annotate mothur/tools/mothur/classify.otu.xml @ 32:ec8df51e841a

Fixes courtesy of Peter Briggs: metagenomics.py: - Groups class: Fix for when second column not present - Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular data uploads being sniffed as this type mothur_wrapper.py: - update cmd_dict['chimera.perseus'], to use correct inputs - add --beta option (needed for chimera.perseus tool) - add function for converting input floats from scientific notation (e.g. 1e-6, which mothur can't handle) to decimal format (e.g. 0.00001, which it can) chimera.perseus.xml: - add output data item for the "accnos" file (not previous captured in the history) trim.flows.xml: - cosmetic change: base name for additional output data items is now "trim.flows", rather than "logfile" (clarifies history items) shhh.flows.xml: - cosmetic change: update default value specified in help for mindiff to be consistent with that given in the mothur documentation

<tool id="mothur_classify_otu" name="Classify.otu" version="1.20.0" force_history_refresh="True">
 <description>Assign sequences to taxonomy</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='classify.otu'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
  --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy','^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$:tax.summary'
  --list=$otu
  --taxonomy=$tax.taxonomy
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name='$name'
  #end if
  #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0:
   --reftaxonomy=$reftax.taxonomy
  #end if
  #if 100 >= int($cutoff.__str__) > 0:
   --cutoff=$cutoff
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --group='$group'
  #end if
  --basis=$basis
  $probs
 </command>
 <inputs>
  <param name="otu" type="data" format="list" label="list - OTU List "/>
  <param name="name" type="data" format="names" optional="true" label="name - taxonomy sequence names"/>
  <conditional name="tax">
   <param name="source" type="select" label="Select Taxonomy from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="ref">
    <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy Reference">
     <options from_file="mothur_taxonomy.loc">
      <column name="name" index="0" />
      <column name="value" index="1" />
     </options>
    </param>
   </when>
   <when value="hist">
    <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
   </when>
  </conditional>
  <conditional name="reftax">
   <param name="source" type="select" label="Select Reference Taxonomy used in Classify.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
    <option value="none">Selection is Optional</option>
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="none"/>
   <when value="ref">
    <param name="taxonomy" type="select" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
     <options from_file="mothur_taxonomy.loc">
      <column name="name" index="0" />
      <column name="value" index="1" />
     </options>
    </param>
   </when>
   <when value="hist">
    <param name="taxonomy" type="data" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
   </when>
  </conditional>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options>
    <filter type="data_meta" ref="otu" key="labels" />
   </options>
  </param>
  <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100">
   <validator type="in_range" message="Confindence percentage cutoff must be between 0 and 100" min="0" max="100"/>
  </param>
  <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/>
  <param name="basis" type="select" label="basis - Summary file gives numbers of" help="">
   <option value="otu">OTU</option>
   <option value="sequence">sequence</option>
  </param>
  <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

Mothur_, initiated by Dr. Patrick Schloss and his software development team
in the Department of Microbiology and Immunology at The University of Michigan,
provides bioinformatics for the microbial ecology community.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The classify.otu_ command assigns sequences to chosen taxonomy outline.

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.

.. _classify.otu: http://www.mothur.org/wiki/Classify.otu


 </help>
</tool>