annotate mothur/tools/mothur/amova.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_amova" name="Amova" version="1.19.0">
 <description>Analysis of molecular variance</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='amova'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.amova$:'$amova
  --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=$alpha
  #end if
 </command>
 <inputs>
  <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
  <param name="design" type="data" format="tabular" label="design - assign groups to new grouping"
         help="design has 2 TAB-separated columns: group and grouping (Tool: Make_Design) "/>
  <param name="alpha" type="float" optional="true" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/>
  <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="amova" label="${tool.name} on ${on_string}: amova"/>
 </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 amova_ command calculates the analysis of molecular variance from a phylip_distance_matrix_, a nonparametric analog of traditional analysis of variance. This method is widely used in population genetics to test the hypothesis that genetic diversity within two populations is not significantly different from that which would result from pooling the two populations.

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
.. _amova: http://www.mothur.org/wiki/Amova


 </help>
</tool>