Mercurial > repos > cpt > cpt_convert_glimmer

comparison cpt_convert_glimmer/macros.xml @ 3:061b5ee5b844 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author cpt
date Thu, 19 May 2022 23:54:32 +0000
parents d09ed5271c24
children 71c68eb1c30f
comparison
equal deleted inserted replaced
2:f62001b83a21 3:061b5ee5b844
7 <requirement type="package" version="1.1.3">cpt_gffparser</requirement> 7 <requirement type="package" version="1.1.3">cpt_gffparser</requirement>
8 <yield/> 8 <yield/>
9 </requirements> 9 </requirements>
10 </xml> 10 </xml>
11 <xml name="genome_selector"> 11 <xml name="genome_selector">
12 <conditional name="reference_genome"> 12 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
13 <param name="reference_genome_source" type="select" label="Reference Genome">
14 <option value="history" selected="True">From History</option>
15 <option value="cached">Locally Cached</option>
16 </param>
17 <when value="cached">
18 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
19 <options from_data_table="all_fasta"/>
20 </param>
21 </when>
22 <when value="history">
23 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
24 </when>
25 </conditional>
26 </xml> 13 </xml>
27 <xml name="gff3_input"> 14 <xml name="gff3_input">
28 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> 15 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
29 </xml> 16 </xml>
30 <xml name="input/gff3+fasta"> 17 <xml name="input/gff3+fasta">
33 </xml> 20 </xml>
34 <token name="@INPUT_GFF@"> 21 <token name="@INPUT_GFF@">
35 "$gff3_data" 22 "$gff3_data"
36 </token> 23 </token>
37 <token name="@INPUT_FASTA@"> 24 <token name="@INPUT_FASTA@">
38 #if str($reference_genome.reference_genome_source) == 'cached':
39 "${reference_genome.fasta_indexes.fields.path}"
40 #else if str($reference_genome.reference_genome_source) == 'history':
41 genomeref.fa 25 genomeref.fa
42 #end if
43 </token> 26 </token>
44 <token name="@GENOME_SELECTOR_PRE@"> 27 <token name="@GENOME_SELECTOR_PRE@">
45 #if $reference_genome.reference_genome_source == 'history': 28 ln -s $genome_fasta genomeref.fa;
46 ln -s $reference_genome.genome_fasta genomeref.fa;
47 #end if
48 </token> 29 </token>
49 <token name="@GENOME_SELECTOR@"> 30 <token name="@GENOME_SELECTOR@">
50 #if str($reference_genome.reference_genome_source) == 'cached':
51 "${reference_genome.fasta_indexes.fields.path}"
52 #else if str($reference_genome.reference_genome_source) == 'history':
53 genomeref.fa 31 genomeref.fa
54 #end if
55 </token> 32 </token>
56 <xml name="input/fasta"> 33 <xml name="input/fasta">
57 <param label="Fasta file" name="sequences" type="data" format="fasta"/> 34 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
58 </xml> 35 </xml>
59 36