|
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 <conditional name="reference_genome">
|
|
|
32 <param name="reference_genome_source" type="select" label="Reference Genome">
|
|
|
33 <option value="history" selected="True">From History</option>
|
|
|
34 <option value="cached">Locally Cached</option>
|
|
|
35 </param>
|
|
|
36 <when value="cached">
|
|
|
37 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
|
|
|
38 <options from_data_table="all_fasta"/>
|
|
|
39 </param>
|
|
|
40 </when>
|
|
|
41 <when value="history">
|
|
|
42 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
|
|
|
43 </when>
|
|
|
44 </conditional>
|
|
|
45 </xml>
|
|
|
46 <xml name="gff3_input">
|
|
|
47 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
|
|
|
48 </xml>
|
|
|
49 <xml name="input/gff3+fasta">
|
|
|
50 <expand macro="gff3_input" />
|
|
|
51 <expand macro="genome_selector" />
|
|
|
52 </xml>
|
|
|
53 <token name="@INPUT_GFF@">
|
|
|
54 "$gff3_data"
|
|
|
55 </token>
|
|
|
56 <token name="@INPUT_FASTA@">
|
|
|
57 #if str($reference_genome.reference_genome_source) == 'cached':
|
|
|
58 "${reference_genome.fasta_indexes.fields.path}"
|
|
|
59 #else if str($reference_genome.reference_genome_source) == 'history':
|
|
|
60 genomeref.fa
|
|
|
61 #end if
|
|
|
62 </token>
|
|
|
63 <token name="@GENOME_SELECTOR_PRE@">
|
|
|
64 #if $reference_genome.reference_genome_source == 'history':
|
|
|
65 ln -s $reference_genome.genome_fasta genomeref.fa;
|
|
|
66 #end if
|
|
|
67 </token>
|
|
|
68 <token name="@GENOME_SELECTOR@">
|
|
|
69 #if str($reference_genome.reference_genome_source) == 'cached':
|
|
|
70 "${reference_genome.fasta_indexes.fields.path}"
|
|
|
71 #else if str($reference_genome.reference_genome_source) == 'history':
|
|
|
72 genomeref.fa
|
|
|
73 #end if
|
|
|
74 </token>
|
|
|
75 <xml name="input/fasta">
|
|
|
76 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
|
|
|
77 </xml>
|
|
|
78
|
|
|
79 <token name="@SEQUENCE@">
|
|
|
80 "$sequences"
|
|
|
81 </token>
|
|
|
82 <xml name="input/fasta/protein">
|
|
|
83 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
|
|
|
84 </xml>
|
|
|
85 </macros>
|
