diff mothur/tools/mothur/libshuff.xml @ 0:3202a38e44d9

Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/libshuff.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,85 @@
+<tool id="mothur_libshuff" name="Libshuff" version="1.15.0">
+ <description>Cramer-von Mises tests communities for the same structure</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='libshuff'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.libshuff\.summary$:'$summary,'^\S+\.libshuff\.coverage$:'$coverage
+  --outputdir='$logfile.extra_files_path'
+  --READ_cmd='read.dist'
+  #if $matrix.format == "column":
+   --READ_column=$matrix.dist
+   --READ_name=$matrix.name
+  #elif $matrix.format == "phylip":
+   --READ_phylip=$matrix.dist
+  #end if
+  --READ_group=$group
+  #if len($iters.__str__) > 0:
+   --iters=$iters
+  #end if
+  #if $form == "discrete":
+   #if 1.0 >= float($form.step.__str__) > 0.0:
+    --step=$form.step
+   #end if
+   #if 1.0 >= float($cutoff.__str__) > 0.0:
+    --cutoff=$form.cutoff
+   #end if
+  #end if
+ </command>
+ <inputs>
+  <conditional name="matrix">
+   <param name="format" type="select" label="Select a Distance Matrix Format" help="">
+    <option value="column">Pairwise Column Matrix</option>
+    <option value="phylip">Phylip Distance Matrix</option>
+   </param>
+   <when value="column">
+    <param name="dist" type="data" format="pair.dist" label="read.dist(column=) - Distance Matrix"/>
+    <param name="name" type="data" format="names" label="read.dist(name) - Sequences Name reference"/>
+   </when>
+   <when value="phylip">
+    <param name="dist" type="data" format="lower.dist,square.dist" label="read.dist(phylip=) - Distance Matrix"/>
+   </when>
+  </conditional>
+  <param name="group" type="data" format="groups" label="read.dist(group=) - Groups"/>
+  <!-- ? conditional - to hide complexity -->
+  <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
+  <conditional name="form">
+   <param name="form" type="select" label="form - Select a Clustering Method" help="">
+    <option value="integral" selected="true">Integral</option>
+    <option value="discrete">Discrete</option>
+   </param>
+   <when value="integral"/>
+   <when value="discrete">
+    <param name="step" type="float" value="0.0" label="step - Step size - ignored if not > 0" 
+                 help="default value 0.10, smaller steps approach integral"/>
+    <param name="cutoff" type="float" value="0.0" label="cutoff - Cutoff threshold - ignored if not > 0" help=""/>
+   </when>
+  </conditional>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary"/>
+  <data format="tabular" name="coverage" label="${tool.name} on ${on_string}: coverage"/>
+ </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 libshuff_ method is a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic. The significance of the test statistic indicates the probability that the communities have the same structure by chance. Because each pairwise comparison requires two significance tests, a correction for multiple comparisons (e.g. Bonferroni's correction) must be applied.
+
+.. _libshuff: http://www.mothur.org/wiki/Libshuff
+
+
+ </help>
+</tool>