diff mothur/tools/mothur/cluster.split.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/cluster.split.xml	Tue Jun 07 17:35:35 2011 -0400
@@ -0,0 +1,136 @@
+<tool id="mothur_cluster_split" name="Cluster.split" version="1.16.0">
+ <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='cluster.split'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist
+  --outputdir='$logfile.extra_files_path'
+  #if $splitby.splitmethod == "distance":
+   #if $splitby.matrix.format == "column":
+    --column=$splitby.matrix.dist
+    --name=$splitby.matrix.name
+   #elif $splitby.matrix.format == "phylip":
+    --phylip=$splitby.matrix.dist
+    #if $splitby.matrix.name.__str__ != "None" and len($splitby.matrix.name.__str__) > 0:
+     --name=$splitby.matrix.name
+    #end if
+   #end if
+   --splitmethod=$splitby.splitmethod
+  #elif $splitby.splitmethod == "classify":
+   --column=$splitby.dist
+   --name=$splitby.name
+   --taxonomy=$splitby.taxonomy
+   #if $splitby.taxlevel > 1:
+    --taxlevel=$splitby.taxlevel
+   #end if
+   --splitmethod=$splitby.splitmethod
+  #elif $splitby.splitmethod == "fasta":
+   --fasta=$splitby.fasta
+   --name=$splitby.name
+   --taxonomy=$splitby.taxonomy
+   #if $splitby.taxlevel > 1:
+    --taxlevel=$splitby.taxlevel
+   #end if
+   --splitmethod=$splitby.splitmethod
+  #end if
+  #if len($method.__str__) > 0:
+   --method=$method
+  #end if
+  #if float($cutoff.__str__) > 0.0:
+   --cutoff=$cutoff
+  #end if
+  $hard
+  #if len($precision.__str__) > 0:
+   --precision=$precision
+  #end if
+  $large
+  --processors=1
+ </command>
+ <inputs>
+  <conditional name="splitby">
+   <param name="splitmethod" type="select" label="Split by" help="">
+    <option value="distance">Distance</option>
+    <option value="classify">Classification</option>
+    <option value="fasta">Classification using fasta</option>
+   </param>
+   <when value="distance">
+    <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="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="phylip - Distance Matrix"/>
+      <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
+     </when>
+    </conditional>
+   </when>
+   <when value="classify">
+    <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
+    <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
+    <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
+    <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" 
+           help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
+   </when>
+   <when value="fasta">
+    <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
+    <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
+    <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
+    <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" 
+           help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
+   </when>
+  </conditional> <!-- splitby -->
+  <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>
+  </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="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - distance matrix is too large to fit in RAM" 
+                 help="If your job fails due to not enough memory error, set this to true to rerun"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
+  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
+  <data format="list" name="otulist" label="${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.split_ command assign sequences to OTUs (Operational Taxonomy Unit). 
+
+.. _cluster.split: http://www.mothur.org/wiki/Cluster.split
+
+
+ </help>
+</tool>