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annotate macros.xml @ 6:706058e804d1 draft

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author cpt
date Fri, 01 Dec 2023 02:48:37 +0000
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children 759ba1430091
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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" version="0.6.4">bcbiogff</requirement>
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5 <yield/>
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6 </requirements>
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7 </xml>
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8 <token name="@WRAPPER_VERSION@">2.4.0</token>
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9 <xml name="citation/progressive_mauve">
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10 <citation type="doi">10.1371/journal.pone.0011147</citation>
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11 </xml>
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12 <xml name="citation/gepard">
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13 <citation type="doi">10.1093/bioinformatics/btm039</citation>
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14 </xml>
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15 <token name="@XMFA_INPUT@">
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16 '$xmfa'
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17 </token>
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18 <xml name="xmfa_input" token_formats="xmfa">
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19 <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
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20 </xml>
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21 <token name="@XMFA_FA_INPUT@">
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22 '$sequences'
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23 </token>
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24 <xml name="xmfa_fa_input">
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25 <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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26 </xml>
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27 <xml name="genome_selector">
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28 <conditional name="reference_genome">
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29 <param name="reference_genome_source" type="select" label="Reference Genome">
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30 <option value="history" selected="True">From History</option>
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31 <option value="cached">Locally Cached</option>
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32 </param>
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33 <when value="cached">
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34 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
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35 <options from_data_table="all_fasta"/>
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36 </param>
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37 </when>
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38 <when value="history">
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39 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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40 </when>
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41 </conditional>
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42 </xml>
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43 <xml name="gff3_input">
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44 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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45 </xml>
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46 <xml name="input/gff3+fasta">
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47 <expand macro="gff3_input"/>
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48 <expand macro="genome_selector"/>
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49 </xml>
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50 <token name="@INPUT_GFF@">
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51 '$gff3_data'
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52 </token>
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53 <token name="@INPUT_FASTA@">
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54 #if str($reference_genome.reference_genome_source) == 'cached':
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55 '${reference_genome.fasta_indexes.fields.path}'
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56 #else if str($reference_genome.reference_genome_source) == 'history':
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57 genomeref.fa
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58 #end if
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59 </token>
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60 <token name="@GENOME_SELECTOR_PRE@">
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61 #if $reference_genome.reference_genome_source == 'history':
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62 ln -s '$reference_genome.genome_fasta' genomeref.fa;
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63 #end if
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64 </token>
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65 <token name="@GENOME_SELECTOR@">
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66 #if str($reference_genome.reference_genome_source) == 'cached':
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67 '${reference_genome.fasta_indexes.fields.path}'
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68 #else if str($reference_genome.reference_genome_source) == 'history':
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69 genomeref.fa
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70 #end if
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71 </token>
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72 </macros>