Mercurial > repos > cpt > cpt_fix_aragorn

annotate cpt-macros.xml @ 4:733cb0807083 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2a0a6b62f75ceb10ac3287e69c1849f09a9cf177
author cpt
date Wed, 30 Aug 2023 01:44:58 +0000
parents f0f0ab9db43f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1 <macros>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2 <xml name="gff_requirements">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3 <requirements>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
4 <requirement type="package" version="2.7">python</requirement>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
5 <requirement type="package" version="1.65">biopython</requirement>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
6 <requirement type="package" version="2.12.1">requests</requirement>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
7 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
8 <yield/>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
9 </requirements>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
10 <version_command>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
11 <![CDATA[
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
12 cd '$__tool_directory__' && git rev-parse HEAD
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
13 ]]>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
14 </version_command>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
15 </xml>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
16 <xml name="citation/mijalisrasche">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
17 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
18 <citation type="bibtex">@unpublished{galaxyTools,
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
19 author = {E. Mijalis, H. Rasche},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
20 title = {CPT Galaxy Tools},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
21 year = {2013-2017},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
22 note = {https://github.com/tamu-cpt/galaxy-tools/}
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
23 }
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
24 </citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
25 </xml>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
26 <xml name="citations">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
27 <citations>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
28 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
29 <citation type="bibtex">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
30 @unpublished{galaxyTools,
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
31 author = {E. Mijalis, H. Rasche},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
32 title = {CPT Galaxy Tools},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
33 year = {2013-2017},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
34 note = {https://github.com/tamu-cpt/galaxy-tools/}
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
35 }
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
36 </citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
37 <yield/>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
38 </citations>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
39 </xml>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
40 <xml name="citations-crr">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
41 <citations>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
42 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
43 <citation type="bibtex">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
44 @unpublished{galaxyTools,
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
45 author = {C. Ross},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
46 title = {CPT Galaxy Tools},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
47 year = {2020-},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
48 note = {https://github.com/tamu-cpt/galaxy-tools/}
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
49 }
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
50 </citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
51 <yield/>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
52 </citations>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
53 </xml>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
54 <xml name="citations-2020">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
55 <citations>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
56 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
57 <citation type="bibtex">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
58 @unpublished{galaxyTools,
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
59 author = {E. Mijalis, H. Rasche},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
60 title = {CPT Galaxy Tools},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
61 year = {2013-2017},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
62 note = {https://github.com/tamu-cpt/galaxy-tools/}
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
63 }
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
64 </citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
65 <citation type="bibtex">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
66 @unpublished{galaxyTools,
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
67 author = {A. Criscione},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
68 title = {CPT Galaxy Tools},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
69 year = {2019-2021},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
70 note = {https://github.com/tamu-cpt/galaxy-tools/}
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
71 }
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
72 </citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
73 <yield/>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
74 </citations>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
75 </xml>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
76 <xml name="citations-2020-AJC-solo">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
77 <citations>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
78 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
79 <citation type="bibtex">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
80 @unpublished{galaxyTools,
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
81 author = {A. Criscione},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
82 title = {CPT Galaxy Tools},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
83 year = {2019-2021},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
84 note = {https://github.com/tamu-cpt/galaxy-tools/}
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
85 }
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
86 </citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
87 <yield/>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
88 </citations>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
89 </xml>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
90 <xml name="citations-clm">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
91 <citations>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
92 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
93 <citation type="bibtex">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
94 @unpublished{galaxyTools,
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
95 author = {C. Maughmer},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
96 title = {CPT Galaxy Tools},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
97 year = {2017-2020},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
98 note = {https://github.com/tamu-cpt/galaxy-tools/}
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
99 }
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
100 </citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
101 <yield/>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
102 </citations>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
103 </xml>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
104 <xml name="sl-citations-clm">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
105 <citation type="bibtex">
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
106 @unpublished{galaxyTools,
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
107 author = {C. Maughmer},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
108 title = {CPT Galaxy Tools},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
109 year = {2017-2020},
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
110 note = {https://github.com/tamu-cpt/galaxy-tools/}
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
111 }
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
112 </citation>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
113 <yield/>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
114 </xml>
f0f0ab9db43f planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
115 </macros>