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annotate macros.xml @ 2:ba370cca3857 draft

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author cpt
date Sun, 23 Jul 2023 20:59:40 +0000
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children 5e8787e39d30
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package">progressivemauve</requirement>
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5 <!--<requirement type="package" version="2.7">python</requirement>-->
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6 <requirement type="package" version="0.6.4">bcbiogff</requirement>
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7 <yield/>
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8 </requirements>
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9 </xml>
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10 <token name="@WRAPPER_VERSION@">2.4.0</token>
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11 <xml name="citation/progressive_mauve">
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12 <citation type="doi">10.1371/journal.pone.0011147</citation>
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13 </xml>
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14 <xml name="citation/gepard">
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15 <citation type="doi">10.1093/bioinformatics/btm039</citation>
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16 </xml>
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17 <token name="@XMFA_INPUT@">
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18 '$xmfa'
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19 </token>
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20 <xml name="xmfa_input" token_formats="xmfa">
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21 <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
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22 </xml>
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23 <token name="@XMFA_FA_INPUT@">
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24 '$sequences'
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25 </token>
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26 <xml name="xmfa_fa_input">
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27 <param type="data" format="fasta" name="sequences" label="Sequences in alignment" help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/>
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28 </xml>
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29 <xml name="genome_selector">
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30 <conditional name="reference_genome">
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31 <param name="reference_genome_source" type="select" label="Reference Genome">
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32 <option value="history" selected="True">From History</option>
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33 <option value="cached">Locally Cached</option>
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34 </param>
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35 <when value="cached">
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36 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
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37 <options from_data_table="all_fasta"/>
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38 </param>
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39 </when>
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40 <when value="history">
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41 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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42 </when>
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43 </conditional>
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44 </xml>
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45 <xml name="gff3_input">
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46 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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47 </xml>
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48 <xml name="input/gff3+fasta">
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49 <expand macro="gff3_input"/>
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50 <expand macro="genome_selector"/>
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51 </xml>
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52 <token name="@INPUT_GFF@">
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53 '$gff3_data'
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54 </token>
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55 <token name="@INPUT_FASTA@">
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56 #if str($reference_genome.reference_genome_source) == 'cached':
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57 '${reference_genome.fasta_indexes.fields.path}'
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58 #else if str($reference_genome.reference_genome_source) == 'history':
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59 genomeref.fa
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60 #end if
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61 </token>
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62 <token name="@GENOME_SELECTOR_PRE@">
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63 #if $reference_genome.reference_genome_source == 'history':
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64 ln -s '$reference_genome.genome_fasta' genomeref.fa;
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65 #end if
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66 </token>
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67 <token name="@GENOME_SELECTOR@">
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68 #if str($reference_genome.reference_genome_source) == 'cached':
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69 '${reference_genome.fasta_indexes.fields.path}'
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70 #else if str($reference_genome.reference_genome_source) == 'history':
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71 genomeref.fa
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72 #end if
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73 </token>
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74 </macros>