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comparison conversion/gbk2rdf/gbktordf.xml @ 29:dd59731d50b5

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Biopython and python3.4 inclusion test.
author Jasper Koehorst <jasperkoehorst@gmail.com>
date Wed, 25 Feb 2015 08:25:32 +0100
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28:3501912295fb 29:dd59731d50b5
1 <tool id="SAPP_genbank_to_ttl" name="EMBL/GBK to RDF" version="0.1">
2 <requirements>
3 <requirement type='package' version="3.4">python</requirement>
4 <requirement type='package' version="1.0">rdflib</requirement>
5 <requirement type="package" version="1.65">biopython</requirement>
6 </requirements>
7 <description>Genbank to RDF conversion</description>
8 <command interpreter="python3.4">gbktordf.py '-input' '$input' -output '$output' -sourcedb "$format" -format "$format"</command>
9 <inputs>
10 <param name="input" type="data" format="gbk,gb,genbank,embl" label="Genbank file"/>
11 <param name="format" type="select" label="EMBL/GBK">
12 <option value="genbank" selected="true"> Genbank</option>
13 <option value="embl"> EMBL </option>
14 </param>
15 </inputs>
16
17 <outputs>
18 <data format="rdf" name="output" label="GBKttl: ${input.name}" />
19 </outputs>
20
21 <tests>
22 <test>
23 <param name="input" value="test-data/NC_010067.gbk"/>
24 <output name="$output" file="NC_010067.rdf"/>
25 <output name="$format" value="genbank"/>
26 <output name="$sourcedb" value="genbank"/>
27 </test>
28 <test>
29 <param name="input" value="test-data/CP009049.embl"/>
30 <output name="$output" file="CP009049.rdf"/>
31 <output name="$format" value="embl"/>
32 <output name="$sourcedb" value="embl"/>
33 </test>
34 </tests>
35
36 <help>
37 Genbank or EMBL to RDF conversion
38 </help>
39 </tool>