view mothur/tools/mothur/phylotype.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_phylotype" name="Phylotype" version="1.19.0">
 <description>Assign sequences to OTUs based on taxonomy</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='phylotype'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist
  --outputdir='$logfile.extra_files_path'
  --taxonomy=$taxonomy
  #if 50 >= int($cutoff.__str__) > 0:
   --cutoff=$cutoff
  #end if
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name='$name'
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
 </command>
 <inputs>
  <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/>
  <param name="name" type="data" format="names" optional="true" label="name - Names reference file for the taxonomy"/>
  <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true">
   <option value="0">0</option>
   <option value="1">1</option>
   <option value="2">2</option>
   <option value="3">3</option>
   <option value="4">4</option>
   <option value="5">5</option>
   <option value="6">6</option>
   <option value="7">7</option>
   <option value="8">8</option>
   <option value="9">9</option>
   <option value="10">10</option>
  </param>
  <param name="cutoff" type="integer" value="-1" label="cutoff - Truncate the taxonomy at depth (Ignored if &lt; 0)"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
  <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
 </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 phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.

.. _list: http://www.mothur.org/wiki/List_file
.. _rabund: http://www.mothur.org/wiki/Rabund_file
.. _sabund: http://www.mothur.org/wiki/Sabund_file
.. _phylotype: http://www.mothur.org/wiki/Phylotype


 </help>
</tool>