Mercurial > repos > cpt > cpt_find_spanins

comparison 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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2:1a7fef71aee3 3:fd70980a516b
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="2019.06.05">regex</requirement>
5 <requirement type="package" version="3.6">python</requirement>
6 <requirement type="package" version="1.77">biopython</requirement>
7 <requirement type="package" version="1.1.7">cpt_gffparser</requirement>
8 <yield/>
9 </requirements>
10 </xml>
11 <token name="@BLAST_TSV@">
12 $blast_tsv
13 </token>
14 <xml name="blast_tsv">
15 <param label="Blast Results" help="TSV/tabular (25 Column)" name="blast_tsv" type="data" format="tabular"/>
16 </xml>
17 <token name="@BLAST_XML@">
18 $blast_xml
19 </token>
20 <xml name="blast_xml">
21 <param label="Blast Results" help="XML format" name="blast_xml" type="data" format="blastxml"/>
22 </xml>
23 <xml name="gff3_with_fasta">
24 <param label="Genome Sequences" name="fasta" type="data" format="fasta"/>
25 <param label="Genome Annotations" name="gff3" type="data" format="gff3"/>
26 </xml>
27 <xml name="genome_selector">
28 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
29 </xml>
30 <xml name="gff3_input">
31 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
32 </xml>
33 <xml name="input/gff3+fasta">
34 <expand macro="gff3_input"/>
35 <expand macro="genome_selector"/>
36 </xml>
37 <token name="@INPUT_GFF@">
38 $gff3_data
39 </token>
40 <token name="@INPUT_FASTA@">
41 genomeref.fa
42 </token>
43 <token name="@GENOME_SELECTOR_PRE@">
44 ln -s $genome_fasta genomeref.fa;
45 </token>
46 <token name="@GENOME_SELECTOR@">
47 genomeref.fa
48 </token>
49 <xml name="input/fasta">
50 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
51 </xml>
52 <token name="@SEQUENCE@">
53 $sequences
54 </token>
55 <xml name="input/fasta/protein">
56 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
57 </xml>
58 </macros>