Mercurial > repos > cpt > cpt_blast_to_xmfa

comparison macros.xml @ 1:c66d6978a5f8 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:14:17 +0000
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children 1623f46fdd2e
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0:84761ea60231 1:c66d6978a5f8
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package">progressivemauve</requirement>
5 <!--<requirement type="package" version="2.7">python</requirement>-->
6 <requirement type="package" version="0.6.4">bcbiogff</requirement>
7 <yield/>
8 </requirements>
9 </xml>
10 <token name="@WRAPPER_VERSION@">2.4.0</token>
11 <xml name="citation/progressive_mauve">
12 <citation type="doi">10.1371/journal.pone.0011147</citation>
13 </xml>
14 <xml name="citation/gepard">
15 <citation type="doi">10.1093/bioinformatics/btm039</citation>
16 </xml>
17 <token name="@XMFA_INPUT@">
18 '$xmfa'
19 </token>
20 <xml name="xmfa_input" token_formats="xmfa">
21 <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
22 </xml>
23 <token name="@XMFA_FA_INPUT@">
24 '$sequences'
25 </token>
26 <xml name="xmfa_fa_input">
27 <param type="data" format="fasta" name="sequences" label="Sequences in alignment" 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"/>
28 </xml>
29 <xml name="genome_selector">
30 <conditional name="reference_genome">
31 <param name="reference_genome_source" type="select" label="Reference Genome">
32 <option value="history" selected="True">From History</option>
33 <option value="cached">Locally Cached</option>
34 </param>
35 <when value="cached">
36 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
37 <options from_data_table="all_fasta"/>
38 </param>
39 </when>
40 <when value="history">
41 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
42 </when>
43 </conditional>
44 </xml>
45 <xml name="gff3_input">
46 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
47 </xml>
48 <xml name="input/gff3+fasta">
49 <expand macro="gff3_input"/>
50 <expand macro="genome_selector"/>
51 </xml>
52 <token name="@INPUT_GFF@">
53 '$gff3_data'
54 </token>
55 <token name="@INPUT_FASTA@">
56 #if str($reference_genome.reference_genome_source) == 'cached':
57 '${reference_genome.fasta_indexes.fields.path}'
58 #else if str($reference_genome.reference_genome_source) == 'history':
59 genomeref.fa
60 #end if
61 </token>
62 <token name="@GENOME_SELECTOR_PRE@">
63 #if $reference_genome.reference_genome_source == 'history':
64 ln -s '$reference_genome.genome_fasta' genomeref.fa;
65 #end if
66 </token>
67 <token name="@GENOME_SELECTOR@">
68 #if str($reference_genome.reference_genome_source) == 'cached':
69 '${reference_genome.fasta_indexes.fields.path}'
70 #else if str($reference_genome.reference_genome_source) == 'history':
71 genomeref.fa
72 #end if
73 </token>
74 </macros>