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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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5 <requirement type="package">progressivemauve</requirement>
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6 <requirement type="package" version="3.8.13">python</requirement>
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7 <requirement type="package" version="1.79">biopython</requirement>
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8 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
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9 <yield/>
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10 </requirements>
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11 </xml>
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12 <token name="@WRAPPER_VERSION@">2.4.0</token>
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13 <xml name="citation/progressive_mauve">
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14 <citation type="doi">10.1371/journal.pone.0011147</citation>
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15 </xml>
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16 <xml name="citation/gepard">
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17 <citation type="doi">10.1093/bioinformatics/btm039</citation>
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18 </xml>
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19
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20 <token name="@XMFA_INPUT@">
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21 "$xmfa"
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22 </token>
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23 <xml name="xmfa_input"
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24 token_formats="xmfa">
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25 <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA" />
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26 </xml>
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27
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28 <token name="@XMFA_FA_INPUT@">
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29 "$sequences"
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30 </token>
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31 <xml name="xmfa_fa_input">
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32 <param type="data" format="fasta" name="sequences" label="Sequences in alignment"
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33 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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34
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35 </xml>
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36 <xml name="genome_selector">
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37 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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38 </xml>
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39 <xml name="gff3_input">
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40 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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41 </xml>
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42 <xml name="input/gff3+fasta">
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43 <expand macro="gff3_input" />
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44 <expand macro="genome_selector" />
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45 </xml>
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46 <token name="@INPUT_GFF@">
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47 "$gff3_data"
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48 </token>
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49 <token name="@INPUT_FASTA@">
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50 genomeref.fa
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51 </token>
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52 <token name="@GENOME_SELECTOR_PRE@">
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53 ln -s $genome_fasta genomeref.fa;
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54 </token>
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55 <token name="@GENOME_SELECTOR@">
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56 genomeref.fa
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57 </token>
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58 </macros>
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