Mercurial > repos > iuc > khmer_normalize_by_median

annotate macros.xml @ 2:6d8793a4923d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
author iuc
date Thu, 03 Dec 2015 18:44:24 -0500
parents 5531deeabd2c
children cd5802b16687
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1 <macros>
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2 <token name="@WRAPPER_VERSION@">2.0</token>
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3 <xml name="requirements">
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4 <requirements>
2
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5 <requirement type="package" version="0.98">bz2file</requirement>
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6 <requirement type="package" version="0.9">screed</requirement>
0
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7 <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement>
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8 </requirements>
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9 </xml>
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10 <xml name="version">
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11 <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command>
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12 </xml>
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13 <xml name="stdio">
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14 <stdio>
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15 <exit_code range="1:" level="fatal" />
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16 </stdio>
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17 </xml>
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18 <token name="@TABLEPARAMS@">
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19 <![CDATA[
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20 #if $parameters.type == "simple"
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21 --ksize=20
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22 --n_tables=4
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23 --max-tablesize=$parameters.tablesize
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24 #else
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25 --ksize=$parameters.ksize
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26 --n_tables=$parameters.n_tables
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27 --max-tablesize="$parameters.tablesize_specific"
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28 #end if
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29 ]]>
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30 </token>
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31 <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
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32 <xml name="tableinputs">
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33 <conditional name="parameters">
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34 <param name="type" type="select" label="Advanced Parameters"
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35 help="ksize, n_tables, a specific tablesize" >
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36 <option value="simple" selected="true">Hide</option>
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37 <option value="specific">Show</option>
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38 </param>
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39 <when value="simple">
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40 <param name="tablesize" type="select" label="Sample Type" display="radio">
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41 <option value="1e9" selected="true">Microbial Genome</option>
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42 <option value="2e9">Animal Transcriptome</option>
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43 <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
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44 <option value="16e9">Large Animal Genome</option>
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45 </param>
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46 </when>
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47 <when value="specific">
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48 <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
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49 <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
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50 <param name="tablesize_specific" type="text" value="1000000.0"
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51 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
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52 </when>
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53 </conditional>
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54 </xml>
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55 <xml name="input_sequences_filenames">
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56 <param name="inputs" multiple="true" type="data" format="fasta,fastq"
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57 label="Sequences in FASTA or FASTQ format"
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58 help="Put in order of precedence such as longest reads first." />
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59 </xml>
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60 <xml name="input_sequence_filename">
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61 <param name="input_sequence_filename" type="data" format="fasta,fastq"
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62 label="Sequence in FASTA or FASTQ format" />
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63 </xml>
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64 <xml name="input_countgraph_filename">
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65 <param name="input_countgraph_filename" type="data" format="oxlicg"
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66 label="the k-mer countgraph to query"
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67 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." />
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68 </xml>
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69 <xml name="abundance-histogram-output">
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70 <data name="output_histogram_filename" format="txt"
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71 label="${tool.name} k-mer abundance histogram. The
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72 columns are: (1) k-mer abundance, (2) k-mer count, (3)
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73 cumulative count, (4) fraction of total distinct k-mers." />
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74 </xml>
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75 <xml name="output_sequences">
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76 <data name="output" format_source="inputs"
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77 label="${tool.name} processed nucleotide sequence file">
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78 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/>
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79 </data>
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80 </xml>
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81 <xml name="output_sequences_single">
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82 <data name="output" format_source="input_sequence_filename"
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83 label="${tool.name} processed nucleotide sequence file" />
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84 </xml>
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85 <xml name="input_zero">
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86 <param name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
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87 help="Output zero count bins (--no-zero)" />
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88 </xml>
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89 <xml name="input_bigcount">
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90 <param name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
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91 checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" />
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92 </xml>
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93 <token name="@HELP_FOOTER@"><![CDATA[
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94 (from the khmer project: http://khmer.readthedocs.org/en/v@WRAPPER_VERSION@/ )]]></token>
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95 <xml name="software-citation">
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96 <citation type="bibtex">@article{khmer2015,
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97 author = "Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine
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98 and Bucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau,
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99 Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton,
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100 Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and
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101 Garland, Phillip and Gluck, Jonathan and González, Iván and Guermond, Sarah
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102 and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and
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103 Hyer, Alex and Härpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David
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104 and Lippi, Justin and Mansour, Tamer and McA'Nulty, Pamela and McDonald, Eric
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105 and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy,
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106 Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory,
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107 Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N and
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108 Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and
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109 Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan,
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110 Ramakrishnan and Standage, Daniel and Stapleton, James A. and Stein, Joe and
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111 Steinman, Susan R and Taylor, Benjamin and Trimble, Will and Wiencko, Heather
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112 L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and zyme, en and
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113 Brown, C. Titus"
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114 title = "The khmer software package: enabling efficient nucleotide
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115 sequence analysis",
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116 year = "2015",
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117 month = "08",
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118 publisher = "F1000",
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119 url = "http://dx.doi.org/10.12688/f1000research.6924.1"
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120 }</citation>
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121 </xml>
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122 <xml name="diginorm-citation">
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123 <citation type="bibtex">@unpublished{diginorm,
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124 author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz,
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125 Alexis B and Brom, Timothy H",
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126 title = "A Reference-Free Algorithm for Computational Normalization of
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127 Shotgun Sequencing Data",
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128 year = "2012",
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129 eprint = "arXiv:1203.4802",
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130 url = "http://arxiv.org/abs/1203.4802",
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131 }</citation></xml>
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132 <xml name="graph-citation">
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133 <citation type="bibtex">@article{Pell2012,
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134 doi = {10.1073/pnas.1121464109},
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135 url = {http://dx.doi.org/10.1073/pnas.1121464109},
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136 year = {2012},
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137 month = {jul},
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138 publisher = {Proceedings of the National Academy of Sciences},
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139 volume = {109},
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140 number = {33},
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141 pages = {13272--13277},
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142 author = {J. Pell and A. Hintze and R. Canino-Koning and A. Howe and J. M. Tiedje and C. T. Brown},
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143 title = {Scaling metagenome sequence assembly with probabilistic de Bruijn graphs},
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144 journal = {Proceedings of the National Academy of Sciences}
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145 }</citation>
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146 </xml>
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147 <xml name="counting-citation">
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148 <citation type="doi">10.1371/journal.pone.0101271</citation>
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149 </xml>
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150 </macros>