Mercurial > repos > jjkoehorst > sapp
diff gbk2rdf.xml @ 35:fa736576c7ed draft
planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
| author | jjkoehorst |
|---|---|
| date | Mon, 04 Jul 2016 10:37:59 -0400 |
| parents | |
| children | 2201c5d61f16 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gbk2rdf.xml Mon Jul 04 10:37:59 2016 -0400 @@ -0,0 +1,24 @@ +<tool id="DGBK2RDF" name="EMBL/GBK to RDF" version="0.1"> + <description>Converts GenBank/EMBL files to RDF</description> + <requirements> + <container type="docker">jjkoehorst/sappdocker:GBK2RDF</container> + </requirements> + <command>java -jar /genbank2rdf/GenBank2RDF-0.0.1-SNAPSHOT-jar-with-dependencies.jar '-input' '$input' -output '$output' -source "$source" -format "$format" -identifier "${input.name}" -codon "$codon" </command> + <inputs> + <param format="gbk,gb,genbank" label="Genbank file" name="input" type="data"/> + <param label="EMBL/GBK" name="format" type="select"> + <option value="gbk">Genbank</option> + <option selected="true" value="embl">EMBL</option> + </param> + <param label="11/4" name="codon" type="select"> + <option selected="true" value="11">11</option> + <option value="4">4</option> + </param> + <param label="Source of annotation eg. RAST/NCBI/EBI" name="source" optional="false" type="text"/> + </inputs> + <outputs> + <data format="ttl" label="GBKttl: ${input.name}" name="output"/> + </outputs> + <help>Java Genbank or EMBL to RDF conversion + </help> +</tool>