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annotate macros.xml @ 3:fd70980a516b draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:42:01 +0000
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children f8f045f436d8
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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="2019.06.05">regex</requirement>
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5 <requirement type="package" version="3.6">python</requirement>
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6 <requirement type="package" version="1.77">biopython</requirement>
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7 <requirement type="package" version="1.1.7">cpt_gffparser</requirement>
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8 <yield/>
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9 </requirements>
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10 </xml>
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11 <token name="@BLAST_TSV@">
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12 $blast_tsv
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13 </token>
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14 <xml name="blast_tsv">
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15 <param label="Blast Results" help="TSV/tabular (25 Column)" name="blast_tsv" type="data" format="tabular"/>
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16 </xml>
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17 <token name="@BLAST_XML@">
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18 $blast_xml
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19 </token>
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20 <xml name="blast_xml">
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21 <param label="Blast Results" help="XML format" name="blast_xml" type="data" format="blastxml"/>
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22 </xml>
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23 <xml name="gff3_with_fasta">
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24 <param label="Genome Sequences" name="fasta" type="data" format="fasta"/>
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25 <param label="Genome Annotations" name="gff3" type="data" format="gff3"/>
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26 </xml>
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27 <xml name="genome_selector">
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28 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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29 </xml>
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30 <xml name="gff3_input">
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31 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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32 </xml>
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33 <xml name="input/gff3+fasta">
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34 <expand macro="gff3_input"/>
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35 <expand macro="genome_selector"/>
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36 </xml>
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37 <token name="@INPUT_GFF@">
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38 $gff3_data
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39 </token>
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40 <token name="@INPUT_FASTA@">
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41 genomeref.fa
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42 </token>
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43 <token name="@GENOME_SELECTOR_PRE@">
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44 ln -s $genome_fasta genomeref.fa;
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45 </token>
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46 <token name="@GENOME_SELECTOR@">
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47 genomeref.fa
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48 </token>
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49 <xml name="input/fasta">
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50 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
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51 </xml>
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52 <token name="@SEQUENCE@">
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53 $sequences
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54 </token>
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55 <xml name="input/fasta/protein">
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56 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
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57 </xml>
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58 </macros>