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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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1
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5 <requirement type="package" version="3.8.13">python</requirement>
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6 <requirement type="package" version="1.79">biopython</requirement>
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7 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
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0
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8 <yield/>
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9 </requirements>
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10 </xml>
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11 <xml name="genome_selector">
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12 <conditional name="reference_genome">
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13 <param name="reference_genome_source" type="select" label="Reference Genome">
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14 <option value="history" selected="True">From History</option>
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15 <option value="cached">Locally Cached</option>
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16 </param>
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17 <when value="cached">
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18 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
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19 <options from_data_table="all_fasta"/>
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20 </param>
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21 </when>
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22 <when value="history">
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23 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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24 </when>
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25 </conditional>
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26 </xml>
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27 <xml name="gff3_input">
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28 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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29 </xml>
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30 <xml name="input/gff3+fasta">
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31 <expand macro="gff3_input" />
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32 <expand macro="genome_selector" />
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33 </xml>
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34 <token name="@INPUT_GFF@">
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35 "$gff3_data"
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36 </token>
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37 <token name="@INPUT_FASTA@">
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38 #if str($reference_genome.reference_genome_source) == 'cached':
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39 "${reference_genome.fasta_indexes.fields.path}"
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40 #else if str($reference_genome.reference_genome_source) == 'history':
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41 genomeref.fa
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42 #end if
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43 </token>
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44 <token name="@GENOME_SELECTOR_PRE@">
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45 #if $reference_genome.reference_genome_source == 'history':
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46 ln -s $reference_genome.genome_fasta genomeref.fa;
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47 #end if
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48 </token>
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49 <token name="@GENOME_SELECTOR@">
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50 #if str($reference_genome.reference_genome_source) == 'cached':
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51 "${reference_genome.fasta_indexes.fields.path}"
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52 #else if str($reference_genome.reference_genome_source) == 'history':
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53 genomeref.fa
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54 #end if
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55 </token>
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56 <xml name="input/fasta">
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57 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
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58 </xml>
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59
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60 <token name="@SEQUENCE@">
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61 "$sequences"
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62 </token>
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63 <xml name="input/fasta/protein">
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64 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
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65 </xml>
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66 </macros>
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