Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/consensus.seqs.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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7 | 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 |
7 | 11 #if $cutoff != None and len($cutoff.__str__) > 0 and 100 > int($cutoff.__str__) > 0: |
12 --cutoff=$cutoff | |
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='$__new_file_path__' |
4 | 21 --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:${fasta.ext}','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$: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> |
4 | 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> |
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39 <filter type="data_meta" ref="list" key="labels" /> |
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40 </options> |
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41 </param> |
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42 </when> |
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43 </conditional> <!-- --> |
7 | 44 <param name="cutoff" type="integer" value="100" optional="True" label="cutoff - set a percentage of sequences that support the base"> |
45 <help>For example: cutoff=95 would return the base that was supported by at least 95% of sequences.</help> | |
46 <validator type="in_range" message="The percentage cutoff must be between 1 and 100" min="1" max="100"/> | |
47 </param> | |
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48 </inputs> |
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49 <outputs> |
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50 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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51 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: cons.summary"> |
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52 <filter>otu['use'] == 'no'</filter> |
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53 </data> |
4 | 54 <data format_source="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta"> |
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55 <filter>otu['use'] == 'no'</filter> |
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56 </data> |
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57 </outputs> |
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58 <requirements> |
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59 <requirement type="package" version="1.27">mothur</requirement> |
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60 </requirements> |
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61 <tests> |
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62 </tests> |
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63 <help> |
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64 **Mothur Overview** |
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65 |
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66 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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67 in the Department of Microbiology and Immunology at The University of Michigan, |
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68 provides bioinformatics for the microbial ecology community. |
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69 |
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70 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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71 |
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72 **Command Documenation** |
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73 |
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74 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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75 |
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76 .. _consensus.seqs: http://www.mothur.org/wiki/Consensus.seqs |
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77 |
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78 </help> |
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79 </tool> |