diff mda_advanced_heatmap_gen.xml @ 39:436f03b71cf6 draft

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author insilico-bob
date Thu, 20 Jun 2019 11:31:24 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mda_advanced_heatmap_gen.xml	Thu Jun 20 11:31:24 2019 -0400
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+<?xml version="1.0" encoding="UTF-8" ?>
+<tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.3">
+  <requirements>
+       <requirement type="package" version="3.4.1">r-base</requirement> 
+		<requirement type="package" version="8.0.144">openjdk</requirement>
+  </requirements>
+  <description> Create Clustered Heat Maps with Advanced Options</description>
+<command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh  "$__tool_directory__" "$__tool_data_path__/" "chm_name|Heat_Map_$hmname" "chm_description|$hmdesc" "summary_width|$summaryDisplayWidth"
+	"row_configuration|order_method|${d_rows.rowOrderMethod}|distance_metric|${d_rows.rowDistanceMeasure}|agglomeration_method|${d_rows.rowAgglomerationMethod}|tree_covar_cuts|${d_rows.rowDendroCut}|data_type|$rowDataType|top_items|$rowTopItems|tree_cuts|${d_rows.rcutrows.rowDendroTreeCut}|${d_rows.rcutrows.raddcuts}|dendro_show|${d_rows.rowDendroShow}|dendro_height|${d_rows.rowDendroHeight}"      
+	"col_configuration|order_method|${d_cols.columnOrderMethod}|distance_metric|${d_cols.columnDistanceMeasure}|agglomeration_method|${d_cols.columnAgglomerationMethod}|tree_covar_cuts|${d_cols.colDendroCut}|data_type|$colDataType|top_items|$colTopItems|tree_cuts|${d_cols.ccutrows.colDendroTreeCut}|${d_cols.ccutrows.caddcuts}|dendro_show|${d_cols.columnDendroShow}|dendro_height|${d_cols.columnDendroHeight}"    
+    #for $attr in $hm_attribute
+      'attribute|${attr.attrbute_key}':'${attr.attrbute_value}'
+    #end for
+    #for $mx in $matrices
+	   'matrix_files|path|$mx.dataLayer|name|${mx.dataLayerName}|summary_method|${mx.summarymethod}|selection_color|${mx.dataLayerSelectionColor}|cuts_color|${mx.dataLayerCutsColor}|grid_color|${mx.dataLayerGridColor}|grid_show|${mx.dataLayerGridShow}|${mx.colorsBreaks.setColorsBreaks}|${mx.colorsBreaks.matrixColor1}|${mx.colorsBreaks.matrixColor2}|${mx.colorsBreaks.matrixColor3}|${mx.colorsBreaks.matrixBreak1}|${mx.colorsBreaks.matrixBreak2}|${mx.colorsBreaks.matrixBreak3}|${mx.colorsBreaks.missingColor}'
+    #end for
+    #for $op in $operations
+       'classification|name|${op.class_name}|path|${op.repeatinput.file_name}|category|${op.cattype.cat}|bar_type|${op.cattype.scatbar.bartype}|height|${op.classHeight}|fg_color|${op.cattype.scatbar.fg_color}|bg_color|${op.cattype.scatbar.bg_color}'
+    #end for
+ 	'output_location|$output' 
+ </command>
+	<stdio>
+      <exit_code range="1:" level="fatal" />
+	</stdio>
+  <inputs>
+    <repeat name="matrices" title="Heat Map Matrices">
+    	<param name="dataLayer" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/>
+    	<param name="dataLayerName" size="40" type="text" value="Data_Layer_name"  label="Data Layer Name" help="Name for data layer (no spaces).">
+           <sanitizer>
+              <valid>
+                <add preset="string.printable"/>
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
+                <remove value=" "/> 
+              </valid>
+           </sanitizer>
+        </param>   
+	    <param name="summarymethod" type="select"  label="Data Summarization Method" help="For large matrices, the selected method is used to aggregate data values in the summary view.">
+			<option value="average">Average</option>
+			<option value="sample">Sample</option>
+			<option value="mode">Mode</option>
+	    </param>
+  		<conditional name="colorsBreaks">
+			<param name="setColorsBreaks" type="select" label="Colors and Breakpoints" help="Select whether to set your own colors and breakpoints or use default values.">
+				<option value="none">Use System Generated Colors and Breakpoints</option>
+				<option value="defined">Define Your Own Colors and Breakpoints</option>	    
+			</param>
+	       	<when value="none">
+	 		    	<param name="matrixColor1" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="matrixBreak1" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="matrixColor2" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="matrixBreak2" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="matrixColor3" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="matrixBreak3" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="missingColor" type="text" size="0" hidden="true" value="0"/>
+	       	</when>
+	       	<when value="defined">
+ 					<param name="matrixColor1" type="color" label="Color for Breakpoint One" value="#ff0000"/>
+ 					<param name="matrixBreak1" type="text" label="Value for Breakpoint One" value="-1"/>
+ 					<param name="matrixColor2" type="color" label="Color for Breakpoint Two" value="#ffffff"/>
+ 					<param name="matrixBreak2" type="text" label="Value for Breakpoint Two" value="0"/>
+ 					<param name="matrixColor3" type="color" label="Color for Breakpoint Three" value="#0000ff"/>
+ 					<param name="matrixBreak3" type="text" label="Value for Breakpoint Three" value="1"/>
+ 					<param name="missingColor" type="color" label="Color for Missing Values" value="#000000"/> 
+	        </when>
+        </conditional>
+	   	<param name="dataLayerSelectionColor" type="color" label="Color for selection box" value="#00ff38"/>
+   		<param name="dataLayerCutsColor" type="color" label="Color for Heat Map Gaps" value="#ffffff"/>
+   		<param name="dataLayerGridColor" type="color" label="Color for Heat Map Grid" value="#ffffff"/>
+	    <param name="dataLayerGridShow" type="select"  label="Show Heat Map Grid">
+			<option value="Y">Yes</option>
+			<option value="N">No</option>
+	    </param>
+    </repeat>
+    <param name="hmname" size="40" type="text" value="Heat_Map_name"  label="Heat Map Name" help="Short Name for heat map (no spaces)."/>
+           <sanitizer>
+              <valid>
+                <add preset="string.printable"/>
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
+                <remove value=" "/> 
+              </valid>
+           </sanitizer>
+    <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="Heat Map Description" help="Longer description of the heat map contents."/>
+           <sanitizer>
+              <valid>
+                <add preset="string.printable"/>
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
+                <remove value=" "/> 
+              </valid>
+           </sanitizer>
+    <param name="summaryDisplayWidth" 	type="select"  label="Summary Display Width %" help="Sets the percentage of the viewer display of the summary panel.">
+		<option value="50">50%</option>
+		<option value="10">10%</option>
+		<option value="20">20%</option>
+		<option value="30">30%</option>
+		<option value="40">40%</option>
+		<option value="60">60%</option>
+		<option value="70">70%</option>
+		<option value="80">80%</option>
+		<option value="90">90%</option>
+    </param>
+      <conditional name="d_rows">
+			<param name="rowOrderMethod" type="select" label="Row ordering method" help="Determine if rows should be clustered, randomized, or remain as is.">
+				<option value="Hierarchical">Hierarchical Clustering</option>
+				<option value="Original">Original Order</option>	    
+				<option value="Random">Random</option>	    
+			</param>
+	        <when value="Hierarchical">
+				<param name="rowDistanceMeasure" type="select"  label="Row Distance Metric" help="For clustering, select the method of determining distance between rows.">
+					<option value="euclidean">Euclidean</option>
+					<!-- <option value="binary">Binary</option> ** breaks dendrogram -->
+					<option value="manhattan">Manhattan</option>
+					<option value="maximum">Maximum</option>
+					<!-- <option value="canberra">Canberra</option>	     ** breaks dendrogram  -->
+					<option value="minkowski">Minkowski</option>	    
+					<!-- <option value="correlation">Correlation</option>  ** breaks dendrogram	 -->    
+				</param>
+				<param name="rowAgglomerationMethod" type="select"  label="Row Clustering Method" help="For clustering, select algorithm for building clusters.">
+					<option value="average">Average Linkage</option>
+					<option value="complete">Complete Linkage</option>
+					<option value="single">Single Linkage</option>
+					<option value="ward" selected="true">Ward</option>
+					<option value="mcquitty">Mcquitty</option>	    
+					<!-- <option value="median">Median</option> ** breaks dendrogram	    
+					<option value="centroid">Centroid</option>	** breaks dendrogram -->    
+				</param>
+				<param name="rowDendroShow" type="select"  label="Show Row Dendrogram" help="For setting the visibility of the row dendrogram.">
+					<option value="ALL">Summary and Detail</option>
+					<option value="SUMMARY">Summary Only</option>
+					<option value="NONE">Hide</option>
+	    		</param>
+				<param name="rowDendroHeight" type="select"  label="Row Dendrogram Display Height" help="For adjusting the displayed height of the dendrogram bar.">
+					<option value="100">100%</option>
+					<option value="50">50%</option>
+					<option value="75">75%</option>
+					<option value="125">125%</option>
+					<option value="150">150%</option>
+					<option value="200">200%</option>
+	    		</param>
+	            <param name="rowDendroCut" type="select" label="Row Cluster Covariate Bar" help="To generate a row covariate bar based on clusters, select the number of clusters(classes) to use.">
+	        		<option value="0" selected="true" >None</option>
+	        		<option value="2" >2</option>
+	        		<option value="3" >3</option>
+	        		<option value="4" >4</option>
+	        		<option value="5" >5</option>
+	        		<option value="6" >6</option>
+	        		<option value="7" >7</option>
+	        		<option value="8" >8</option>
+	        		<option value="9" >9</option>
+	        		<option value="10" >10</option>
+	            </param>
+     			<conditional name="rcutrows">
+					<param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
+						<option value="none">None</option>
+						<option value="treecuts">Cluster-Based Gaps</option>	    
+						<option value="positional">Fixed Gaps</option>	    
+					</param>
+		        	<when value="none">
+		  		    	<param name="rowDendroTreeCut" type="text" size="0" hidden="true"   value="0"/>
+		        	</when>
+		        	<when value="treecuts">
+			            <param name="rowDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters." >
+			        		<option value="0" selected="true" >None</option>
+			        		<option value="2" >2</option>
+			        		<option value="3" >3</option>
+			        		<option value="4" >4</option>
+			        		<option value="5" >5</option>
+			        		<option value="6" >6</option>
+			        		<option value="7" >7</option>
+			        		<option value="8" >8</option>
+			        		<option value="9" >9</option>
+			        		<option value="10" >10</option>
+			            </param>
+			        </when>
+		        	<when value="positional">
+		  		    	<param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
+					</when>
+			    </conditional>
+	        </when>
+	        <when value="Original">
+			    <param name="rowDistanceMeasure" type="text" size="0"   hidden="true"   value="n/a"/>
+			    <param name="rowAgglomerationMethod" type="text" size="0"  hidden="true"    value="n/a"/>
+	  		    <param name="rowDendroCut" type="text" size="0" hidden="true"   value="0"/>
+     			<conditional name="rcutrows">
+					<param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
+						<option value="none">None</option>
+						<option value="positional">Fixed Gaps</option>	    
+					</param>
+		        	<when value="none">
+  		    			<param name="rowDendroTreeCut" type="text" size="100" value="None"  hidden="true"/>
+		        	</when>
+		        	<when value="positional">
+  		    			<param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
+		        	</when>
+		        </conditional>
+	        </when>
+	        <when value="Random">
+			    <param name="rowDistanceMeasure" type="text" size="0"  hidden="true"    value="n/a"/>
+			    <param name="rowAgglomerationMethod" type="text" size="0"  hidden="true"    value="n/a"/>
+	 		    <param name="rowDendroCut" type="text" size="0" hidden="true"    value="0"/>
+     			<conditional name="rcutrows">
+					<param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
+						<option value="none">None</option>
+						<option value="positional">Fixed Gaps</option>	    
+					</param>
+		        	<when value="none">
+  		    			<param name="rowDendroTreeCut" type="text" size="100" value="None"  hidden="true"/>
+		        	</when>
+		        	<when value="positional">
+  		    			<param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
+		        	</when>
+		        </conditional>
+	        </when>
+    </conditional>
+	<param name="rowTopItems" size="100" type="text" value="None" label="Row Top Items" help="A few rows can be labeled in the full summary heat map. To do so provide a comma delimited list of row labels."/>
+    <param name="rowDataType" type="select" label="Row Label Type" help="Enable label driven link-outs by specifying the type of row labels.">
+        <option value="labels" selected="true" >None</option>
+        <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
+        <option value="bio.feature.agilent" >Agilent Id</option>
+        <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
+        <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
+        <option value="bio.gene.entrez" >Gene Entrez Id</option>
+        <option value="bio.gene.hugo" >Gene HUGO symbol</option>
+        <option value="bio.go" >Gene Ontology (GO) Id</option>
+        <option value="bio.geo.acc" >GEO Accession Id</option>
+        <option value="bio.probe.illumina" >Illumina Probe Id</option>
+        <option value="bio.probe.infinium" >Infinium Probe Id</option>
+        <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
+        <option value="bio.mirna" >miRNA Id</option>
+        <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
+        <option value="bio.pubmed" >Pubmed Id</option>
+        <option value="bio.pubmed.search" >Pubmed Search Term</option>
+        <option value="scholar" >Scholarly term</option>
+        <option value="bio.gene.unigene" >Unigene CId</option>
+        <option value="bio.protein.uniprot" >UniProt Id</option>
+    </param>    
+	<conditional name="d_cols">
+		<param name="columnOrderMethod" type="select" label="Column ordering method" help="Determine if columns should be clustered, randomized, or remain as is.">
+			<option value="Hierarchical">Hierarchical Clustering</option>
+			<option value="Original">Original Order</option>	    
+			<option value="Random">Random</option>	    
+		</param>
+        <when value="Hierarchical">
+			<param name="columnDistanceMeasure" type="select"  label="Column Distance Metric" help="For clustering, select the method of determining distance between columns.">
+				<option value="euclidean">Euclidean</option>
+				<!-- <option value="binary">Binary</option> ** breaks dendrogram  -->
+				<option value="manhattan">Manhattan</option>
+				<option value="maximum">Maximum</option>
+				<!-- <option value="canberra">Canberra</option> ** breaks dendrogram  -->	    
+				<option value="minkowski">Minkowski</option>	    
+				<!-- <option value="correlation">Correlation</option>	** breaks dendrogram     -->
+			</param>
+			<param name="columnAgglomerationMethod" type="select"  label="Column Clustering Method" help="For clustering, select algorithm for building clusters.">
+				<option value="average">Average Linkage</option>
+				<option value="complete">Complete Linkage</option>
+				<option value="single">Single Linkage</option>
+				<option value="ward" selected="true">Ward</option>
+				<option value="mcquitty">Mcquitty</option>	    
+				<!-- <option value="median">Median</option>	  ** breaks dendrogram  
+				<option value="centroid">Centroid</option>	** breaks dendrogram     -->
+			</param>
+			<param name="columnDendroShow" type="select"  label="Show Column Dendrogram" help="For setting the visibility of the column dendrogram.">
+					<option value="ALL">Summary and Detail</option>
+					<option value="SUMMARY">Summary Only</option>
+					<option value="NONE">Hide</option>
+    		</param>
+			<param name="columnDendroHeight" type="select"  label="Column Dendrogram Display Height" help="For adjusting the displayed height of the dendrogram bar.">
+					<option value="100">100%</option>
+					<option value="50">50%</option>
+					<option value="75">75%</option>
+					<option value="125">125%</option>
+					<option value="150">150%</option>
+					<option value="200">200%</option>
+    		</param>
+           <param name="colDendroCut" type="select" label="Column Cluster Covariate Bar" help="To generate a column covariate bar based on clusters, select the number of clusters(classes) to use.">
+        		<option value="0" selected="true" >None</option>
+        		<option value="2" >2</option>
+        		<option value="3" >3</option>
+        		<option value="4" >4</option>
+        		<option value="5" >5</option>
+        		<option value="6" >6</option>
+        		<option value="7" >7</option>
+        		<option value="8" >8</option>
+        		<option value="9" >9</option>
+        		<option value="10" >10</option>
+            </param>
+   			<conditional name="ccutrows">
+				<param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
+					<option value="none">None</option>
+					<option value="treecuts">Cluster-Based Gaps</option>	    
+					<option value="positional">Fixed Gaps</option>	    
+				</param>
+	        	<when value="none">
+	  		    	<param name="colDendroTreeCut" type="text" size="0" hidden="true"   value="0"/>
+	        	</when>
+	        	<when value="treecuts">
+		            <param name="colDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters.">
+		        		<option value="0" selected="true" >None</option>
+		        		<option value="2" >2</option>
+		        		<option value="3" >3</option>
+		        		<option value="4" >4</option>
+		        		<option value="5" >5</option>
+		        		<option value="6" >6</option>
+		        		<option value="7" >7</option>
+		        		<option value="8" >8</option>
+		        		<option value="9" >9</option>
+		        		<option value="10" >10</option>
+		            </param>
+		        </when>
+	        	<when value="positional">
+	  		    	<param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
+		        </when>
+		    </conditional>
+        </when>
+        <when value="Original">
+		    <param name="columnDistanceMeasure" type="text" size="0" hidden="true"    value="n/a"/>
+		    <param name="columnAgglomerationMethod" type="text" size="0"   hidden="true"  value="n/a"/>
+		    <param name="colDendroCut" type="text" size="0"  hidden="true"   value="0"/>
+   			<conditional name="ccutrows">
+				<param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
+					<option value="none">None</option>
+					<option value="positional">Fixed Gaps</option>	    
+				</param>
+	        	<when value="none">
+ 		    			<param name="colDendroTreeCut" type="text" size="100" value="None"  hidden="true"/>
+	        	</when>
+	        	<when value="positional">
+ 		    			<param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
+	        	</when>
+	        </conditional>
+         </when>
+        <when value="Random">
+		    <param name="columnDistanceMeasure" type="text" size="0"  hidden="true"   value="n/a"/>
+		    <param name="columnAgglomerationMethod" type="text" size="0"  hidden="true"   value="n/a"/>
+		    <param name="colDendroCut" type="text" size="0"  hidden="true"   value="0"/>
+   			<conditional name="ccutrows">
+				<param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
+					<option value="none">None</option>
+					<option value="positional">Fixed Gaps</option>	    
+				</param>
+	        	<when value="none">
+ 		    			<param name="colDendroTreeCut" type="text" size="100" value="None"  hidden="true"/>
+	        	</when>
+	        	<when value="positional">
+ 		    			<param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
+	        	</when>
+	        </conditional>
+        </when>
+    </conditional>
+	<param name="colTopItems" size="100" type="text" value="None" label="Column Top Items" help="A few columns can be labeled in the full summary heat map. To do so provide a comma delimited list of column labels."/>
+    <param name="colDataType" type="select" label="Column Label Type" help="Enable label driven link-outs by specifying the type of column labels.">
+        <option value="labels" selected="true" >None</option>
+        <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
+        <option value="bio.feature.agilent" >Agilent Id</option>
+        <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
+        <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
+        <option value="bio.gene.entrez" >Gene Entrez Id</option>
+        <option value="bio.gene.hugo" >Gene HUGO symbol</option>
+        <option value="bio.go" >Gene Ontology (GO) Id</option>
+        <option value="bio.geo.acc" >GEO Accession Id</option>
+        <option value="bio.probe.illumina" >Illumina Probe Id</option>
+        <option value="bio.probe.infinium" >Infinium Probe Id</option>
+        <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
+        <option value="bio.mirna" >miRNA Id</option>
+        <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
+        <option value="bio.pubmed" >Pubmed Id</option>
+        <option value="bio.pubmed.search" >Pubmed Search Term</option>
+        <option value="scholar" >Scholarly term</option>
+        <option value="bio.gene.unigene" >Unigene CId</option>
+        <option value="bio.protein.uniprot" >UniProt Id</option>
+    </param>    
+    <repeat name="operations" title="Covariate Bars">
+        <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label.">
+           <sanitizer>
+              <valid>
+                <add preset="string.printable"/>
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
+                <remove value=" "/> 
+              </valid>
+           </sanitizer>
+        </param>
+        <param name="repeatinput" type="data" format="Tabular" label="Covariate File" help="Tab delimited text file with row or column label and covariate value on each line."/>
+		<param name="classHeight" size="10" type="text" value="15" label="Covariate Display Height" help="Set the display height for column covariates and width for row covariates."/>
+        <conditional name="cattype">
+			<param name="cat" type="select" label="Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values.">
+			  <option value="row_discrete" >Row Categorical</option>
+			  <option value="row_continuous" >Row Continuous</option>
+			  <option value="column_discrete" >Column Categorical</option>
+			  <option value="column_continuous" >Column Continuous</option>
+			</param>
+	        <when value="row_continuous">
+        		<conditional name="scatbar">
+			 		<param name="bartype" type="select" label="Display Type">
+					  <option value="color_plot" >Standard</option>
+					  <option value="bar_plot" >Bar Plot</option>
+					  <option value="scatter_plot" >Scatter Plot</option>
+					</param>
+	        		<when value="color_plot">
+ 						<param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
+ 						<param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
+	        		</when>
+	        		<when value="bar_plot">
+ 						<param name="bg_color" type="color" label="Color for Bar Plot Background" value="#ffffff"/>
+ 						<param name="fg_color" type="color" label="Color for Bar Plot Foreground" value="#000000"/>
+	        		</when>
+	        		<when value="scatter_plot">
+ 						<param name="bg_color" type="color" label="Color for Scatter Plot Background" value="#ffffff"/>
+ 						<param name="fg_color" type="color" label="Color for Scatter Plot Foreground" value="#000000"/>
+	        		</when>
+	        	</conditional>
+	        </when>
+	        <when value="column_continuous">
+        		<conditional name="scatbar">
+			 		<param name="bartype" type="select" label="Display Type">
+					  <option value="color_plot" >Standard</option>
+					  <option value="bar_plot" >Bar Plot</option>
+					  <option value="scatter_plot" >Scatter Plot</option>
+					</param>
+	        		<when value="color_plot">
+ 						<param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
+ 						<param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
+	        		</when>
+	        		<when value="bar_plot">
+ 						<param name="bg_color" type="color" label="Color for Bar Plot Background" value="#ffffff"/>
+ 						<param name="fg_color" type="color" label="Color for Bar Plot Foreground" value="#000000"/>
+	        		</when>
+	        		<when value="scatter_plot">
+ 						<param name="bg_color" type="color" label="Color for Scatter Plot Background" value="#ffffff"/>
+ 						<param name="fg_color" type="color" label="Color for Scatter Plot Foreground" value="#000000"/>
+	        		</when>
+	        	</conditional>
+	        </when>
+	        <when value="column_discrete">
+         		<conditional name="scatbar">
+					<param name="bartype" type="select" hidden="true">
+					  <option value="color_plot" >Standard</option>
+					</param>
+ 	        		<when value="color_plot">
+						<param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
+ 						<param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
+ 					</when>
+	        	</conditional>
+	        </when>
+	        <when value="row_discrete">
+         		<conditional name="scatbar">
+					<param name="bartype" type="select" hidden="true">
+					  <option value="color_plot" >Standard</option>
+					</param>
+ 	        		<when value="color_plot">
+						<param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
+ 						<param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
+ 					</when>
+	        	</conditional>
+	        </when>
+	 	</conditional>
+     </repeat>       
+     <repeat name="hm_attribute" title="Heat Map Attributes">
+        <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attribute Key" help="For map level attributes. Enter the key (no spaces).">
+           <sanitizer invalid_char="_">
+              <valid initial="">
+                <add preset="string.letters"/>
+                <add preset="string.digits"/>
+              </valid>
+              <mapping initial="">
+              </mapping>
+           </sanitizer>
+        </param>
+        <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes Value" help="For map level attributes. Enter the value (no spaces).">
+           <sanitizer invalid_char="_">
+              <valid initial="">
+                <add preset="string.letters"/>
+                <add preset="string.digits"/>
+              </valid>
+              <mapping initial="">
+              </mapping>
+           </sanitizer>
+        </param>
+    </repeat>       
+  </inputs>
+  <outputs>
+    <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
+  </outputs>
+ <tests>
+    <test>
+      <param name="inputmatrix" value="400x400.txt" />
+      <param name="hmname" value="testRun" />
+      <param name="$hmdesc" value="validateTool" />
+      <param name="summarymethod" value="Average" />
+      <param name="rowOrderMethod" value="Hierarchical" />
+      <param name="rowDistanceMeasure" value="Manhattan" />
+      <param name="rowAgglomerationMethod" value="Ward" />
+      <param name="columnOrderMethod" value="Hierarchical" />
+      <param name="columnDistanceMeasure" value="Manhattan" />
+      <param name="columnAgglomerationMethod" value="Ward" />
+      <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />     
+
+    </test>
+<!--   galaxy/test-data/    dir where the input and output file that should match tool output will be copied -->
+  </tests>
+ </tool>