Mercurial > repos > iuc > khmer_normalize_by_median

comparison macros.xml @ 6:bfd859f04a89 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author iuc
date Fri, 07 Sep 2018 11:01:41 -0400
parents cd5802b16687
children 557cc16931f4
comparison
equal deleted inserted replaced
5:f0290a079720 6:bfd859f04a89
1 <macros> 1 <macros>
2 <token name="@WRAPPER_VERSION@">2.0</token> 2 <token name="@WRAPPER_VERSION@">3.0.0a1</token>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.98">bz2file</requirement>
6 <requirement type="package" version="0.9">screed</requirement>
7 <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement> 5 <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement>
8 </requirements> 6 </requirements>
9 </xml> 7 </xml>
10 <xml name="version"> 8 <xml name="version">
11 <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command> 9 <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command>
45 </param> 43 </param>
46 </when> 44 </when>
47 <when value="specific"> 45 <when value="specific">
48 <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" /> 46 <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
49 <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" /> 47 <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
50 <param name="tablesize_specific" type="text" value="1000000.0" 48 <param name="tablesize_specific" type="text" value="1000000.0"
51 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" /> 49 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
52 </when> 50 </when>
53 </conditional> 51 </conditional>
54 </xml> 52 </xml>
55 <xml name="input_sequences_filenames"> 53 <xml name="input_sequences_filenames">
91 checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" /> 89 checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" />
92 </xml> 90 </xml>
93 <token name="@HELP_FOOTER@"><![CDATA[ 91 <token name="@HELP_FOOTER@"><![CDATA[
94 (from the khmer project: http://khmer.readthedocs.org/en/v2.0/ )]]></token> 92 (from the khmer project: http://khmer.readthedocs.org/en/v2.0/ )]]></token>
95 <xml name="software-citation"> 93 <xml name="software-citation">
96 <citation type="bibtex">@article{khmer2015, 94 <citation type="doi">10.12688/f1000research.6924.1</citation>
97 author = "Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine
98 and Bucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau,
99 Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton,
100 Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and
101 Garland, Phillip and Gluck, Jonathan and González, Iván and Guermond, Sarah
102 and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and
103 Hyer, Alex and Härpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David
104 and Lippi, Justin and Mansour, Tamer and McA'Nulty, Pamela and McDonald, Eric
105 and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy,
106 Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory,
107 Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N and
108 Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and
109 Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan,
110 Ramakrishnan and Standage, Daniel and Stapleton, James A. and Stein, Joe and
111 Steinman, Susan R and Taylor, Benjamin and Trimble, Will and Wiencko, Heather
112 L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and zyme, en and
113 Brown, C. Titus"
114 title = "The khmer software package: enabling efficient nucleotide
115 sequence analysis",
116 year = "2015",
117 month = "08",
118 publisher = "F1000",
119 url = "http://dx.doi.org/10.12688/f1000research.6924.1"
120 }</citation>
121 </xml> 95 </xml>
122 <xml name="diginorm-citation"> 96 <xml name="diginorm-citation">
123 <citation type="bibtex">@unpublished{diginorm, 97 <citation type="bibtex">@unpublished{diginorm,
124 author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz, 98 author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz,
125 Alexis B and Brom, Timothy H", 99 Alexis B and Brom, Timothy H",
128 year = "2012", 102 year = "2012",
129 eprint = "arXiv:1203.4802", 103 eprint = "arXiv:1203.4802",
130 url = "http://arxiv.org/abs/1203.4802", 104 url = "http://arxiv.org/abs/1203.4802",
131 }</citation></xml> 105 }</citation></xml>
132 <xml name="graph-citation"> 106 <xml name="graph-citation">
133 <citation type="bibtex">@article{Pell2012, 107 <citation type="doi">10.1073/pnas.1121464109</citation>
134 doi = {10.1073/pnas.1121464109},
135 url = {http://dx.doi.org/10.1073/pnas.1121464109},
136 year = {2012},
137 month = {jul},
138 publisher = {Proceedings of the National Academy of Sciences},
139 volume = {109},
140 number = {33},
141 pages = {13272--13277},
142 author = {J. Pell and A. Hintze and R. Canino-Koning and A. Howe and J. M. Tiedje and C. T. Brown},
143 title = {Scaling metagenome sequence assembly with probabilistic de Bruijn graphs},
144 journal = {Proceedings of the National Academy of Sciences}
145 }</citation>
146 </xml> 108 </xml>
147 <xml name="counting-citation"> 109 <xml name="counting-citation">
148 <citation type="doi">10.1371/journal.pone.0101271</citation> 110 <citation type="doi">10.1371/journal.pone.0101271</citation>
149 </xml> 111 </xml>
150 </macros> 112 </macros>