Mercurial > repos > iuc > khmer_extract_partitions

annotate macros.xml @ 7:b7cc017efa4d 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 10:52:57 -0400
parents 991fd8dcddbe
children f388b06c8f48
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1 <macros>
7
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2 <token name="@WRAPPER_VERSION@">3.0.0a1</token>
0
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement>
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6 </requirements>
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7 </xml>
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8 <xml name="version">
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9 <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command>
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10 </xml>
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11 <xml name="stdio">
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12 <stdio>
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13 <exit_code range="1:" level="fatal" />
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14 </stdio>
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15 </xml>
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16 <token name="@TABLEPARAMS@">
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17 <![CDATA[
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18 #if $parameters.type == "simple"
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19 --ksize=20
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20 --n_tables=4
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21 --max-tablesize=$parameters.tablesize
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22 #else
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23 --ksize=$parameters.ksize
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24 --n_tables=$parameters.n_tables
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25 --max-tablesize="$parameters.tablesize_specific"
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26 #end if
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27 ]]>
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28 </token>
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29 <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
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30 <xml name="tableinputs">
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31 <conditional name="parameters">
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32 <param name="type" type="select" label="Advanced Parameters"
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33 help="ksize, n_tables, a specific tablesize" >
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34 <option value="simple" selected="true">Hide</option>
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35 <option value="specific">Show</option>
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36 </param>
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37 <when value="simple">
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38 <param name="tablesize" type="select" label="Sample Type" display="radio">
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39 <option value="1e9" selected="true">Microbial Genome</option>
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40 <option value="2e9">Animal Transcriptome</option>
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41 <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
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42 <option value="16e9">Large Animal Genome</option>
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43 </param>
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44 </when>
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45 <when value="specific">
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46 <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
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47 <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
7
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48 <param name="tablesize_specific" type="text" value="1000000.0"
0
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49 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
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50 </when>
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51 </conditional>
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52 </xml>
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53 <xml name="input_sequences_filenames">
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54 <param name="inputs" multiple="true" type="data" format="fasta,fastq"
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55 label="Sequences in FASTA or FASTQ format"
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56 help="Put in order of precedence such as longest reads first." />
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57 </xml>
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58 <xml name="input_sequence_filename">
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59 <param name="input_sequence_filename" type="data" format="fasta,fastq"
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60 label="Sequence in FASTA or FASTQ format" />
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61 </xml>
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62 <xml name="input_countgraph_filename">
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63 <param name="input_countgraph_filename" type="data" format="oxlicg"
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64 label="the k-mer countgraph to query"
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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." />
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66 </xml>
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67 <xml name="abundance-histogram-output">
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68 <data name="output_histogram_filename" format="txt"
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69 label="${tool.name} k-mer abundance histogram. The
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70 columns are: (1) k-mer abundance, (2) k-mer count, (3)
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71 cumulative count, (4) fraction of total distinct k-mers." />
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72 </xml>
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73 <xml name="output_sequences">
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74 <data name="output" format_source="inputs"
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75 label="${tool.name} processed nucleotide sequence file">
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76 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/>
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77 </data>
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78 </xml>
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79 <xml name="output_sequences_single">
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80 <data name="output" format_source="input_sequence_filename"
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81 label="${tool.name} processed nucleotide sequence file" />
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82 </xml>
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83 <xml name="input_zero">
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84 <param name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
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85 help="Output zero count bins (--no-zero)" />
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86 </xml>
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87 <xml name="input_bigcount">
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88 <param name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
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89 checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" />
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90 </xml>
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91 <token name="@HELP_FOOTER@"><![CDATA[
5
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92 (from the khmer project: http://khmer.readthedocs.org/en/v2.0/ )]]></token>
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93 <xml name="software-citation">
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94 <citation type="doi">10.12688/f1000research.6924.1</citation>
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95 </xml>
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96 <xml name="diginorm-citation">
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97 <citation type="bibtex">@unpublished{diginorm,
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98 author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz,
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99 Alexis B and Brom, Timothy H",
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100 title = "A Reference-Free Algorithm for Computational Normalization of
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101 Shotgun Sequencing Data",
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102 year = "2012",
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103 eprint = "arXiv:1203.4802",
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104 url = "http://arxiv.org/abs/1203.4802",
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105 }</citation></xml>
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106 <xml name="graph-citation">
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107 <citation type="doi">10.1073/pnas.1121464109</citation>
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108 </xml>
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109 <xml name="counting-citation">
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110 <citation type="doi">10.1371/journal.pone.0101271</citation>
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111 </xml>
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112 </macros>