Mercurial > repos > cpt > cpt_shinefind
annotate cpt-macros.xml @ 4:5004ddb62700 draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author | cpt |
---|---|
date | Mon, 05 Jun 2023 02:53:31 +0000 |
parents | |
children |
rev | line source |
---|---|
4
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
1 <macros> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
2 <xml name="gff_requirements"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
3 <requirements> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
4 <requirement type="package" version="2.7">python</requirement> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
5 <requirement type="package" version="1.65">biopython</requirement> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
6 <requirement type="package" version="2.12.1">requests</requirement> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
7 <requirement type="package" version="1.2.2">cpt_gffparser</requirement> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
8 <yield/> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
9 </requirements> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
10 <version_command> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
11 <![CDATA[ |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
12 cd '$__tool_directory__' && git rev-parse HEAD |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
13 ]]> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
14 </version_command> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
15 </xml> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
16 <xml name="citation/mijalisrasche"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
17 <citation type="doi">10.1371/journal.pcbi.1008214</citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
18 <citation type="bibtex">@unpublished{galaxyTools, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
19 author = {E. Mijalis, H. Rasche}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
20 title = {CPT Galaxy Tools}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
21 year = {2013-2017}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
22 note = {https://github.com/tamu-cpt/galaxy-tools/} |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
23 } |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
24 </citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
25 </xml> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
26 <xml name="citations"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
27 <citations> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
28 <citation type="doi">10.1371/journal.pcbi.1008214</citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
29 <citation type="bibtex"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
30 @unpublished{galaxyTools, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
31 author = {E. Mijalis, H. Rasche}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
32 title = {CPT Galaxy Tools}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
33 year = {2013-2017}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
34 note = {https://github.com/tamu-cpt/galaxy-tools/} |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
35 } |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
36 </citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
37 <yield/> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
38 </citations> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
39 </xml> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
40 <xml name="citations-crr"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
41 <citations> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
42 <citation type="doi">10.1371/journal.pcbi.1008214</citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
43 <citation type="bibtex"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
44 @unpublished{galaxyTools, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
45 author = {C. Ross}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
46 title = {CPT Galaxy Tools}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
47 year = {2020-}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
48 note = {https://github.com/tamu-cpt/galaxy-tools/} |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
49 } |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
50 </citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
51 <yield/> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
52 </citations> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
53 </xml> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
54 <xml name="citations-2020"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
55 <citations> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
56 <citation type="doi">10.1371/journal.pcbi.1008214</citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
57 <citation type="bibtex"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
58 @unpublished{galaxyTools, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
59 author = {E. Mijalis, H. Rasche}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
60 title = {CPT Galaxy Tools}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
61 year = {2013-2017}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
62 note = {https://github.com/tamu-cpt/galaxy-tools/} |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
63 } |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
64 </citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
65 <citation type="bibtex"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
66 @unpublished{galaxyTools, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
67 author = {A. Criscione}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
68 title = {CPT Galaxy Tools}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
69 year = {2019-2021}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
70 note = {https://github.com/tamu-cpt/galaxy-tools/} |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
71 } |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
72 </citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
73 <yield/> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
74 </citations> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
75 </xml> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
76 <xml name="citations-2020-AJC-solo"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
77 <citations> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
78 <citation type="doi">10.1371/journal.pcbi.1008214</citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
79 <citation type="bibtex"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
80 @unpublished{galaxyTools, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
81 author = {A. Criscione}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
82 title = {CPT Galaxy Tools}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
83 year = {2019-2021}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
84 note = {https://github.com/tamu-cpt/galaxy-tools/} |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
85 } |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
86 </citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
87 <yield/> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
88 </citations> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
89 </xml> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
90 <xml name="citations-clm"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
91 <citations> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
92 <citation type="doi">10.1371/journal.pcbi.1008214</citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
93 <citation type="bibtex"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
94 @unpublished{galaxyTools, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
95 author = {C. Maughmer}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
96 title = {CPT Galaxy Tools}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
97 year = {2017-2020}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
98 note = {https://github.com/tamu-cpt/galaxy-tools/} |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
99 } |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
100 </citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
101 <yield/> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
102 </citations> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
103 </xml> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
104 <xml name="sl-citations-clm"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
105 <citation type="bibtex"> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
106 @unpublished{galaxyTools, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
107 author = {C. Maughmer}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
108 title = {CPT Galaxy Tools}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
109 year = {2017-2020}, |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
110 note = {https://github.com/tamu-cpt/galaxy-tools/} |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
111 } |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
112 </citation> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
113 <yield/> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
114 </xml> |
5004ddb62700
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
115 </macros> |