|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <macros>
|
|
|
3 <xml name="requirements">
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="3.7">python</requirement>
|
|
|
6 <requirement type="package" version="1.77">biopython</requirement>
|
|
|
7 <requirement type="package" version="1.1.3">cpt_gffparser</requirement>
|
|
|
8 <yield/>
|
|
|
9 </requirements>
|
|
|
10 </xml>
|
|
|
11 <xml name="genome_selector">
|
|
3
|
12 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
|
|
0
|
13 </xml>
|
|
|
14 <xml name="gff3_input">
|
|
|
15 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
|
|
|
16 </xml>
|
|
|
17 <xml name="input/gff3+fasta">
|
|
|
18 <expand macro="gff3_input" />
|
|
|
19 <expand macro="genome_selector" />
|
|
|
20 </xml>
|
|
|
21 <token name="@INPUT_GFF@">
|
|
|
22 "$gff3_data"
|
|
|
23 </token>
|
|
|
24 <token name="@INPUT_FASTA@">
|
|
|
25 genomeref.fa
|
|
|
26 </token>
|
|
|
27 <token name="@GENOME_SELECTOR_PRE@">
|
|
3
|
28 ln -s $genome_fasta genomeref.fa;
|
|
0
|
29 </token>
|
|
|
30 <token name="@GENOME_SELECTOR@">
|
|
|
31 genomeref.fa
|
|
|
32 </token>
|
|
|
33 <xml name="input/fasta">
|
|
|
34 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
|
|
|
35 </xml>
|
|
|
36
|
|
|
37 <token name="@SEQUENCE@">
|
|
|
38 "$sequences"
|
|
|
39 </token>
|
|
|
40 <xml name="input/fasta/protein">
|
|
|
41 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
|
|
|
42 </xml>
|
|
|
43 </macros>
|
