Mercurial > repos > cpt > cpt_psm_recombine

annotate macros.xml @ 1:97ef96676b48 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:51:26 +0000
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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="5.26.2">perl</requirement>
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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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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 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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13 </xml>
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14 <xml name="gff3_input">
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15 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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16 </xml>
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17 <xml name="input/gff3+fasta">
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18 <expand macro="gff3_input"/>
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19 <expand macro="genome_selector"/>
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20 </xml>
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21 <token name="@INPUT_GFF@">
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22 $gff3_data
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23 </token>
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24 <token name="@INPUT_FASTA@">
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25 genomeref.fa
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26 </token>
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27 <token name="@GENOME_SELECTOR_PRE@">
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28 ln -s $genome_fasta genomeref.fa;
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29 </token>
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30 <token name="@GENOME_SELECTOR@">
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31 genomeref.fa
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32 </token>
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33 <xml name="input/fasta">
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34 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
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35 </xml>
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36 <token name="@SEQUENCE@">
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37 $sequences
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38 </token>
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39 <xml name="input/fasta/protein">
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40 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
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41 </xml>
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42 </macros>