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comparison tools/SADI-Docker/SADI-Docker-tab2rdf.xml @ 0:54c48f9ca32b default tip

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first release
author Mikel Egana <mikel.egana.aranguren@gmail.com>
date Fri, 04 Sep 2015 23:24:45 +0200
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1 <tool id="SADI-Docker-tab2rdf" name="SADI - Tab-to-RDF" version="0.1">
2
3 <!-- Modified by Mikel Egaña Aranguren, very hacky -->
4
5 <description>Converter</description>
6
7 <requirements>
8 <container type="docker">mikeleganaaranguren/sadi:v6</container>
9 </requirements>
10 <command>
11 #if $namespace.choose_namespace=="none"
12 python /sadi/tab2rdf.py $input_file $output_file $output_format none
13 #for $i in $triples
14 ${i.s_col} ${i.p_val} ${i.o_col} ${i.o_type}
15 #end for
16 #else
17 python /sadi/tab2rdf.py $input_file $output_file $output_format $namespace.choosen_namespace
18 #for $i in $triples
19 ${i.s_col} ${i.p_val} ${i.o_col} ${i.o_type}
20 #end for
21 #end if
22 </command>
23 <inputs>
24 <param name="input_file" type="data" format="tabular" label="Input File (tabular)"/>
25
26 <conditional name="namespace">
27 <param name="choose_namespace" type="select" label="Add namespace?">
28 <option value="none">No (The tab file includes complete URIs for each resource)</option>
29 <option value="yes_choose_namespace">Yes</option>
30 </param>
31 <when value="yes_choose_namespace">
32 <param name="choosen_namespace" type="text" size="50" value="http://localhost/" label="Namespace" />
33 </when>
34 </conditional>
35
36 <param name="output_format" type="select" label="Output Format">
37 <option value="ntriples">N-Triples</option>
38 <option value="turtle">Turtle</option>
39 <option value="rdfxml">RDF/XML</option>
40 </param>
41 <repeat name="triples" title="Triples">
42 <param name="s_col" type="data_column" data_ref="input_file" label="Subject (column)" />
43 <param name="p_val" type="text" size="50" value="a" label="Predicate (text)">
44 <sanitizer sanitize="False"/>
45 </param>
46 <param name="o_col" type="data_column" data_ref="input_file" label="Object (column)" />
47 <param name="o_type" label="Check if this object is Literal (Keep unchecked if this object is URI)" type="boolean" truevalue="1" falsevalue="0" checked="False"/>
48 </repeat>
49 </inputs>
50 <outputs>
51 <data name="output_file" format="rdf" label="${tool.name} on ${on_string}"/>
52 </outputs>
53 <help>
54
55 **Important note**
56
57 This is a modified version of Tab2RDF, local to SADI-Docker-Galaxy (http://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy).
58
59 **What it does**
60
61 Sample Input::
62
63 name age superviser
64 Micheal 42 John
65 Anne 30 Micheal
66
67 Sample Parameters::
68
69 Namespace - 'http://localhost/'
70 Triple 1 - c1 'age' c2(literal)
71 Triple 2 - c3 'supervises' c1(URI)
72
73 Sample Output::
74
75 &lt;http://localhost/Michael&gt; &lt;http://localhost/age&gt; "42"
76 &lt;http://localhost/Anne&gt; &lt;http://localhost/age&gt; "30"
77 &lt;http://localhost/John&gt; &lt;http://localhost/supervises&gt; &lt;http://localhost/Micheal&gt;
78 &lt;http://localhost/Micheal&gt; &lt;http://localhost/supervises&gt; &lt;http://localhost/Anne&gt;
79
80 **Output Format**
81
82 Output RDF format is N-Triples by default.
83
84 </help>
85 </tool>