# HG changeset patch
# User kellrott
# Date 1343233402 14400
# Node ID cde61e2fea1ee1eef10dfc8839e6eb3257264093

Uploaded

diff -r 000000000000 -r cde61e2fea1e cluster3.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster3.xml	Wed Jul 25 12:23:22 2012 -0400
@@ -0,0 +1,131 @@
+<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>