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comparison cpt_mist3/macros.xml @ 0:1a9603d09814 draft default tip

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author cpt
date Fri, 17 Jun 2022 02:58:50 +0000
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-1:000000000000 0:1a9603d09814
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package">progressivemauve</requirement>
6 <requirement type="package" version="3.8.13">python</requirement>
7 <requirement type="package" version="1.79">biopython</requirement>
8 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
9 <yield/>
10 </requirements>
11 </xml>
12 <token name="@WRAPPER_VERSION@">2.4.0</token>
13 <xml name="citation/progressive_mauve">
14 <citation type="doi">10.1371/journal.pone.0011147</citation>
15 </xml>
16 <xml name="citation/gepard">
17 <citation type="doi">10.1093/bioinformatics/btm039</citation>
18 </xml>
19
20 <token name="@XMFA_INPUT@">
21 "$xmfa"
22 </token>
23 <xml name="xmfa_input"
24 token_formats="xmfa">
25 <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA" />
26 </xml>
27
28 <token name="@XMFA_FA_INPUT@">
29 "$sequences"
30 </token>
31 <xml name="xmfa_fa_input">
32 <param type="data" format="fasta" name="sequences" label="Sequences in alignment"
33 help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/>
34
35 </xml>
36 <xml name="genome_selector">
37 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
38 </xml>
39 <xml name="gff3_input">
40 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
41 </xml>
42 <xml name="input/gff3+fasta">
43 <expand macro="gff3_input" />
44 <expand macro="genome_selector" />
45 </xml>
46 <token name="@INPUT_GFF@">
47 "$gff3_data"
48 </token>
49 <token name="@INPUT_FASTA@">
50 genomeref.fa
51 </token>
52 <token name="@GENOME_SELECTOR_PRE@">
53 ln -s $genome_fasta genomeref.fa;
54 </token>
55 <token name="@GENOME_SELECTOR@">
56 genomeref.fa
57 </token>
58 </macros>