view mothur/tools/mothur/anosim.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_anosim" name="Anosim" version="1.19.0">
 <description>Non-parametric multivariate analysis of changes in community structure</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='anosim'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.anosim$:'$anosim
  --outputdir='$logfile.extra_files_path'
  --phylip=$dist
  --design=$design
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  #if float($alpha.__str__) > 0.0:
   --alpha=$alpha
  #end if
 </command>
 <inputs>
  <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
  <param name="design" type="data" format="tabular" label="design - assign groups to new grouping"
         help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
  <param name="alpha" type="float" optional="true" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/>
  <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="anosim" label="${tool.name} on ${on_string}: anosim"/>
 </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 anosim_ command uses a phylip_distance_matrix_ and a design file to calculate the non-parametric multivariate analysis of changes in community structure.

A design file partitions a list of names into groups.  It is a tab-delimited file with 2 columns: name and group, e.g. :
        ======= =======
        duck    bird
        cow     mammal
        pig     mammal
        goose   bird
        cobra   reptile
        ======= =======

The Make_Design tool can construct a design file from a Mothur dataset that contains group names.


.. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _anosim: http://www.mothur.org/wiki/Anosim


 </help>
</tool>