diff mothur/tools/mothur/homova.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/homova.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -0,0 +1,62 @@
+<tool id="mothur_homova" name="Homova" version="1.19.0">
+ <description>Homogeneity of molecular variance</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='homova'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.homova$:'$homova
+  --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 ${on_string}: logfile" />
+  <data format="tabular" name="homova" label="${tool.name} on ${on_string}: homova"/>
+ </outputs>
+ <requirements>
+  <requirement type="binary">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 homova_ command calculates the homogeneity of molecular variance (HOMOVA) from a phylip_distance_matrix_, a nonparametric analog of Bartlett's test for homo- geneity of variance, which has been used in population genetics to test the hypothesis that the genetic diversity within two or more populations is homogeneous.
+
+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
+.. _homova: http://www.mothur.org/wiki/Homova
+
+
+ </help>
+</tool>