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<tool id="cluster3" name="Cluster 3" version="1.0.0">
  <description>Cluster 3.0</description>
  <command interpreter="python">$scriptfile</command>
  <inputs>
	  <param name="filename" type="data" format="tab" label="Matrix"/>
      <param name="row_center" type="select" label="Row Center (gene)">
         <option value="x">No row Center</option>
         <option value="a">Substact mean of row</option>
         <option value="m">Substact median of row</option>
      </param>
      <param name="log_transform" type="boolean" label="Log transform data" default="false"/>
      <param name="row_normalize" type="boolean" label="Normalize Rows (gene)"/>
      
      <param name="col_center" type="select" label="Column Center (sample)">
         <option value="x">No column Center</option>
         <option value="a">Substact mean of column</option>
         <option value="m">Substact median of column</option>
      </param>
      <param name="col_normalize" type="boolean" label="Normalize Columns (sample)"/>
      
      
      <param name="col_algorithm" type="select" label="Column (sample) clustering">
		<option value="0">No clustering</option>
		<option value="1">Uncentered correlation</option>
		<option value="2">Pearson correlation</option>
		<option value="3">Uncentered correlation, absolute value</option>
		<option value="4">Pearson correlation, absolute value</option>
		<option value="5">Spearman's rank correlation</option>
		<option value="6">Kendall's tau</option>
		<option value="7">Euclidean distance</option>
		<option value="8">City-block distance</option>
      </param>
      
      <param name="row_algorithm" type="select" label="Row (gene) clustering">
		<option value="0">No clustering</option>
		<option value="1">Uncentered correlation</option>
		<option value="2">Pearson correlation</option>
		<option value="3">Uncentered correlation, absolute value</option>
		<option value="4">Pearson correlation, absolute value</option>
		<option value="5">Spearman's rank correlation</option>
		<option value="6">Kendall's tau</option>
		<option value="7">Euclidean distance</option>
		<option value="8">City-block distance</option>
      </param>
      
      <param name="hclustermethod" type="select" label="Hierarchical clustering method">
		<option value="x">Off</option>
		<option value="m">Pairwise complete-linkage</option>
		<option value="s">Pairwise single-linkage</option>
		<option value="c">Pairwise centroid-linkage</option>
		<option value="a">Pairwise average-linkage</option>
      </param>
      
      <param name="knum" type="integer" optional="true" label="K-Means count"/>
      <param name="kcount" type="integer" optional="true" label="K-Means run count"/>
      
      <param name="prow" type="boolean" label="Principal Component Analysis to rows (genes) instead of clustering"/>
      <param name="pcol" type="boolean" label="Principal Component Analysis to cols (samples) instead of clustering"/>
      
      
  </inputs>
  <outputs>
      <data name="cdtfile" format="cdt"/>
       <data format="atr" name="atrfile" >
          <filter>col_algorithm != "0"</filter>
       </data>
       <data format="atr" name="atrfile" >
          <filter>col_algorithm != "0"</filter>
       </data>
       <data format="gtr" name="gtrfile" >
          <filter>row_algorithm != "0"</filter>
       </data>       
  </outputs>
  	<configfiles>

  <configfile name="scriptfile"><![CDATA[#!/usr/bin/env python
import subprocess
import shutil

cmd = ["cluster", "-f", "$filename", "-u", "galaxy_cluster"]

if "$col_algorithm" != "0":
	cmd.extend( ['-e', '$col_algorithm'] )

if "$row_algorithm" != "0":
	cmd.extend( ['-g', '$row_algorithm'] )

if len("$knum"):
	cmd.extend(['-k', '$knum'])

if len("$kcount"):
	cmd.extend(['-k', '$kcount'])

if "$col_normalize" == "true":
	cmd.append("-na")

if "$row_normalize" == "true":
	cmd.append("-ng")

if "$log_transform" == "true":
	cmd.append("-l")

print cmd

proc = subprocess.Popen(cmd)
proc.communicate()

shutil.move("galaxy_cluster" + ".cdt", "$cdtfile")

if "$col_algorithm" != "0":
	shutil.move("galaxy_cluster" + ".atr", "$atrfile")

if "$row_algorithm" != "0":
	shutil.move("galaxy_cluster" + ".gtr", "$gtrfile")


]]></configfile>
  	</configfiles>
<help>

A Wrapper for the Cluster3.0 library http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm

Source code at http://bonsai.hgc.jp/~mdehoon/software/cluster/cluster-1.50.tar.gz

For command line version, 
./configure --without-x
make
make install

</help>
</tool>