Mercurial > repos > cpt > cpt_gff_rebase

annotate macros.xml @ 2:d0b52c1d6b25 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:52:31 +0000
parents 4f4b413056f6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1 <macros>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2 <xml name="requirements">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3 <requirements>
2
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
4 <requirement type="package" version="3.9">python</requirement>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
5 <requirement type="package" version="1.81">biopython</requirement>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
6 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
1
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
7 <yield/>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
8 </requirements>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
9 </xml>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
10 <token name="@WRAPPER_VERSION@">2.4.0</token>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
11 <xml name="citation/gepard">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
12 <citation type="doi">10.1093/bioinformatics/btm039</citation>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
13 </xml>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
14 <token name="@XMFA_INPUT@">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
15 '$xmfa'
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
16 </token>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
17 <xml name="xmfa_input" token_formats="xmfa">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
18 <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
19 </xml>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
20 <token name="@XMFA_FA_INPUT@">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
21 '$sequences'
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
22 </token>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
23 <xml name="xmfa_fa_input">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
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"/>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
25 </xml>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
26 <xml name="genome_selector">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
27 <conditional name="reference_genome">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
28 <param name="reference_genome_source" type="select" label="Reference Genome">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
29 <option value="history" selected="True">From History</option>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
30 <option value="cached">Locally Cached</option>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
31 </param>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
32 <when value="cached">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
33 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
34 <options from_data_table="all_fasta"/>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
35 </param>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
36 </when>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
37 <when value="history">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
38 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
39 </when>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
40 </conditional>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
41 </xml>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
42 <xml name="gff3_input">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
43 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
44 </xml>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
45 <xml name="input/gff3+fasta">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
46 <expand macro="gff3_input"/>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
47 <expand macro="genome_selector"/>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
48 </xml>
2
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
49 <xml name="citation/mijalisrasche">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
50 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
51 <citation type="bibtex">@unpublished{galaxyTools,
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
52 author = {E. Mijalis, H. Rasche},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
53 title = {CPT Galaxy Tools},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
54 year = {2013-2017},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
55 note = {https://github.com/tamu-cpt/galaxy-tools/}
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
56 }
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
57 </citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
58 </xml>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
59 <xml name="citations">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
60 <citations>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
61 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
62 <citation type="bibtex">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
63 @unpublished{galaxyTools,
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
64 author = {E. Mijalis, H. Rasche},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
65 title = {CPT Galaxy Tools},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
66 year = {2013-2017},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
67 note = {https://github.com/tamu-cpt/galaxy-tools/}
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
68 }
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
69 </citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
70 <yield/>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
71 </citations>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
72 </xml>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
73 <xml name="citations-crr">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
74 <citations>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
75 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
76 <citation type="bibtex">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
77 @unpublished{galaxyTools,
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
78 author = {C. Ross},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
79 title = {CPT Galaxy Tools},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
80 year = {2020-},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
81 note = {https://github.com/tamu-cpt/galaxy-tools/}
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
82 }
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
83 </citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
84 <yield/>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
85 </citations>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
86 </xml>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
87 <xml name="citations-2020">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
88 <citations>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
89 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
90 <citation type="bibtex">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
91 @unpublished{galaxyTools,
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
92 author = {E. Mijalis, H. Rasche},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
93 title = {CPT Galaxy Tools},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
94 year = {2013-2017},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
95 note = {https://github.com/tamu-cpt/galaxy-tools/}
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
96 }
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
97 </citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
98 <citation type="bibtex">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
99 @unpublished{galaxyTools,
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
100 author = {A. Criscione},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
101 title = {CPT Galaxy Tools},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
102 year = {2019-2021},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
103 note = {https://github.com/tamu-cpt/galaxy-tools/}
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
104 }
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
105 </citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
106 <yield/>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
107 </citations>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
108 </xml>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
109 <xml name="citations-2020-AJC-solo">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
110 <citations>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
111 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
112 <citation type="bibtex">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
113 @unpublished{galaxyTools,
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
114 author = {A. Criscione},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
115 title = {CPT Galaxy Tools},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
116 year = {2019-2021},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
117 note = {https://github.com/tamu-cpt/galaxy-tools/}
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
118 }
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
119 </citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
120 <yield/>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
121 </citations>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
122 </xml>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
123 <xml name="citations-clm">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
124 <citations>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
125 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
126 <citation type="bibtex">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
127 @unpublished{galaxyTools,
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
128 author = {C. Maughmer},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
129 title = {CPT Galaxy Tools},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
130 year = {2017-2020},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
131 note = {https://github.com/tamu-cpt/galaxy-tools/}
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
132 }
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
133 </citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
134 <yield/>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
135 </citations>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
136 </xml>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
137 <xml name="sl-citations-clm">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
138 <citation type="bibtex">
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
139 @unpublished{galaxyTools,
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
140 author = {C. Maughmer},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
141 title = {CPT Galaxy Tools},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
142 year = {2017-2020},
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
143 note = {https://github.com/tamu-cpt/galaxy-tools/}
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
144 }
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
145 </citation>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
146 <yield/>
d0b52c1d6b25 planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
cpt
parents: 1
diff changeset
147 </xml>
1
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
148 <token name="@INPUT_GFF@">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
149 '$gff3_data'
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
150 </token>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
151 <token name="@INPUT_FASTA@">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
152 #if str($reference_genome.reference_genome_source) == 'cached':
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
153 '${reference_genome.fasta_indexes.fields.path}'
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
154 #else if str($reference_genome.reference_genome_source) == 'history':
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
155 genomeref.fa
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
156 #end if
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
157 </token>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
158 <token name="@GENOME_SELECTOR_PRE@">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
159 #if $reference_genome.reference_genome_source == 'history':
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
160 ln -s '$reference_genome.genome_fasta' genomeref.fa;
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
161 #end if
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
162 </token>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
163 <token name="@GENOME_SELECTOR@">
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
164 #if str($reference_genome.reference_genome_source) == 'cached':
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
165 '${reference_genome.fasta_indexes.fields.path}'
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
166 #else if str($reference_genome.reference_genome_source) == 'history':
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
167 genomeref.fa
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
168 #end if
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
169 </token>
4f4b413056f6 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
170 </macros>