annotate mothur/tools/mothur/consensus.seqs.xml @ 11:11867a45a43d

Change make.shared param name from unique to groups
author Jim Johnson <jj@umn.edu>
date Thu, 14 Jul 2011 15:21:01 -0500
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1 <tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.20.0" force_history_refresh="True">
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2 <description>Find a consensus sequence for each OTU or phylotype</description>
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3 <command interpreter="python">
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4 mothur_wrapper.py
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5 --cmd='consensus.seqs'
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6 --outputdir='$logfile.extra_files_path'
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7 --fasta=$fasta
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8 #if $name.__str__ != "None" and len($name.__str__) > 0:
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9 --name=$name
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10 #end if
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11 #if $cutoff != None and len($cutoff.__str__) > 0 and 100 > int($cutoff.__str__) > 0:
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12 --cutoff=$cutoff
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13 #end if
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14 #if $otu.use == 'yes':
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15 --list=$otu.list
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16 #if $otu.label.__str__ != "None" and len($otu.label.__str__) > 0:
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17 --label='$otu.label'
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18 #end if
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19 --result='^mothur.\S+\.logfile$:'$logfile
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20 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
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21 --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:${fasta.ext}','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$:names','^\S+?\.(((unique|[0-9.]*)\.)?cons\.summary)$:tabular'
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22 #else
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23 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.cons\.summary$:'$summary,'^\S+\.cons\.fasta$:'$cons_fasta
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24 #end if
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25 </command>
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26 <inputs>
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27 <param name="fasta" type="data" format="align" label="fasta - Sequences to Bin" help="Sequences must be the same length"/>
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28 <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
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29 <conditional name="otu">
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30 <param name="use" type="select" label="Consensus sequence">
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31 <option value="no">Single consensus sequence</option>
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32 <option value="yes">Consensus sequence for each OTU in list</option>
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33 </param>
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34 <when value="no"/>
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35 <when value="yes">
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36 <param name="list" type="data" format="list" label="list - OTU List"/>
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37 <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true">
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38 <options from_dataset="list">
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39 <column name="name" index="0"/>
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40 <column name="value" index="0"/>
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41 </options>
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42 </param>
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43 </when>
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44 </conditional> <!-- -->
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45 <param name="cutoff" type="integer" value="100" optional="True" label="cutoff - set a percentage of sequences that support the base">
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46 <help>For example: cutoff=95 would return the base that was supported by at least 95% of sequences.</help>
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47 <validator type="in_range" message="The percentage cutoff must be between 1 and 100" min="1" max="100"/>
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48 </param>
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49 </inputs>
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50 <outputs>
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51 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
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52 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: cons.summary">
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53 <filter>otu['use'] == 'no'</filter>
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54 </data>
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55 <data format_source="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta">
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56 <filter>otu['use'] == 'no'</filter>
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57 </data>
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58 </outputs>
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59 <requirements>
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60 <requirement type="binary">mothur</requirement>
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61 </requirements>
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62 <tests>
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63 </tests>
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64 <help>
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65 **Mothur Overview**
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66
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67 Mothur_, initiated by Dr. Patrick Schloss and his software development team
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68 in the Department of Microbiology and Immunology at The University of Michigan,
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69 provides bioinformatics for the microbial ecology community.
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71 .. _Mothur: http://www.mothur.org/wiki/Main_Page
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72
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73 **Command Documenation**
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74
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75 The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.
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76
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77 .. _consensus.seqs: http://www.mothur.org/wiki/Consensus.seqs
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78
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79 </help>
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80 </tool>