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1 <tool id="DGBK2RDF" name="EMBL/GBK to RDF" version="0.1">
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2 <description>Converts GenBank/EMBL files to RDF</description>
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3 <requirements>
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4 <container type="docker">jjkoehorst/sappdocker:GBK2RDF</container>
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5 </requirements>
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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>
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7 <inputs>
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8 <param format="gbk,gb,genbank" label="Genbank file" name="input" type="data"/>
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9 <param label="EMBL/GBK" name="format" type="select">
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10 <option value="gbk">Genbank</option>
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11 <option selected="true" value="embl">EMBL</option>
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12 </param>
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13 <param label="11/4" name="codon" type="select">
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14 <option selected="true" value="11">11</option>
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15 <option value="4">4</option>
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16 </param>
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17 <param label="Source of annotation eg. RAST/NCBI/EBI" name="source" optional="false" type="text"/>
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18 </inputs>
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19 <outputs>
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20 <data format="ttl" label="GBKttl: ${input.name}" name="output"/>
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21 </outputs>
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22 <help>Java Genbank or EMBL to RDF conversion
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23 </help>
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24 </tool>
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