|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <macros>
|
|
|
3 <xml name="requirements">
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="3.8.13">python</requirement>
|
|
|
6 <requirement type="package" version="1.79">biopython</requirement>
|
|
|
7 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
|
|
|
8 <yield/>
|
|
|
9 </requirements>
|
|
|
10 </xml>
|
|
|
11 <token name="@BLAST_TSV@">
|
|
|
12 "$blast_tsv"
|
|
|
13 </token>
|
|
|
14 <xml name="blast_tsv">
|
|
|
15 <param label="Blast Results" help="TSV/tabular (25 Column)"
|
|
|
16 name="blast_tsv" type="data" format="tabular" />
|
|
|
17 </xml>
|
|
|
18
|
|
|
19 <token name="@BLAST_XML@">
|
|
|
20 "$blast_xml"
|
|
|
21 </token>
|
|
|
22 <xml name="blast_xml">
|
|
|
23 <param label="Blast Results" help="XML format"
|
|
|
24 name="blast_xml" type="data" format="blastxml" />
|
|
|
25 </xml>
|
|
|
26 <xml name="gff3_with_fasta">
|
|
|
27 <param label="Genome Sequences" name="fasta" type="data" format="fasta" />
|
|
|
28 <param label="Genome Annotations" name="gff3" type="data" format="gff3" />
|
|
|
29 </xml>
|
|
|
30 <xml name="genome_selector">
|
|
|
31 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
|
|
|
32 </xml>
|
|
|
33 <xml name="gff3_input">
|
|
|
34 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
|
|
|
35 </xml>
|
|
|
36 <xml name="input/gff3+fasta">
|
|
|
37 <expand macro="gff3_input" />
|
|
|
38 <expand macro="genome_selector" />
|
|
|
39 </xml>
|
|
|
40 <token name="@INPUT_GFF@">
|
|
|
41 "$gff3_data"
|
|
|
42 </token>
|
|
|
43 <token name="@INPUT_FASTA@">
|
|
|
44 genomeref.fa
|
|
|
45 </token>
|
|
|
46 <token name="@GENOME_SELECTOR_PRE@">
|
|
|
47 ln -s $genome_fasta genomeref.fa;
|
|
|
48 </token>
|
|
|
49 <token name="@GENOME_SELECTOR@">
|
|
|
50 genomeref.fa
|
|
|
51 </token>
|
|
|
52 <xml name="input/fasta">
|
|
|
53 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
|
|
|
54 </xml>
|
|
|
55
|
|
|
56 <token name="@SEQUENCE@">
|
|
|
57 "$sequences"
|
|
|
58 </token>
|
|
|
59 <xml name="input/fasta/protein">
|
|
|
60 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
|
|
|
61 </xml>
|
|
|
62 </macros>
|
