comparison macros.xml @ 0:c07433531fd3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
author iuc
date Wed, 11 Nov 2015 09:46:38 -0500
parents
children 5915ca16931b
comparison
equal deleted inserted replaced
-1:000000000000 0:c07433531fd3
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><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></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 <![CDATA[
18 #if $parameters.type == "simple"
19 --ksize=20
20 --n_tables=4
21 --max-tablesize=$parameters.tablesize
22 #else
23 --ksize=$parameters.ksize
24 --n_tables=$parameters.n_tables
25 --max-tablesize="$parameters.tablesize_specific"
26 #end if
27 ]]>
28 </token>
29 <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
30 <xml name="tableinputs">
31 <conditional name="parameters">
32 <param name="type" type="select" label="Advanced Parameters"
33 help="ksize, n_tables, a specific tablesize" >
34 <option value="simple" selected="true">Hide</option>
35 <option value="specific">Show</option>
36 </param>
37 <when value="simple">
38 <param name="tablesize" type="select" label="Sample Type" display="radio">
39 <option value="1e9" selected="true">Microbial Genome</option>
40 <option value="2e9">Animal Transcriptome</option>
41 <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
42 <option value="16e9">Large Animal Genome</option>
43 </param>
44 </when>
45 <when value="specific">
46 <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
47 <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
48 <param name="tablesize_specific" type="text" value="1000000.0"
49 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
50 </when>
51 </conditional>
52 </xml>
53 <xml name="input_sequences_filenames">
54 <param name="inputs" multiple="true" type="data" format="fasta,fastq"
55 label="Sequences in FASTA or FASTQ format"
56 help="Put in order of precedence such as longest reads first." />
57 </xml>
58 <xml name="input_sequence_filename">
59 <param name="input_sequence_filename" type="data" format="fasta,fastq"
60 label="Sequence in FASTA or FASTQ format" />
61 </xml>
62 <xml name="input_countgraph_filename">
63 <param name="input_countgraph_filename" type="data" format="oxlicg"
64 label="the k-mer countgraph to query"
65 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." />
66 </xml>
67 <xml name="abundance-histogram-output">
68 <data name="output_histogram_filename" format="txt"
69 label="${tool.name} k-mer abundance histogram. The
70 columns are: (1) k-mer abundance, (2) k-mer count, (3)
71 cumulative count, (4) fraction of total distinct k-mers." />
72 </xml>
73 <xml name="output_sequences">
74 <data name="output" format_source="inputs"
75 label="${tool.name} processed nucleotide sequence file">
76 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/>
77 </data>
78 </xml>
79 <xml name="output_sequences_single">
80 <data name="output" format_source="input_sequence_filename"
81 label="${tool.name} processed nucleotide sequence file" />
82 </xml>
83 <xml name="input_zero">
84 <param name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
85 help="Output zero count bins (--no-zero)" />
86 </xml>
87 <xml name="input_bigcount">
88 <param name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
89 checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" />
90 </xml>
91 <token name="@HELP_FOOTER@"><![CDATA[
92 (from the khmer project: http://khmer.readthedocs.org/en/v@WRAPPER_VERSION@/ )]]></token>
93 <xml name="software-citation">
94 <citation type="bibtex">@article{khmer2015,
95 author = "Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine
96 and Bucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau,
97 Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton,
98 Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and
99 Garland, Phillip and Gluck, Jonathan and González, Iván and Guermond, Sarah
100 and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and
101 Hyer, Alex and Härpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David
102 and Lippi, Justin and Mansour, Tamer and McA'Nulty, Pamela and McDonald, Eric
103 and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy,
104 Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory,
105 Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N and
106 Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and
107 Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan,
108 Ramakrishnan and Standage, Daniel and Stapleton, James A. and Stein, Joe and
109 Steinman, Susan R and Taylor, Benjamin and Trimble, Will and Wiencko, Heather
110 L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and zyme, en and
111 Brown, C. Titus"
112 title = "The khmer software package: enabling efficient nucleotide
113 sequence analysis",
114 year = "2015",
115 month = "08",
116 publisher = "F1000",
117 url = "http://dx.doi.org/10.12688/f1000research.6924.1"
118 }</citation>
119 </xml>
120 <xml name="diginorm-citation">
121 <citation type="bibtex">@unpublished{diginorm,
122 author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz,
123 Alexis B and Brom, Timothy H",
124 title = "A Reference-Free Algorithm for Computational Normalization of
125 Shotgun Sequencing Data",
126 year = "2012",
127 eprint = "arXiv:1203.4802",
128 url = "http://arxiv.org/abs/1203.4802",
129 }</citation></xml>
130 <xml name="graph-citation">
131 <citation type="bibtex">@article{Pell2012,
132 doi = {10.1073/pnas.1121464109},
133 url = {http://dx.doi.org/10.1073/pnas.1121464109},
134 year = {2012},
135 month = {jul},
136 publisher = {Proceedings of the National Academy of Sciences},
137 volume = {109},
138 number = {33},
139 pages = {13272--13277},
140 author = {J. Pell and A. Hintze and R. Canino-Koning and A. Howe and J. M. Tiedje and C. T. Brown},
141 title = {Scaling metagenome sequence assembly with probabilistic de Bruijn graphs},
142 journal = {Proceedings of the National Academy of Sciences}
143 }</citation>
144 </xml>
145 <xml name="counting-citation">
146 <citation type="doi">10.1371/journal.pone.0101271</citation>
147 </xml>
148 </macros>