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1 <tool id="DFASTA2RDF" name="FASTA to RDF" version="0.1">
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2 <description></description>
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3 <requirements>
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4 <container type="docker">jjkoehorst/sappdocker:FASTA2RDF</container>
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5 </requirements>
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6 <command interpreter="docker">java -jar /fasta2rdf/target/FASTA2RDF-0.1-jar-with-dependencies.jar
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7 '--type' '$source.fastaType' '--ignorestop' '$IgnoreStopCodon'
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8 '--input' '$input' '--output' '$output' '-organism' '$organism'
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9 '--ncbi_taxid' '$ncbi_taxid'
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10 #if len(str($identification_tag))==0
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11 '--idtag' ${input.name}
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12 #else
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13 '--idtag' '$identification_tag'
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14 #end if
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15 --source SAPP
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16
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17 #for $index, $id in enumerate( $ids )
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18 '--id_alternative' '$id.id_tag'
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19 #end for
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20 '--id_alternative' '$input.name'
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21 '--codon' '$table'
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22 </command>
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23 <inputs>
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24 <param size="60" name="input" type="data" format="fasta" label="Fasta file for conversion" />
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25
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26 <conditional name="source">
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27 <param name="fastaType" type="select"
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28 label="Select if it is a Genome/Gene/Protein or program wont start!">
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29 <option value="">To be chosen</option>
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30 <option value="genome"> Genome </option>
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31 <option value="gene"> Gene</option>
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32 <option value="protein"> Protein </option>
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33 <validator type="empty_field"
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34 message="Please select if it is a Genome, Gene or Protein" />
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35 </param>
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36 </conditional>
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37
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38 <param name="table" type="select" label="Codon table">
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39 <option value="1"> 1 - UNIVERSAL </option>
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40 <option value="2"> 2 - VERTEBRATE_MITOCHONDRIAL </option>
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41 <option value="3"> 3 - YEAST_MITOCHONDRIAL </option>
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42 <option value="4"> 4 - MOLD_MITOCHONDRIAL </option>
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43 <option value="5"> 5 - INVERTEBRATE_MITOCHONDRIAL </option>
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44 <option value="6"> 6 - CILIATE_NUCLEAR </option>
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45 <option value="9"> 9 - ECHINODERM_MITOCHONDRIAL </option>
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46 <option value="10"> 10 - EUPLOTID_NUCLEAR </option>
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47 <option value="11" selected="true"> 11 - BACTERIAL </option>
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48 <option value="12"> 12 - ALTERNATIVE_YEAST_NUCLEAR </option>
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49 <option value="13"> 13 - ASCIDIAN_MITOCHONDRIAL </option>
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50 <option value="14"> 14 - FLATWORM_MITOCHONDRIAL </option>
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51 <option value="15"> 15 - BLEPHARISMA_MACRONUCLEAR </option>
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52 <option value="16"> 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL </option>
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53 <option value="21"> 21 - TREMATODE_MITOCHONDRIAL </option>
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54 <option value="23"> 23 - SCENEDESMUS_MITOCHONDRIAL </option>
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55 </param>
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56 <param size="60" name="organism" type="text" format="text"
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57 label="organism name" />
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58 <param name='IgnoreStopCodon' type='boolean'
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59 label='Ignore if stop codon within protein sequence' truevalue='true'
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60 falsevalue='false' checked="false" help='' />
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61
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62 <param size="60" name="ncbi_taxid" type="integer" value="0"
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63 label="NCBI taxonomy ID" optional="False">
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64 <validator type="in_range" min="1"
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65 message="Minimum taxonomy value is 1" />
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66 </param>
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67 <param size="60" name="identification_tag" type="text" format="text"
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68 label="An identification tag used for RDF storage !Needs to be very unique!"
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69 optional="True" />
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70 <repeat name="ids" title="Identification tags">
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71 <param size="60" name="id_tag" type="text" format="text"
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72 label="An identification tag used by other consortiums" />
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73 </repeat>
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74 </inputs>
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75 <outputs>
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76 <data format="ttl" name="output" label="FASTA2RDF: ${input.name}" />
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77 </outputs>
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78 <help>
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79 RDF creation from a multi (gene/protein/genome) fasta file
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80 </help>
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81 </tool>
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82
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