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comparison macros.xml @ 0:0187f18785a3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
author iuc
date Sat, 17 Oct 2015 04:02:33 -0400
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-1:000000000000 0:0187f18785a3
1 <macros>
2 <token name="@WRAPPER_VERSION@">2.0</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement>
6 </requirements>
7 </xml>
8 <xml name="version">
9 <version_command>@BINARY@ --version</version_command>
10 </xml>
11 <xml name="stdio">
12 <stdio>
13 <exit_code range="1:" level="fatal" />
14 </stdio>
15 </xml>
16 <token name="@TABLEPARAMS@">
17 #if $parameters.type == "simple"
18 --ksize=20
19 --n_tables=4
20 --max-tablesize=$parameters.tablesize
21 #else
22 --ksize=$parameters.ksize
23 --n_tables=$parameters.n_tables
24 --max-tablesize="$parameters.tablesize_specific"
25 #end if
26 </token>
27 <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
28 <xml name="tableinputs">
29 <conditional name="parameters">
30 <param name="type" type="select" label="Advanced Parameters"
31 help="ksize, n_tables, a specific tablesize" >
32 <option value="simple" selected="true">Hide</option>
33 <option value="specific">Show</option>
34 </param>
35 <when value="simple">
36 <param name="tablesize" type="select" label="Sample Type" display="radio">
37 <option value="1e9" selected="true">Microbial Genome</option>
38 <option value="2e9">Animal Transcriptome</option>
39 <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
40 <option value="16e9">Large Animal Genome</option>
41 </param>
42 </when>
43 <when value="specific">
44 <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
45 <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
46 <param name="tablesize_specific" type="text" value="1000000.0"
47 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
48 </when>
49 </conditional>
50 </xml>
51 <xml name="input_sequences_filenames">
52 <param name="inputs" multiple="true" type="data" format="fasta,fastq"
53 label="Sequences in FASTA or FASTQ format"
54 help="Put in order of precedence such as longest reads first." />
55 </xml>
56 <xml name="input_sequence_filename">
57 <param name="input_sequence_filename" type="data" format="fasta,fastq"
58 label="Sequence in FASTA or FASTQ format" />
59 </xml>
60 <xml name="input_countgraph_filename">
61 <param name="input_countgraph_filename" type="data" format="oxlicg"
62 label="the k-mer countgraph to query"
63 help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer countgraph." />
64 </xml>
65 <xml name="abundance-histogram-output">
66 <data name="output_histogram_filename" format="txt"
67 label="${tool.name} k-mer abundance histogram. The
68 columns are: (1) k-mer abundance, (2) k-mer count, (3)
69 cumulative count, (4) fraction of total distinct k-mers." />
70 </xml>
71 <xml name="output_sequences">
72 <data name="output" format_source="inputs"
73 label="${tool.name} processed nucleotide sequence file">
74 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/>
75 </data>
76 </xml>
77 <xml name="output_sequences_single">
78 <data name="output" format_source="input_sequence_filename"
79 label="${tool.name} processed nucleotide sequence file" />
80 </xml>
81 <xml name="input_zero">
82 <param name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
83 help="Output zero count bins (--no-zero)" />
84 </xml>
85 <xml name="input_bigcount">
86 <param name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
87 checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" />
88 </xml>
89 <token name="@HELP_FOOTER@"><![CDATA[
90 (from the khmer project: http://khmer.readthedocs.org/en/v@WRAPPER_VERSION@/ )]]></token>
91 <xml name="software-citation">
92 <citation type="bibtex">@article{khmer2015,
93 author = "Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine
94 and Bucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau,
95 Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton,
96 Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and
97 Garland, Phillip and Gluck, Jonathan and González, Iván and Guermond, Sarah
98 and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and
99 Hyer, Alex and Härpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David
100 and Lippi, Justin and Mansour, Tamer and McA'Nulty, Pamela and McDonald, Eric
101 and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy,
102 Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory,
103 Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N and
104 Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and
105 Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan,
106 Ramakrishnan and Standage, Daniel and Stapleton, James A. and Stein, Joe and
107 Steinman, Susan R and Taylor, Benjamin and Trimble, Will and Wiencko, Heather
108 L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and zyme, en and
109 Brown, C. Titus"
110 title = "The khmer software package: enabling efficient nucleotide
111 sequence analysis",
112 year = "2015",
113 month = "08",
114 publisher = "F1000",
115 url = "http://dx.doi.org/10.12688/f1000research.6924.1"
116 }</citation>
117 </xml>
118 <xml name="diginorm-citation">
119 <citation type="bibtex">@unpublished{diginorm,
120 author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz,
121 Alexis B and Brom, Timothy H",
122 title = "A Reference-Free Algorithm for Computational Normalization of
123 Shotgun Sequencing Data",
124 year = "2012",
125 eprint = "arXiv:1203.4802",
126 url = "http://arxiv.org/abs/1203.4802",
127 }</citation></xml>
128 <xml name="graph-citation">
129 <citation type="bibtex">@article{Pell2012,
130 doi = {10.1073/pnas.1121464109},
131 url = {http://dx.doi.org/10.1073/pnas.1121464109},
132 year = {2012},
133 month = {jul},
134 publisher = {Proceedings of the National Academy of Sciences},
135 volume = {109},
136 number = {33},
137 pages = {13272--13277},
138 author = {J. Pell and A. Hintze and R. Canino-Koning and A. Howe and J. M. Tiedje and C. T. Brown},
139 title = {Scaling metagenome sequence assembly with probabilistic de Bruijn graphs},
140 journal = {Proceedings of the National Academy of Sciences}
141 }</citation>
142 </xml>
143 <xml name="counting-citation">
144 <citation type="doi">10.1371/journal.pone.0101271</citation>
145 </xml>
146 </macros>