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1 <tool id="SAPP_protein_rdf" name="Protein FASTA to RDF" version="0.1">
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2 <requirements>
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3 <requirement type='package' version="3.4">python</requirement>
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4 <requirement type='package' version="1.0">rdflib</requirement>
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5 </requirements>
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6 <description></description>
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7 <command interpreter="python3.4">protein_to_ttl.py '-input' '$input' '-output' '$output' '-organism' '$organism' '-ncbi_taxid' '$ncbi_taxid' '-idtag' '$identification_tag' '-diagnosis' '$diagnosis' '-country' '$country' '-location' '$location' '-date' '$date' -sourcedb SAPP
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8 #for $index, $id in enumerate( $ids )
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9 '-ids' '$id.id_tag'
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10 #end for
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11 '-id_alternative' '$input.name'
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12 </command>
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13 <inputs>
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14 <param size="60" name="input" type="data" format="fasta,fa" label="File for annotation, file types used fasta,fa"/>
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15 <param size="60" name="organism" type="text" format="text" label="organism name"/>
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16 <param size="60" name="diagnosis" type="text" format="text" label="Diagnosis of host if applicable"/>
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17 <param size="60" name="ncbi_taxid" type="text" format="text" label="NCBI taxonomy ID"/>
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18 <param size="60" name="country" type="text" format="text" label="Country of sample"/>
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19 <param size="60" name="location" type="text" format="text" label="Location of sample e.g., river, city, hospital"/>
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20 <param size="60" name="date" type="text" format="text" label="Sample date"/>
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21 <param size="60" name="identification_tag" type="text" format="text" label="An identification tag used for RDF storage !Needs to be very unique!"/>
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22 <repeat name="ids" title="Identification tags">
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23 <param size="60" name="id_tag" type="text" format="text" label="An identification tag used by other consortiums"/>
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24 </repeat>
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25 </inputs>
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26
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27 <outputs>
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28 <data format="rdf" name="output" label="proteinTTL: ${input.name}" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input" value="test-data/NC_017117.faa"/>
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33 <output name="$output" file="NC_017117.rdf"/>
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34 <output name="$ncbi_taxid" value="634455"/>
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35 <output name="$idtag" value="Acetobacter pasteurianus IFO 3283-22"/>
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36 <output name="$organism" value="Acetobacter pasteurianus IFO 3283-22"/>
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37 </test>
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38 </tests>
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39 <help>
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40 RDF creation from a multi protein fasta file
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41 </help>
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42 </tool>
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