Mercurial > repos > iuc > mothur_classify_otu

annotate classify.otu.xml @ 8:970693ff9731 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 14:07:09 -0400
parents 5301655f34bb
children
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1 <tool profile="16.07" id="mothur_classify_otu" name="Classify.otu" version="@WRAPPER_VERSION@.0">
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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>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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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 ## create symlinks to input datasets
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13 ln -s '$otu' otu.dat &&
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14 ln -s '$tax.taxonomy' tax.taxonomy.dat &&
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15 ln -s '$name' name.dat &&
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16 ln -s '$count' count.dat &&
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17 ln -s '$group' group.dat &&
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18
3
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19 echo 'classify.otu(
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20 list=otu.dat,
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21 taxonomy=tax.taxonomy.dat,
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22 #if $name:
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23 name=name.dat,
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24 #end if
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25 #if $count:
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26 count=count.dat,
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27 #end if
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28 #if $label:
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29 label=${ str($label).replace(",","-") },
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30 #end if
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31 #if $group:
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32 group=group.dat,
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33 #end if
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34 basis=$basis,
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35 probs=$probs,
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36 persample=$persample,
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37 cutoff=$cutoff,
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38 relabund=$relabund,
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39 output=$output,
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40 printlevel=$printlevel
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41 )'
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42 | sed 's/ //g' ## mothur trips over whitespace
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43 | mothur
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44 | tee mothur.out.log
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45 ]]></command>
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46 <inputs>
3
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47 <param argument="list" name="otu" type="data" format="mothur.list" label="list - OTU List "/>
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48 <param argument="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
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49 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - used to represent the number of duplicate sequences for a given representative sequence"/>
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50 <conditional name="tax">
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51 <param name="source" type="select" label="Select Taxonomy from" help="">
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52 <option value="hist">History</option>
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53 <option value="ref">Cached Reference</option>
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54 </param>
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55 <when value="ref">
3
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56 <param argument="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference">
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57 <options from_data_table="mothur_taxonomy"/>
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58 </param>
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59 </when>
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60 <when value="hist">
3
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61 <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
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62 </when>
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63 </conditional>
3
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64 <param argument="label" type="select" label="label - OTU Labels" multiple="true">
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65 <expand macro="labeloptions"/>
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66 </param>
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67 <param argument="cutoff" type="integer" value="60" min="0" max="100" label="cutoff - Confindence percentage cutoff between 1 and 100"/>
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68 <param argument="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
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69 <param argument="basis" type="select" label="basis - Summary file gives numbers of" help="">
0
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70 <option value="otu">OTU</option>
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71 <option value="sequence">sequence</option>
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72 </param>
3
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73 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
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74 <param argument="persample" type="boolean" falsevalue="false" truevalue="true" checked="false"
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75 label="persample - allows you to find a consensus taxonomy for each group"
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76 help="default false"/>
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77 <param argument="relabund" type="boolean" checked="false" truevalue="T" falsevalue="F" label="Relative abundance values?"
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78 help="use relative abundances rather than raw abundances for the tax.summary file"/>
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79 <expand macro="param-output"/>
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80 <expand macro="param-printlevel"/>
5
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81 <expand macro="param-savelog"/>
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82 </inputs>
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83 <outputs>
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84 <expand macro="logfile-output"/>
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85 <collection name="taxsummaries" type="list" label="${tool.name} on ${on_string}: tax.summary">
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86 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.tax\.summary" format="mothur.tax.summary"/>
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87 </collection>
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88 <collection name="taxonomies" type="list" label="${tool.name} on ${on_string}: taxonomy">
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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89 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.taxonomy" format="mothur.cons.taxonomy"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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90 </collection>
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91 </outputs>
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92 <tests>
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93 <test><!-- test with defaults -->
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94 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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95 <param name="source" value="hist"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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96 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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97 <output_collection name="taxonomies" count="36">
3
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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98 <element name="0.18" ftype="mothur.cons.taxonomy">
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99 <assert_contents>
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100 <expand macro="test-taxonomy-format"/>
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101 <has_text text="Otu01"/>
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102 </assert_contents>
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103 </element>
0
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104 </output_collection>
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105 <output_collection name="taxsummaries" count="36">
3
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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106 <element name="0.18" ftype="mothur.tax.summary">
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107 <assert_contents>
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108 <expand macro="test-taxsummary-format"/>
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109 <has_text text="Root"/>
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110 </assert_contents>
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111 </element>
0
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112 </output_collection>
5
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113 <param name="savelog" value="true"/>
0
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114 <expand macro="logfile-test"/>
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115 </test>
3
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116 <test><!-- test with names file and label select -->
0
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117 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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118 <param name="name" value="amazon1.names" ftype="mothur.names"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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119 <param name="source" value="hist"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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120 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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121 <param name="sum" value="abrecovery.pds.wang.tree.sum"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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122 <param name="label" value="unique,0.05,0.18"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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123 <output_collection name="taxonomies" count="3">
3
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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124 <element name="0.18" ftype="mothur.cons.taxonomy">
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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125 <assert_contents>
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126 <expand macro="test-taxonomy-format"/>
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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127 <has_text text="Otu01"/>
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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128 </assert_contents>
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129 </element>
0
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130 </output_collection>
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131 <output_collection name="taxsummaries" count="3">
3
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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132 <element name="0.18" ftype="mothur.tax.summary">
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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133 <assert_contents>
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134 <expand macro="test-taxsummary-format"/>
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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135 <has_text text="Root"/>
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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136 </assert_contents>
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137 </element>
0
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138 </output_collection>
5
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139 <param name="savelog" value="true"/>
0
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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140 <expand macro="logfile-test"/>
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141 </test>
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142 <test><!-- test with count table -->
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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143 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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144 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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145 <param name="source" value="hist"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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146 <param name="label" value="unique,0.05,0.18"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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147 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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148 <output_collection name="taxonomies" count="3">
3
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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149 <element name="0.18" ftype="mothur.cons.taxonomy">
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150 <assert_contents>
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151 <expand macro="test-taxonomy-format"/>
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152 <has_text text="Otu01"/>
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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153 </assert_contents>
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154 </element>
0
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155 </output_collection>
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156 <output_collection name="taxsummaries" count="3">
3
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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157 <element name="0.18" ftype="mothur.tax.summary">
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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158 <assert_contents>
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159 <expand macro="test-taxsummary-format"/>
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160 <has_text text="Root"/>
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161 </assert_contents>
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162 </element>
0
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163 </output_collection>
5
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164 <param name="savelog" value="true"/>
0
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165 <expand macro="logfile-test"/>
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166 </test>
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167 <test><!-- test with group file -->
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168 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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169 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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170 <param name="source" value="hist"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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171 <param name="label" value="unique,0.05,0.18"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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172 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
21adc0e62211 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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173 <output_collection name="taxonomies" count="3">
3
ccbf829666b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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174 <element name="0.18" ftype="mothur.cons.taxonomy">
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175 <assert_contents>
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176 <expand macro="test-taxonomy-format"/>
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177 <has_text text="Otu01"/>
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178 </assert_contents>
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179 </element>
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180 </output_collection>
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181 <output_collection name="taxsummaries" count="3">
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182 <element name="0.18" ftype="mothur.tax.summary">
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183 <assert_contents>
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184 <expand macro="test-taxsummary-format"/>
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185 <has_text text="Root"/>
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186 </assert_contents>
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187 </element>
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188 </output_collection>
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189 <param name="savelog" value="true"/>
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190 <expand macro="logfile-test"/>
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191 </test>
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192 </tests>
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193 <help><![CDATA[
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194
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195 @MOTHUR_OVERVIEW@
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196
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197 **Command Documentation**
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198
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199 The classify.otu_ command assigns sequences to chosen taxonomy outline.
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200
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201 The basis parameter allows you indicate what you want the summary file to represent, options are otu and sequence. Default is otu. For example consider the following basis=sequence could give Clostridiales 3 105 16 43 46, where 105 is the total number of sequences whose otu classified to Clostridiales. 16 is the number of sequences in the otus from groupA, 43 is the number of sequences in the otus from groupB, and 46 is the number of sequences in the otus from groupC. Now for basis=otu could give Clostridiales 3 7 6 1 2, where 7 is the number of otus that classified to Clostridiales. 6 is the number of otus containing sequences from groupA, 1 is the number of otus containing sequences from groupB, and 2 is the number of otus containing sequences from groupC.
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202
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203 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
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204
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205 v1.21.0: Updated to use Mothur 1.33. Added count parameter (1.28.0) and persample parameter (1.29.0)
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206
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207 ]]></help>
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208 <expand macro="citations">
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209 <citation type="doi">10.1128/AEM.02810-10</citation>
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210 </expand>
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211 </tool>