Mercurial > repos > kellrott > cluster3
diff cluster3.xml @ 0:cde61e2fea1e draft default tip
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author | kellrott |
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date | Wed, 25 Jul 2012 12:23:22 -0400 |
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--- /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>