +--------+--------+---------+--------+---------+--------+---------+
121
122 For help contact: jochen.bick@usys.ethz.ch
123 ]]></help>
124 </tool>