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comparison cpt_starts/macros.xml @ 1:0a9dafaa81fc draft

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author cpt
date Thu, 19 May 2022 23:59:59 +0000
parents 9f2517655a1e
children 204a23a39c58
comparison
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0:9f2517655a1e 1:0a9dafaa81fc
26 <xml name="gff3_with_fasta"> 26 <xml name="gff3_with_fasta">
27 <param label="Genome Sequences" name="fasta" type="data" format="fasta" /> 27 <param label="Genome Sequences" name="fasta" type="data" format="fasta" />
28 <param label="Genome Annotations" name="gff3" type="data" format="gff3" /> 28 <param label="Genome Annotations" name="gff3" type="data" format="gff3" />
29 </xml> 29 </xml>
30 <xml name="genome_selector"> 30 <xml name="genome_selector">
31 <conditional name="reference_genome"> 31 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
32 <param name="reference_genome_source" type="select" label="Reference Genome">
33 <option value="history" selected="True">From History</option>
34 <option value="cached">Locally Cached</option>
35 </param>
36 <when value="cached">
37 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
38 <options from_data_table="all_fasta"/>
39 </param>
40 </when>
41 <when value="history">
42 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
43 </when>
44 </conditional>
45 </xml> 32 </xml>
46 <xml name="gff3_input"> 33 <xml name="gff3_input">
47 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> 34 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
48 </xml> 35 </xml>
49 <xml name="input/gff3+fasta"> 36 <xml name="input/gff3+fasta">
52 </xml> 39 </xml>
53 <token name="@INPUT_GFF@"> 40 <token name="@INPUT_GFF@">
54 "$gff3_data" 41 "$gff3_data"
55 </token> 42 </token>
56 <token name="@INPUT_FASTA@"> 43 <token name="@INPUT_FASTA@">
57 #if str($reference_genome.reference_genome_source) == 'cached':
58 "${reference_genome.fasta_indexes.fields.path}"
59 #else if str($reference_genome.reference_genome_source) == 'history':
60 genomeref.fa 44 genomeref.fa
61 #end if
62 </token> 45 </token>
63 <token name="@GENOME_SELECTOR_PRE@"> 46 <token name="@GENOME_SELECTOR_PRE@">
64 #if $reference_genome.reference_genome_source == 'history': 47 ln -s $genome_fasta genomeref.fa;
65 ln -s $reference_genome.genome_fasta genomeref.fa;
66 #end if
67 </token> 48 </token>
68 <token name="@GENOME_SELECTOR@"> 49 <token name="@GENOME_SELECTOR@">
69 #if str($reference_genome.reference_genome_source) == 'cached':
70 "${reference_genome.fasta_indexes.fields.path}"
71 #else if str($reference_genome.reference_genome_source) == 'history':
72 genomeref.fa 50 genomeref.fa
73 #end if
74 </token> 51 </token>
75 <xml name="input/fasta"> 52 <xml name="input/fasta">
76 <param label="Fasta file" name="sequences" type="data" format="fasta"/> 53 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
77 </xml> 54 </xml>
78 55