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comparison cpt_related_genome_nuc/macros.xml @ 0:5a5fe0a6f78d draft default tip

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author cpt
date Fri, 10 Jun 2022 08:45:13 +0000
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-1:000000000000 0:5a5fe0a6f78d
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>