Mercurial > repos > iuc > mothur_classify_otu

comparison classify.otu.xml @ 1:225b9e8ba32d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:15:05 -0400
parents 21adc0e62211
children ccbf829666b6
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0:21adc0e62211 1:225b9e8ba32d
2 <description>Assign sequences to taxonomy</description> 2 <description>Assign sequences to taxonomy</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat && 13 ln -s "$otu" otu.dat &&
11 ln -s "$tax.taxonomy" tax.taxonomy.dat && 14 ln -s "$tax.taxonomy" tax.taxonomy.dat &&
12 ln -s "$name" name.dat && 15 ln -s "$name" name.dat &&
13 ln -s "$count" count.dat && 16 ln -s "$count" count.dat &&
40 persample=$persample, 43 persample=$persample,
41 cutoff=$cutoff 44 cutoff=$cutoff
42 )' 45 )'
43 | sed 's/ //g' ## mothur trips over whitespace 46 | sed 's/ //g' ## mothur trips over whitespace
44 | mothur 47 | mothur
48 | tee mothur.out.log
45 ]]></command> 49 ]]></command>
46 <inputs> 50 <inputs>
47 <param name="otu" type="data" format="mothur.list" label="list - OTU List "/> 51 <param name="otu" type="data" format="mothur.list" label="list - OTU List "/>
48 <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/> 52 <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
49 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - used to represent the number of duplicate sequences for a given representative sequence"/> 53 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - used to represent the number of duplicate sequences for a given representative sequence"/>
162 <help> 166 <help>
163 <![CDATA[ 167 <![CDATA[
164 168
165 @MOTHUR_OVERVIEW@ 169 @MOTHUR_OVERVIEW@
166 170
167 **Command Documenation** 171 **Command Documentation**
168 172
169 The classify.otu_ command assigns sequences to chosen taxonomy outline. 173 The classify.otu_ command assigns sequences to chosen taxonomy outline.
170 174
171 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. 175 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.
172 176
173 .. _classify.otu: http://www.mothur.org/wiki/Classify.otu 177 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
174 178
175 v1.21.0: Updated to use Mothur 1.33. Added count parameter (1.28.0) and persample parameter (1.29.0) 179 v1.21.0: Updated to use Mothur 1.33. Added count parameter (1.28.0) and persample parameter (1.29.0)
176 ]]> 180 ]]>
177 </help> 181 </help>
178 <expand macro="citations"/> 182 <expand macro="citations"/>