annotate mothur/tools/mothur/summary.tax.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_summary_tax" name="Summary.tax" version="1.22.0">
 <description>Assign sequences to taxonomy</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='summary.tax'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tax\.summary$:'$tax_summary
  --outputdir='$logfile.extra_files_path'
  --taxonomy=$tax.taxonomy
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name='$name'
  #end if
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --group='$group'
  #end if
  #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0:
   --reftaxonomy=$reftax.taxonomy
  #end if
 </command>
 <inputs>
  <conditional name="tax">
   <param name="source" type="select" label="Select Taxonomy from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="ref">
    <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy Reference">
     <options from_file="mothur_taxonomy.loc">
      <column name="name" index="0" />
      <column name="value" index="1" />
     </options>
    </param>
   </when>
   <when value="hist">
    <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
   </when>
  </conditional>
  <param name="name" type="data" format="names" optional="true" label="name - taxonomy sequence names"/>
  <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/>
  <conditional name="reftax">
   <param name="source" type="select" label="Select Reference Taxonomy used in Summary.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
    <option value="none">Selection is Optional</option>
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="none"/>
   <when value="ref">
    <param name="taxonomy" type="select" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
     <options from_file="mothur_taxonomy.loc">
      <column name="name" index="0" />
      <column name="value" index="1" />
     </options>
    </param>
   </when>
   <when value="hist">
    <param name="taxonomy" type="data" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
   </when>
  </conditional>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="summary" name="tax_summary" label="${tool.name} on ${on_string}: summary" />
 </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 summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information.

.. _summary.tax: http://www.mothur.org/wiki/Summary.otu

 </help>
</tool>