Mercurial > repos > cpt > cpt_export_seq_unique
comparison cpt_export_seq_unique/macros.xml @ 0:aaed5a0c774c draft
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author | cpt |
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date | Fri, 01 Jul 2022 13:43:49 +0000 |
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-1:000000000000 | 0:aaed5a0c774c |
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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 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> | |
32 </xml> | |
33 <xml name="gff3_input"> | |
34 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> | |
35 </xml> | |
36 <xml name="input/gff3+fasta"> | |
37 <expand macro="gff3_input" /> | |
38 <expand macro="genome_selector" /> | |
39 </xml> | |
40 <token name="@INPUT_GFF@"> | |
41 "$gff3_data" | |
42 </token> | |
43 <token name="@INPUT_FASTA@"> | |
44 genomeref.fa | |
45 </token> | |
46 <token name="@GENOME_SELECTOR_PRE@"> | |
47 ln -s $genome_fasta genomeref.fa; | |
48 </token> | |
49 <token name="@GENOME_SELECTOR@"> | |
50 genomeref.fa | |
51 </token> | |
52 <xml name="input/fasta"> | |
53 <param label="Fasta file" name="sequences" type="data" format="fasta"/> | |
54 </xml> | |
55 | |
56 <token name="@SEQUENCE@"> | |
57 "$sequences" | |
58 </token> | |
59 <xml name="input/fasta/protein"> | |
60 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/> | |
61 </xml> | |
62 </macros> |