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comparison cpt_trnascanse_to_gff/macros.xml @ 0:b4134ad44443 draft

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author cpt
date Fri, 13 May 2022 18:03:32 +0000
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children 7bf46fd8d62e
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-1:000000000000 0:b4134ad44443
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 <xml name="input/fasta">
57 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
58 </xml>
59
60 <token name="@SEQUENCE@">
61 "$sequences"
62 </token>
63 <xml name="input/fasta/protein">
64 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
65 </xml>
66 </macros>