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comparison macros.xml @ 2:0a02ef22ce17 draft

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:56:25 +0000
parents 4e02e6e9e77d
children
comparison
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1:4e02e6e9e77d 2:0a02ef22ce17
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package">progressivemauve</requirement> 4 <requirement type="package" version="3.9">python</requirement>
5 <!--<requirement type="package" version="2.7">python</requirement>--> 5 <requirement type="package" version="1.81">biopython</requirement>
6 <requirement type="package" version="0.6.4">bcbiogff</requirement> 6 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
7 <yield/> 7 <yield/>
8 </requirements> 8 </requirements>
9 </xml> 9 </xml>
10 <token name="@WRAPPER_VERSION@">2.4.0</token> 10 <token name="@WRAPPER_VERSION@">2.4.0</token>
11 <xml name="citation/progressive_mauve">
12 <citation type="doi">10.1371/journal.pone.0011147</citation>
13 </xml>
14 <xml name="citation/gepard"> 11 <xml name="citation/gepard">
15 <citation type="doi">10.1093/bioinformatics/btm039</citation> 12 <citation type="doi">10.1093/bioinformatics/btm039</citation>
16 </xml> 13 </xml>
17 <token name="@XMFA_INPUT@"> 14 <token name="@XMFA_INPUT@">
18 '$xmfa' 15 '$xmfa'
47 </xml> 44 </xml>
48 <xml name="input/gff3+fasta"> 45 <xml name="input/gff3+fasta">
49 <expand macro="gff3_input"/> 46 <expand macro="gff3_input"/>
50 <expand macro="genome_selector"/> 47 <expand macro="genome_selector"/>
51 </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@unpublished{galaxyTools,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63 @unpublished{galaxyTools,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>
52 <token name="@INPUT_GFF@"> 148 <token name="@INPUT_GFF@">
53 '$gff3_data' 149 '$gff3_data'
54 </token> 150 </token>
55 <token name="@INPUT_FASTA@"> 151 <token name="@INPUT_FASTA@">
56 #if str($reference_genome.reference_genome_source) == 'cached': 152 #if str($reference_genome.reference_genome_source) == 'cached':