Mercurial > repos > mikel-egana-aranguren > sadi_docker

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
first release
author Mikel Egana <mikel.egana.aranguren@gmail.com>
date Fri, 04 Sep 2015 23:24:45 +0200
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
1 <tool id="SADI-Docker-tab2rdf" name="SADI - Tab-to-RDF" version="0.1">
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
2
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
3 <!-- Modified by Mikel Egaña Aranguren, very hacky -->
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
4
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
5 <description>Converter</description>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
6
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
7 <requirements>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
8 <container type="docker">mikeleganaaranguren/sadi:v6</container>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
9 </requirements>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
10 <command>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
11 #if $namespace.choose_namespace=="none"
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
12 python /sadi/tab2rdf.py $input_file $output_file $output_format none
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
13 #for $i in $triples
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
14 ${i.s_col} ${i.p_val} ${i.o_col} ${i.o_type}
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
15 #end for
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
16 #else
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
17 python /sadi/tab2rdf.py $input_file $output_file $output_format $namespace.choosen_namespace
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
18 #for $i in $triples
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
19 ${i.s_col} ${i.p_val} ${i.o_col} ${i.o_type}
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
20 #end for
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
21 #end if
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
22 </command>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
23 <inputs>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
24 <param name="input_file" type="data" format="tabular" label="Input File (tabular)"/>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
25
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
26 <conditional name="namespace">
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
27 <param name="choose_namespace" type="select" label="Add namespace?">
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
28 <option value="none">No (The tab file includes complete URIs for each resource)</option>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
29 <option value="yes_choose_namespace">Yes</option>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
30 </param>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
31 <when value="yes_choose_namespace">
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
32 <param name="choosen_namespace" type="text" size="50" value="http://localhost/" label="Namespace" />
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
33 </when>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
34 </conditional>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
35
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
36 <param name="output_format" type="select" label="Output Format">
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
37 <option value="ntriples">N-Triples</option>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
38 <option value="turtle">Turtle</option>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
39 <option value="rdfxml">RDF/XML</option>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
40 </param>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
41 <repeat name="triples" title="Triples">
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
42 <param name="s_col" type="data_column" data_ref="input_file" label="Subject (column)" />
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
43 <param name="p_val" type="text" size="50" value="a" label="Predicate (text)">
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
44 <sanitizer sanitize="False"/>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
45 </param>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
46 <param name="o_col" type="data_column" data_ref="input_file" label="Object (column)" />
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
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"/>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
48 </repeat>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
49 </inputs>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
50 <outputs>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
51 <data name="output_file" format="rdf" label="${tool.name} on ${on_string}"/>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
52 </outputs>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
53 <help>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
54
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
55 **Important note**
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
56
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
57 This is a modified version of Tab2RDF, local to SADI-Docker-Galaxy (http://github.com/mikel-egana-aranguren/SADI-Docker-Galaxy).
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
58
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
59 **What it does**
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
60
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
61 Sample Input::
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
62
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
63 name age superviser
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
64 Micheal 42 John
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
65 Anne 30 Micheal
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
66
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
67 Sample Parameters::
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
68
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
69 Namespace - 'http://localhost/'
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
70 Triple 1 - c1 'age' c2(literal)
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
71 Triple 2 - c3 'supervises' c1(URI)
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
72
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
73 Sample Output::
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
74
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
75 &lt;http://localhost/Michael&gt; &lt;http://localhost/age&gt; "42"
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
76 &lt;http://localhost/Anne&gt; &lt;http://localhost/age&gt; "30"
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
77 &lt;http://localhost/John&gt; &lt;http://localhost/supervises&gt; &lt;http://localhost/Micheal&gt;
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
78 &lt;http://localhost/Micheal&gt; &lt;http://localhost/supervises&gt; &lt;http://localhost/Anne&gt;
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
79
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
80 **Output Format**
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
81
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
82 Output RDF format is N-Triples by default.
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
83
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
84 </help>
54c48f9ca32b first release
Mikel Egana <mikel.egana.aranguren@gmail.com>
parents:
diff changeset
85 </tool>