|
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">
|
|
|
12 <conditional name="reference_genome">
|
|
|
13 <param name="reference_genome_source" type="select" label="Reference Genome">
|
|
|
14 <option value="history" selected="True">From History</option>
|
|
|
15 <option value="cached">Locally Cached</option>
|
|
|
16 </param>
|
|
|
17 <when value="cached">
|
|
|
18 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
|
|
|
19 <options from_data_table="all_fasta"/>
|
|
|
20 </param>
|
|
|
21 </when>
|
|
|
22 <when value="history">
|
|
|
23 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
|
|
|
24 </when>
|
|
|
25 </conditional>
|
|
|
26 </xml>
|
|
|
27 <xml name="gff3_input">
|
|
|
28 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
|
|
|
29 </xml>
|
|
|
30 <xml name="input/gff3+fasta">
|
|
|
31 <expand macro="gff3_input" />
|
|
|
32 <expand macro="genome_selector" />
|
|
|
33 </xml>
|
|
|
34 <token name="@INPUT_GFF@">
|
|
|
35 "$gff3_data"
|
|
|
36 </token>
|
|
|
37 <token name="@INPUT_FASTA@">
|
|
|
38 #if str($reference_genome.reference_genome_source) == 'cached':
|
|
|
39 "${reference_genome.fasta_indexes.fields.path}"
|
|
|
40 #else if str($reference_genome.reference_genome_source) == 'history':
|
|
|
41 genomeref.fa
|
|
|
42 #end if
|
|
|
43 </token>
|
|
|
44 <token name="@GENOME_SELECTOR_PRE@">
|
|
|
45 #if $reference_genome.reference_genome_source == 'history':
|
|
|
46 ln -s $reference_genome.genome_fasta genomeref.fa;
|
|
|
47 #end if
|
|
|
48 </token>
|
|
|
49 <token name="@GENOME_SELECTOR@">
|
|
|
50 #if str($reference_genome.reference_genome_source) == 'cached':
|
|
|
51 "${reference_genome.fasta_indexes.fields.path}"
|
|
|
52 #else if str($reference_genome.reference_genome_source) == 'history':
|
|
|
53 genomeref.fa
|
|
|
54 #end if
|
|
|
55 </token>
|
|
|
56 </macros>
|
