diff mothur/tools/mothur/amova.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/amova.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -0,0 +1,63 @@
+<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="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 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>