diff mothur/tools/mothur/cluster.classic.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/cluster.classic.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,97 @@
+<tool id="mothur_cluster_classic" name="Cluster.classic" version="1.15.0">
+ <description>Assign sequences to OTUs (Dotur implementation)</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='cluster.classic'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist
+  --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
+   #if $matrix.name.__str__ != "None" and len($matrix.name.__str__) > 0:
+    --READ_name=$matrix.name
+   #end if
+  #end if
+  $sim
+  #if float($cutoff.__str__) > 0.0:
+   --READ_cutoff=$cutoff
+  #end if
+  $hard
+  #if len($precision.__str__) > 0:
+   --READ_precision=$precision
+  #end if
+  #if len($method.__str__) > 0:
+   --method=$method
+  #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"/>
+    <param name="name" type="data" format="names" optional="true" label="read.dist(name=) - Sequences Name reference"/>
+   </when>
+  </conditional>
+  <!-- ? conditional - to hide complexity -->
+  <param name="method" type="select" label="method - Select a Clustering Method" help="">
+   <option value="furthest" selected="true">Furthest neighbor</option>
+   <option value="nearest">Nearest neighbor</option>
+   <option value="average">Average neighbor</option>
+   <option value="weighted">Weighted</option>
+  </param>
+  <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" 
+                 help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
+  <param name="hard" type="boolean" checked="false" truevalue="--hard=true" falsevalue="" label="hard - Use hard cutoff instead of rounding" 
+                 help=""/>
+  <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
+                 help="Set higher precision for longer genome scale sequence lengths">
+   <option value="10">.1</option>
+   <option value="100" selected="true">.01</option>
+   <option value="1000">.001</option>
+   <option value="10000">.0001</option>
+   <option value="100000">.00001</option>
+   <option value="1000000">.000001</option>
+  </param>
+  <param name="sim" type="boolean" checked="false" truevalue="--READ_sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" 
+                 help=""/>
+
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank)"/>
+  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species)"/>
+  <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
+ </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 cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit). 
+
+.. _cluster.classic: http://www.mothur.org/wiki/Cluster.classic
+
+
+ </help>
+</tool>