Mercurial > repos > iuc > khmer_normalize_by_median

annotate macros.xml @ 10:4d23ab83ea29 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author iuc
date Thu, 03 Oct 2024 13:46:42 +0000
parents b1fe2ef3d244
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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5531deeabd2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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1 <macros>
8
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2 <token name="@TOOL_VERSION@">3.0.0a3</token>
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3 <token name="@VERSION_SUFFIX@">3</token>
8
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4 <token name="@PROFILE@">20.01</token>
9
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5 <xml name="bio_tools">
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6 <xrefs>
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7 <xref type="bio.tools">khmer</xref>
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8 </xrefs>
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9 </xml>
0
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10 <xml name="requirements">
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">khmer</requirement>
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13 <yield/>
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14 </requirements>
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15 </xml>
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16 <xml name="version">
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17 <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command>
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18 </xml>
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19 <xml name="stdio">
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20 <stdio>
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21 <exit_code range="1:" level="fatal" />
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22 </stdio>
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23 </xml>
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24 <token name="@TABLEPARAMS@">
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25 <![CDATA[
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26 #if $parameters.type == "simple"
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27 --ksize=20
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28 --n_tables=4
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29 --max-tablesize=$parameters.tablesize
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30 #else
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31 --ksize=$parameters.ksize
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32 --n_tables=$parameters.n_tables
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33 --max-tablesize="$parameters.tablesize_specific"
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34 #end if
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35 ]]>
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36 </token>
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37 <token name="@THREADS@">--threads "\${GALAXY_SLOTS:-4}"</token>
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38 <xml name="tableinputs">
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39 <conditional name="parameters">
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40 <param name="type" type="select" label="Advanced Parameters"
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41 help="ksize, n_tables, a specific tablesize" >
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42 <option value="simple" selected="true">Hide</option>
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43 <option value="specific">Show</option>
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44 </param>
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45 <when value="simple">
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46 <param argument="--max-tablesize" name="tablesize" type="select" label="Sample Type" display="radio">
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47 <option value="1e9" selected="true">Microbial Genome</option>
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48 <option value="2e9">Animal Transcriptome</option>
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49 <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
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50 <option value="16e9">Large Animal Genome</option>
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51 </param>
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52 </when>
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53 <when value="specific">
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54 <param argument="--ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
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55 <param argument="--n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
7
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56 <param argument="--max-tablesize" name="tablesize_specific" type="text" value="1000000.0"
0
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57 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
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58 </when>
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59 </conditional>
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60 </xml>
7
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61 <token name="@LINK_SEQUENCES@">
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62 <![CDATA[
557cc16931f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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63 #import re
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64 mkdir input/ &&
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65 #set gzip=""
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66 #for $num, $input in enumerate($inputs)
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67 ln -s '${input}' 'input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext' &&
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68 #if str($input).endswith(".gz"):
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69 #set gzip="--gzip"
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70 #end if
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71 #end for]]></token>
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72 <token name="@USE_SEQUENCES@">
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73 <![CDATA[
557cc16931f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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74 #for $num, $input in enumerate($inputs)
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75 '../input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext'
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76 #end for]]></token>
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77
0
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78 <xml name="input_sequences_filenames">
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79 <param name="inputs" multiple="true" type="data" format="fasta,fastq,fasta.gz,fastq.gz"
0
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80 label="Sequences in FASTA or FASTQ format"
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81 help="Put in order of precedence such as longest reads first." />
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82 </xml>
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83 <xml name="input_sequence_filename">
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84 <param name="input_sequence_filename" type="data" format="fasta,fastq,fasta.gz,fastq.gz"
0
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85 label="Sequence in FASTA or FASTQ format" />
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86 </xml>
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87 <xml name="input_countgraph_filename">
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88 <param name="input_countgraph_filename" type="data" format="oxlicg"
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89 label="the k-mer countgraph to query"
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90 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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91 </xml>
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92 <xml name="abundance-histogram-output">
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93 <data name="output_histogram_filename" format="csv"
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94 label="${tool.name} on ${on_string}: k-mer abundance histogram" />
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95 </xml>
10
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96 <token name="@ABUNDANCE_HISTOGRAM_OUTPUT_HELP@"><![CDATA[
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97 The columns of the k-mer abundance histogram are: (1) k-mer abundance, (2) k-mer count, (3) cumulative count, (4) fraction of total distinct k-mers.
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98 ]]></token>
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99
7
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100 <xml name="output_sequences" token_extension="">
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101 <collection name="sequences" type="list">
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102 <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;fast[aq](\.gz)?)\.@EXTENSION@" directory="output" />
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103 </collection>
0
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104 </xml>
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105 <xml name="output_sequences_single">
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106 <data name="output" format_source="input_sequence_filename"
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107 label="${tool.name} on ${on_string}: processed nucleotide sequence file" />
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108 </xml>
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109 <xml name="input_zero">
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110 <param argument="--no-zero" name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
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111 help="Output zero count bins" />
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112 </xml>
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113 <xml name="input_bigcount">
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114 <param argument="--no-bigcount" name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
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115 checked="true" help="Count k-mers past 255 occurences" />
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116 </xml>
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117 <token name="@HELP_FOOTER@"><![CDATA[
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118 (from the khmer project: http://khmer.readthedocs.org/en/v2.0/ )]]></token>
0
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119 <xml name="software-citation">
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120 <citation type="doi">10.12688/f1000research.6924.1</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="doi">10.1073/pnas.1121464109</citation>
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134 </xml>
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135 <xml name="counting-citation">
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136 <citation type="doi">10.1371/journal.pone.0101271</citation>
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137 </xml>
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138 </macros>