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comparison macros.xml @ 6:f8f045f436d8 draft

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planemo upload commit 8de686c21d1ceac09660bb2c95583e1463744782
author cpt
date Fri, 20 Sep 2024 04:44:18 +0000
parents fd70980a516b
children
comparison
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5:46b252c89e9e 6:f8f045f436d8
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2019.06.05">regex</requirement> 4 <requirement type="package" version="3.9">python</requirement>
5 <requirement type="package" version="3.6">python</requirement> 5 <requirement type="package" version="1.81">biopython</requirement>
6 <requirement type="package" version="1.77">biopython</requirement> 6 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
7 <requirement type="package" version="1.1.7">cpt_gffparser</requirement>
8 <yield/> 7 <yield/>
9 </requirements> 8 </requirements>
10 </xml> 9 </xml>
11 <token name="@BLAST_TSV@"> 10 <token name="@WRAPPER_VERSION@">2.4.0</token>
12 $blast_tsv 11 <xml name="citation/gepard">
12 <citation type="doi">10.1093/bioinformatics/btm039</citation>
13 </xml>
14 <token name="@XMFA_INPUT@">
15 '$xmfa'
13 </token> 16 </token>
14 <xml name="blast_tsv"> 17 <xml name="xmfa_input" token_formats="xmfa">
15 <param label="Blast Results" help="TSV/tabular (25 Column)" name="blast_tsv" type="data" format="tabular"/> 18 <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
16 </xml> 19 </xml>
17 <token name="@BLAST_XML@"> 20 <token name="@XMFA_FA_INPUT@">
18 $blast_xml 21 '$sequences'
19 </token> 22 </token>
20 <xml name="blast_xml"> 23 <xml name="xmfa_fa_input">
21 <param label="Blast Results" help="XML format" name="blast_xml" type="data" format="blastxml"/> 24 <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"/>
22 </xml>
23 <xml name="gff3_with_fasta">
24 <param label="Genome Sequences" name="fasta" type="data" format="fasta"/>
25 <param label="Genome Annotations" name="gff3" type="data" format="gff3"/>
26 </xml> 25 </xml>
27 <xml name="genome_selector"> 26 <xml name="genome_selector">
28 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> 27 <conditional name="reference_genome">
28 <param name="reference_genome_source" type="select" label="Reference Genome">
29 <option value="history" selected="True">From History</option>
30 <option value="cached">Locally Cached</option>
31 </param>
32 <when value="cached">
33 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
34 <options from_data_table="all_fasta"/>
35 </param>
36 </when>
37 <when value="history">
38 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
39 </when>
40 </conditional>
29 </xml> 41 </xml>
30 <xml name="gff3_input"> 42 <xml name="gff3_input">
31 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> 43 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
32 </xml> 44 </xml>
33 <xml name="input/gff3+fasta"> 45 <xml name="input/gff3+fasta">
34 <expand macro="gff3_input"/> 46 <expand macro="gff3_input"/>
35 <expand macro="genome_selector"/> 47 <expand macro="genome_selector"/>
36 </xml> 48 </xml>
49 <xml name="citation/mijalisrasche">
50 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
51 <citation type="bibtex">@unpublished{galaxyTools,
52 author = {E. Mijalis, H. Rasche},
53 title = {CPT Galaxy Tools},
54 year = {2013-2017},
55 note = {https://github.com/tamu-cpt/galaxy-tools/}
56 }
57 </citation>
58 </xml>
59 <xml name="citations">
60 <citations>
61 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
62 <citation type="bibtex">
63 @unpublished{galaxyTools,
64 author = {E. Mijalis, H. Rasche},
65 title = {CPT Galaxy Tools},
66 year = {2013-2017},
67 note = {https://github.com/tamu-cpt/galaxy-tools/}
68 }
69 </citation>
70 <yield/>
71 </citations>
72 </xml>
73 <xml name="citations-crr">
74 <citations>
75 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
76 <citation type="bibtex">
77 @unpublished{galaxyTools,
78 author = {C. Ross},
79 title = {CPT Galaxy Tools},
80 year = {2020-},
81 note = {https://github.com/tamu-cpt/galaxy-tools/}
82 }
83 </citation>
84 <yield/>
85 </citations>
86 </xml>
87 <xml name="citations-2020">
88 <citations>
89 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
90 <citation type="bibtex">
91 @unpublished{galaxyTools,
92 author = {E. Mijalis, H. Rasche},
93 title = {CPT Galaxy Tools},
94 year = {2013-2017},
95 note = {https://github.com/tamu-cpt/galaxy-tools/}
96 }
97 </citation>
98 <citation type="bibtex">
99 @unpublished{galaxyTools,
100 author = {A. Criscione},
101 title = {CPT Galaxy Tools},
102 year = {2019-2021},
103 note = {https://github.com/tamu-cpt/galaxy-tools/}
104 }
105 </citation>
106 <yield/>
107 </citations>
108 </xml>
109 <xml name="citations-2020-AJC-solo">
110 <citations>
111 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
112 <citation type="bibtex">
113 @unpublished{galaxyTools,
114 author = {A. Criscione},
115 title = {CPT Galaxy Tools},
116 year = {2019-2021},
117 note = {https://github.com/tamu-cpt/galaxy-tools/}
118 }
119 </citation>
120 <yield/>
121 </citations>
122 </xml>
123 <xml name="citations-clm">
124 <citations>
125 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
126 <citation type="bibtex">
127 @unpublished{galaxyTools,
128 author = {C. Maughmer},
129 title = {CPT Galaxy Tools},
130 year = {2017-2020},
131 note = {https://github.com/tamu-cpt/galaxy-tools/}
132 }
133 </citation>
134 <yield/>
135 </citations>
136 </xml>
137 <xml name="sl-citations-clm">
138 <citation type="bibtex">
139 @unpublished{galaxyTools,
140 author = {C. Maughmer},
141 title = {CPT Galaxy Tools},
142 year = {2017-2020},
143 note = {https://github.com/tamu-cpt/galaxy-tools/}
144 }
145 </citation>
146 <yield/>
147 </xml>
37 <token name="@INPUT_GFF@"> 148 <token name="@INPUT_GFF@">
38 $gff3_data 149 '$gff3_data'
39 </token> 150 </token>
40 <token name="@INPUT_FASTA@"> 151 <token name="@INPUT_FASTA@">
41 genomeref.fa 152 #if str($reference_genome.reference_genome_source) == 'cached':
153 '${reference_genome.fasta_indexes.fields.path}'
154 #else if str($reference_genome.reference_genome_source) == 'history':
155 genomeref.fa
156 #end if
42 </token> 157 </token>
43 <token name="@GENOME_SELECTOR_PRE@"> 158 <token name="@GENOME_SELECTOR_PRE@">
44 ln -s $genome_fasta genomeref.fa; 159 #if $reference_genome.reference_genome_source == 'history':
160 ln -s '$reference_genome.genome_fasta' genomeref.fa;
161 #end if
45 </token> 162 </token>
46 <token name="@GENOME_SELECTOR@"> 163 <token name="@GENOME_SELECTOR@">
47 genomeref.fa 164 #if str($reference_genome.reference_genome_source) == 'cached':
165 '${reference_genome.fasta_indexes.fields.path}'
166 #else if str($reference_genome.reference_genome_source) == 'history':
167 genomeref.fa
168 #end if
48 </token> 169 </token>
49 <xml name="input/fasta">
50 <param label="Fasta file" name="sequences" type="data" format="fasta"/>
51 </xml>
52 <token name="@SEQUENCE@">
53 $sequences
54 </token>
55 <xml name="input/fasta/protein">
56 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
57 </xml>
58 </macros> 170 </macros>