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comparison sappDocker/gbk2rdf.xml @ 31:957156367442 draft

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author jjkoehorst
date Wed, 29 Jun 2016 01:36:58 -0400
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30:0a947cb25a3d 31:957156367442
1 <tool id="DGBK2RDF" name="EMBL/GBK to RDF" version="0.1">
2 <description>Converts GenBank/EMBL files to RDF</description>
3 <requirements>
4 <container type="docker">jjkoehorst/sappdocker:GBK2RDF</container>
5 </requirements>
6 <command>java -jar /genbank2rdf/target/GenBank2RDF-0.0.1-SNAPSHOT-jar-with-dependencies.jar '-input' '$input' -output '$output' -source "$source" -format "$format" -identifier "${input.name}" -codon "$codon" </command>
7 <inputs>
8 <param format="gbk,gb,genbank" label="Genbank file" name="input" type="data"/>
9 <param label="EMBL/GBK" name="format" type="select">
10 <option value="gbk">Genbank</option>
11 <option selected="true" value="embl">EMBL</option>
12 </param>
13 <param label="11/4" name="codon" type="select">
14 <option selected="true" value="11">11</option>
15 <option value="4">4</option>
16 </param>
17 <param label="Source of annotation eg. RAST/NCBI/EBI" name="source" optional="false" type="text"/>
18 </inputs>
19 <outputs>
20 <data format="ttl" label="GBKttl: ${input.name}" name="output"/>
21 </outputs>
22 <help>Java Genbank or EMBL to RDF conversion
23 </help>
24 </tool>