Mercurial > repos > iuc > mothur_classify_seqs

annotate classify.seqs.xml @ 6:65b370206748 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author iuc
date Fri, 03 Aug 2018 14:37:59 -0400
parents 5b53b77232dc
children
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2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_classify_seqs" name="Classify.seqs" version="@WRAPPER_VERSION@.0">
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Assign sequences to taxonomy</description>
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3 <macros>
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4 <import>macros.xml</import>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
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6 <expand macro="requirements"/>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## enable mothur to find blast
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13 ln -s `dirname \$(which mothur)`/* . &&
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14
3
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15 ## create symlinks to input datasets
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16 ln -s '$fasta' fasta.dat &&
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 ln -s '$alignment.template' alignment.template.dat &&
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 ln -s '$tax.taxonomy' tax.taxonomy.dat &&
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 ln -s '$count' count.dat &&
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 ln -s '$name' name.dat &&
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21
3
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22 echo 'classify.seqs(
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 fasta=fasta.dat,
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 reference=alignment.template.dat,
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 taxonomy=tax.taxonomy.dat,
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26 method=$classify.method,
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27 #if $classify.method == "wang":
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28 ksize=$classify.ksize,
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 iters=$classify.iters,
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30 cutoff=$classify.cutoff,
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31 probs=$classify.probs,
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 #elif $classify.method == "knn":
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33 numwanted=$classify.numwanted,
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34 search=$classify.search.algorithm,
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 #if $classify.search.algorithm == "kmer":
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36 ksize=$classify.search.ksize,
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 #elif $classify.search.algorithm == "blast":
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 match=$classify.search.match,
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 mismatch=$classify.search.mismatch,
5b53b77232dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 gapopen=$classify.search.gapopen,
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41 gapextend=$classify.search.gapextend,
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42 #end if
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43 #end if
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44 #if $count:
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45 count=count.dat,
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46 #end if
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47 #if $name:
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48 name=name.dat,
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49 #end if
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50 relabund=$relabund,
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51 output=$output,
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52 printlevel=$printlevel,
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53 processors='\${GALAXY_SLOTS:-8}'
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54 )'
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55 | sed 's/ //g' ## mothur trips over whitespace
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56 | ./mothur
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57 | tee mothur.out.log
0
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58 ]]></command>
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59 <inputs>
3
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60 <param argument="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
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61 <conditional name="alignment">
3
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62 <param name="source" type="select" label="Select Reference Template from">
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63 <option value="hist">History</option>
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64 <option value="ref">Cached Reference</option>
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65 </param>
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66 <when value="ref">
3
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67 <param argument="reference" name="template" type="select" label="reference - Select an alignment database " help="">
0
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68 <options from_data_table="mothur_aligndb">
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69 </options>
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70 </param>
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71 </when>
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72 <when value="hist">
3
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73 <param argument="reference" name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
0
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74 </when>
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75 </conditional>
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76 <conditional name="tax">
3
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77 <param name="source2" type="select" label="Select Taxonomy from">
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78 <option value="ref">Cached Reference</option>
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79 <option value="hist">History</option>
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80 </param>
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81 <when value="ref">
3
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82 <param argument="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference">
0
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83 <options from_data_table="mothur_taxonomy"/>
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84 </param>
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85 </when>
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86 <when value="hist">
3
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87 <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference"/>
0
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 </when>
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89 </conditional>
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90 <conditional name="classify">
3
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91 <param argument="method" type="select" label="method - Select a classification method">
2
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92 <option value="wang" selected="true">Wang (default)</option>
0
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 <option value="knn">K-Nearest Neighbor (knn)</option>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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94 </param>
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95 <when value="wang">
3
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96 <param argument="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
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97 <param argument="iters" type="integer" value="100" min="1" label="iters - iterations to do when calculating the bootstrap confidence score"/>
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98 <param argument="cutoff" type="integer" value="80" min="0" label="cutoff - specify a bootstrap confidence threshold for your taxonomy"/>
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99 <param argument="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
0
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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100 </when>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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101 <when value="knn">
3
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102 <param argument="numwanted" type="integer" value="10" label="numwanted - the number of sequence matches you want with the knn method"/>
0
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103 <conditional name="search">
3
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104 <param argument="search" name="algorithm" type="select" label="algorithm - " help="">
0
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105 <option value="kmer" selected="true">Kmer (default)</option>
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106 <option value="blast">BLAST</option>
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107 <option value="suffix">Suffix Tree</option>
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108 <option value="distance">Distance</option>
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109 </param>
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110 <when value="kmer">
3
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111 <param argument="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
0
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112 </when>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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113 <when value="blast">
3
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114 <param argument="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
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115 <param argument="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
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116 <param argument="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
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117 <param argument="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
0
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118 </when>
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119 <when value="suffix"/>
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120 <when value="distance"/>
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121 </conditional>
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122 </when>
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123 </conditional>
3
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124 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count file"/>
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125 <param argument="name" type="data" format="mothur.names" optional="true" label="names file"/>
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126 <param argument="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false"
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127 label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances"/>
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128 <expand macro="param-output"/>
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129 <expand macro="param-printlevel"/>
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130 <expand macro="param-savelog"/>
0
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131 </inputs>
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132 <outputs>
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133 <expand macro="logfile-output"/>
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134 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="fasta*.taxonomy" label="${tool.name} on ${on_string}: taxonomy"/>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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135 <data name="tax_summary" format="mothur.tax.summary" from_work_dir="fasta*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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136 <data name="tree_sum" format="tabular" from_work_dir="tax.taxonomy*.tree.sum" label="${tool.name} on ${on_string}: tree.sum"/>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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137 </outputs>
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138 <tests>
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139 <test><!-- test with wang method -->
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140 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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141 <param name="source" value="hist"/>
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142 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
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143 <param name="source2" value="hist"/>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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144 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
3
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145 <output name="tax_summary" ftype="mothur.tax.summary">
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146 <assert_contents>
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147 <expand macro="test-taxsummary-format"/>
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148 <has_text text="Root"/>
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149 <has_text text="Bacteria"/>
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150 </assert_contents>
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151 </output>
0
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152 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
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153 <assert_contents>
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154 <has_text text="Bacteria"/>
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155 <has_text text="U68589"/>
2a0d8b8c3ade planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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156 </assert_contents>
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157 </output>
3
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158 <output name="tree_sum" md5="b44a392a719cf083e5a26d45904926c6" ftype="tabular">
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159 <assert_contents>
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160 <has_text text="@WRAPPER_VERSION@"/>
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161 <has_text text="Root"/>
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162 <has_text text="Bacteria"/>
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163 </assert_contents>
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164 </output>
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165 <param name="savelog" value="true"/>
0
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166 <expand macro="logfile-test"/>
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167 </test>
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168 <test><!-- test with knn method -->
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169 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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170 <param name="source" value="hist"/>
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171 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
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172 <param name="source2" value="hist"/>
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173 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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174 <param name="method" value="knn"/>
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175 <output name="tax_summary" ftype="mothur.tax.summary">
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176 <assert_contents>
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177 <expand macro="test-taxsummary-format"/>
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178 <has_text text="Root"/>
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179 <has_text text="Bacteria"/>
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180 </assert_contents>
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181 </output>
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182 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
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183 <assert_contents>
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184 <has_text text="Bacteria"/>
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185 <has_text text="U68589"/>
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186 </assert_contents>
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187 </output>
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188 <param name="savelog" value="true"/>
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189 <expand macro="logfile-test"/>
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190 </test>
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191 <test><!-- test with knn method and blast algorithm -->
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192 <param name="fasta" value="abrecovery.fasta" ftype="fasta"/>
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193 <param name="source" value="hist"/>
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194 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
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195 <param name="source2" value="hist"/>
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196 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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197 <param name="method" value="knn"/>
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198 <param name="algorithm" value="blast"/>
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199 <output name="tax_summary" ftype="mothur.tax.summary">
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200 <assert_contents>
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201 <expand macro="test-taxsummary-format"/>
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202 <has_text text="Root"/>
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203 <has_text text="Bacteria"/>
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204 </assert_contents>
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205 </output>
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206 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
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207 <assert_contents>
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208 <has_text text="Bacteria"/>
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209 <has_text text="AY457914"/>
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210 </assert_contents>
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211 </output>
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212 <param name="savelog" value="true"/>
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213 <expand macro="logfile-test"/>
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214 </test>
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215 </tests>
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216 <help><![CDATA[
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217
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218 @MOTHUR_OVERVIEW@
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219
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220 **Command Documentation**
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221
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222 The classify.seqs_ command assigns sequences to chosen taxonomy outline.
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223
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224 .. _classify.seqs: https://www.mothur.org/wiki/Classify.seqs
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225
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226
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227 v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang.
3
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228
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229 ]]></help>
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230 <expand macro="citations">
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231 <citation type="doi">10.1128/AEM.00062-07</citation>
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232 <citation type="doi">10.1093/nar/25.17.3389</citation>
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233 <citation type="doi"> 10.1128/AEM.03006-05</citation>
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234 </expand>
0
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235 </tool>