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annotate cpt_stops/macros.xml @ 3:486f1a167acc draft default tip

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author cpt
date Fri, 20 May 2022 09:06:11 +0000
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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" 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 <token name="@BLAST_TSV@">
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12 "$blast_tsv"
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13 </token>
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14 <xml name="blast_tsv">
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15 <param label="Blast Results" help="TSV/tabular (25 Column)"
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16 name="blast_tsv" type="data" format="tabular" />
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17 </xml>
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18
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19 <token name="@BLAST_XML@">
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20 "$blast_xml"
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21 </token>
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22 <xml name="blast_xml">
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23 <param label="Blast Results" help="XML format"
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24 name="blast_xml" type="data" format="blastxml" />
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25 </xml>
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26 <xml name="gff3_with_fasta">
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27 <param label="Genome Sequences" name="fasta" type="data" format="fasta" />
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28 <param label="Genome Annotations" name="gff3" type="data" format="gff3" />
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29 </xml>
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30 <xml name="genome_selector">
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31 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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32 </xml>
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33 <xml name="gff3_input">
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34 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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35 </xml>
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36 <xml name="input/gff3+fasta">
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37 <expand macro="gff3_input" />
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38 <expand macro="genome_selector" />
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39 </xml>
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40 <token name="@INPUT_GFF@">
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41 "$gff3_data"
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42 </token>
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43 <token name="@INPUT_FASTA@">
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44 genomeref.fa
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45 </token>
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46 <token name="@GENOME_SELECTOR_PRE@">
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47 ln -s $genome_fasta genomeref.fa;
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48 </token>
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49 <token name="@GENOME_SELECTOR@">
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50 genomeref.fa
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51 </token>
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52 <xml name="input/fasta">
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53 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
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54 </xml>
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56 <token name="@SEQUENCE@">
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57 "$sequences"
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58 </token>
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59 <xml name="input/fasta/protein">
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60 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
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61 </xml>
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62 </macros>