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

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

--- a/mothur/tools/mothur/cluster.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/cluster.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,27 +1,26 @@
-<tool id="mothur_cluster" name="Cluster" version="1.16.0">
+<tool id="mothur_cluster" name="Cluster" version="1.19.0">
  <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='cluster'
   --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=$matrix.name
+   --column=$matrix.dist
+   --name=$matrix.name
   #elif $matrix.format == "phylip":
-   --READ_phylip=$matrix.dist
+   --phylip=$matrix.dist
    #if $matrix.name.__str__ != "None" and len($matrix.name.__str__) > 0:
-    --READ_name=$matrix.name
+    --name=$matrix.name
    #end if
   #end if
   $sim
   #if float($cutoff.__str__) > 0.0:
-   --READ_cutoff=$cutoff
+   --cutoff=$cutoff
   #end if
   $hard
   #if len($precision.__str__) > 0:
-   --READ_precision=$precision
+   --precision=$precision
   #end if
   #if len($method.__str__) > 0:
    --method=$method
@@ -34,24 +33,24 @@
     <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"/>
+    <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
+    <param name="name" type="data" format="names" label="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"/>
+    <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
+    <param name="name" type="data" format="names" optional="true" label="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="furthest">Furthest neighbor</option>
    <option value="nearest">Nearest neighbor</option>
-   <option value="average">Average neighbor</option>
+   <option value="average" selected="true">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" 
+  <param name="hard" type="boolean" checked="true" truevalue="--hard=true" falsevalue="--hard=false" 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">
@@ -62,7 +61,7 @@
    <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" 
+  <param name="sim" type="boolean" checked="false" truevalue="--sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" 
                  help=""/>
 
  </inputs>
@@ -88,8 +87,14 @@
 
 **Command Documenation**
 
-The cluster_ command assign sequences to OTUs (Operational Taxonomy Unit). 
+The cluster_ command assign sequences to OTUs (Operational Taxonomy Unit).  The assignment is based on a phylip-formatted_distance_matrix_ or a  column-formatted_distance_matrix_ and name_ file.  It generates a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
 
+.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
+.. _name: http://www.mothur.org/wiki/Name_file
+.. _list: http://www.mothur.org/wiki/List_file
+.. _rabund: http://www.mothur.org/wiki/Rabund_file
+.. _sabund: http://www.mothur.org/wiki/Sabund_file
 .. _cluster: http://www.mothur.org/wiki/Cluster