view mothur/tools/mothur/pcoa.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_pcoa" name="Pcoa" version="1.19.0" >
 <description>Principal Coordinate Analysis for a distance matrix</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='pcoa'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pcoa\.axes$:'$pcoa,'^\S+\.pcoa.loadings$:'$loadings
  --outputdir='$logfile.extra_files_path'
  --phylip=$phylip
  $metric
 </command>
 <inputs>
  <param name="phylip" type="data" format="lower.dist,square.dist" label="phylip - Phylip Distance Matrix"/>
  <param name="metric" type="boolean" truevalue="" falsevalue="--metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" />
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="axes" name="pcoa" label="${tool.name} on ${on_string}: pcoa.axes" />
  <data format="tabular" name="loadings" label="${tool.name} on ${on_string}: loadings" />
 </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 pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_.

.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _pcoa: http://www.mothur.org/wiki/Pcoa

 </help>
</tool>