Mercurial > repos > cpt > cpt_req_phage_start

annotate cpt_req_phage_start/macros.xml @ 2:19af10ba2fc2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author cpt
date Fri, 20 May 2022 07:32:32 +0000
parents dca61f5e2d43
children 67e5202e43c9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
1 <?xml version="1.0"?>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
2 <macros>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
3 <xml name="requirements">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
4 <requirements>
2
19af10ba2fc2 Uploaded
cpt
parents: 1
diff changeset
5 <requirement type="package" version="3.8.13">python</requirement>
0
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
6 <requirement type="package" version="1.77">biopython</requirement>
2
19af10ba2fc2 Uploaded
cpt
parents: 1
diff changeset
7 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
0
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
8 <yield/>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
9 </requirements>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
10 </xml>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
11 <token name="@BLAST_TSV@">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
12 "$blast_tsv"
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
13 </token>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
14 <xml name="blast_tsv">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
15 <param label="Blast Results" help="TSV/tabular (25 Column)"
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
16 name="blast_tsv" type="data" format="tabular" />
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
17 </xml>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
18
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
19 <token name="@BLAST_XML@">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
20 "$blast_xml"
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
21 </token>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
22 <xml name="blast_xml">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
23 <param label="Blast Results" help="XML format"
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
24 name="blast_xml" type="data" format="blastxml" />
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
25 </xml>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
26 <xml name="gff3_with_fasta">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
27 <param label="Genome Sequences" name="fasta" type="data" format="fasta" />
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
28 <param label="Genome Annotations" name="gff3" type="data" format="gff3" />
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
29 </xml>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
30 <xml name="genome_selector">
1
dca61f5e2d43 Uploaded
cpt
parents: 0
diff changeset
31 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
0
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
32 </xml>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
33 <xml name="gff3_input">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
34 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
35 </xml>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
36 <xml name="input/gff3+fasta">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
37 <expand macro="gff3_input" />
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
38 <expand macro="genome_selector" />
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
39 </xml>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
40 <token name="@INPUT_GFF@">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
41 "$gff3_data"
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
42 </token>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
43 <token name="@INPUT_FASTA@">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
44 genomeref.fa
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
45 </token>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
46 <token name="@GENOME_SELECTOR_PRE@">
1
dca61f5e2d43 Uploaded
cpt
parents: 0
diff changeset
47 ln -s $genome_fasta genomeref.fa;
0
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
48 </token>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
49 <token name="@GENOME_SELECTOR@">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
50 genomeref.fa
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
51 </token>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
52 <xml name="input/fasta">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
53 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
54 </xml>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
55
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
56 <token name="@SEQUENCE@">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
57 "$sequences"
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
58 </token>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
59 <xml name="input/fasta/protein">
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
60 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
61 </xml>
45a5cf6b0ff4 Uploaded
cpt
parents:
diff changeset
62 </macros>