diff mothur/tools/mothur/mantel.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/mantel.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -0,0 +1,52 @@
+<tool id="mothur_mantel" name="Mantel" version="1.19.0">
+ <description>Mantel correlation coefficient between two matrices.</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='mantel'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.mantel$:'$mantel
+  --outputdir='$logfile.extra_files_path'
+  --phylip=$dist
+  --phylip2=$dist2
+  --method=$method
+  #if int($iters.__str__) > 0:
+   --iters=$iters
+  #end if
+ </command>
+ <inputs>
+  <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
+  <param name="dist2" type="data" format="lower.dist,square.dist" label="phylip2 - Distance Matrix"/>
+  <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson" >
+    <option value="pearson" selected="true">pearson</option>
+    <option value="spearman">spearman</option>
+    <option value="kendall">kendall</option>
+  </param>
+  <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 ${on_string}: logfile" />
+  <data format="tabular" name="mantel" label="${tool.name} on ${on_string}: mantel"/>
+ </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 mantel_ command calculates the Mantel correlation coefficient between two matrices_.
+
+.. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _mantel: http://www.mothur.org/wiki/Mantel
+
+
+ </help>
+</tool>