Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/consensus.seqs.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
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children | fcc0778f6987 |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.15.0" 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 $otu.use == 'yes': |
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12 --list=$otu.list |
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13 #if $otu.label.__str__ != "None" and len($otu.label.__str__) > 0: |
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14 --label='$otu.label' |
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15 #end if |
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16 --result='^mothur.\S+\.logfile$:'$logfile |
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17 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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18 --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:fasta','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$:names','^\S+?\.(((unique|[0-9.]*)\.)?cons\.summary)$:tabular' |
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19 #else |
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20 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.cons\.summary$:'$summary,'^\S+\.cons\.fasta$:'$cons_fasta |
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21 #end if |
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22 </command> |
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23 <inputs> |
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24 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin" help="Sequences must be the same length"/> |
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25 <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
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26 <conditional name="otu"> |
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27 <param name="use" type="select" label="Consensus sequence"> |
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28 <option value="no">Single consensus sequence</option> |
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29 <option value="yes">Consensus sequence for each OTU in list</option> |
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30 </param> |
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31 <when value="no"/> |
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32 <when value="yes"> |
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33 <param name="list" type="data" format="list" label="list - OTU List"/> |
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34 <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true"> |
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35 <options from_dataset="list"> |
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36 <column name="name" index="0"/> |
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37 <column name="value" index="0"/> |
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38 </options> |
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39 </param> |
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40 </when> |
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41 </conditional> <!-- --> |
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42 </inputs> |
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43 <outputs> |
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44 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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45 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: cons.summary"> |
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46 <filter>otu['use'] == 'no'</filter> |
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47 </data> |
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48 <data format="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta"> |
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49 <filter>otu['use'] == 'no'</filter> |
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50 </data> |
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51 </outputs> |
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52 <requirements> |
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53 <requirement type="binary">mothur</requirement> |
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54 </requirements> |
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55 <tests> |
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56 </tests> |
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57 <help> |
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58 **Mothur Overview** |
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59 |
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60 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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61 in the Department of Microbiology and Immunology at The University of Michigan, |
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62 provides bioinformatics for the microbial ecology community. |
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63 |
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64 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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65 |
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66 **Command Documenation** |
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67 |
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68 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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69 |
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70 .. _consensus.seqs: http://www.mothur.org/wiki/Consensus.seqs |
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71 |
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72 </help> |
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73 </tool> |