Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced

changeset 7:c5489978071a draft

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Uploaded
author insilico-bob
date Tue, 28 Jan 2020 15:33:09 -0500
parents 1f13d304ddbd
children c1be063b2454
files GalaxyMapGen.jar heatmap_advanced.sh mda_advanced_heatmap_gen.xml mda_heatmap_viz.zip
diffstat 4 files changed, 56 insertions(+), 40 deletions(-) [+]
line wrap: on
line diff
Binary file GalaxyMapGen.jar has changed
--- a/heatmap_advanced.sh	Thu Jun 20 11:36:53 2019 -0400
+++ b/heatmap_advanced.sh	Tue Jan 28 15:33:09 2020 -0500
@@ -59,11 +59,17 @@
 	if [ $ctr -gt 1 ]
 	then
 		currParm=$(cut -d'|' -f1 <<< $i)
-		if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "attribute" ]
+		if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "attribute" ] && [ $currParm != "chm_name" ]
 		then
 			#Parse pipe-delimited parameter parameter
 			parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",'
 	  	fi
+		if [ $currParm = "chm_name" ]
+		then
+			currVal=$(cut -d'|' -f2 <<< $i)
+			currEdit=$(echo "$currVal"  | sed 's/\//_/g')		
+			parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$currEdit'",'
+	  	fi
 		if [ $currParm = "row_configuration" ]
 		then
 			rowOrder=$(cut -d'|' -f3 <<< $i)
@@ -318,7 +324,10 @@
 		classIter=$((classIter+1))
 		className=$(cut -d'|' -f3 <<< $i)
 		#Parse pipe-delimited 3-part classification bar parameter
-		classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"'
+		if [[ -z "$className" ]]; then
+		   className="covar"$classIter
+		fi
+		classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$className'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"'
 		classCat=$(cut -d'|' -f7 <<< $i)
 		classColorType=$(cut -d'_' -f2 <<< $classCat)
 		classJson=$classJson','
@@ -357,8 +366,12 @@
   if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
   then
     echo "";
-    echo "NOTE 1: This error can occur when a covariate file has inadvertently been selected as an Input Matrix.  Check your Input Matrix entry.";
-    echo "NOTE 2: This error can occur when there is no variation in a data rows or columns in the input matrix.  Try a different distance measure or remove rows/columns without variation.";
+    echo "";
+    echo "R CLUSTERING: Error in clustering the matrix provided (View Details  stdout).   "
+    echo "Note: This error can occur when:"
+    echo "   1. There is invalid numeric data in the matrix provided. Try using Matrix Manipulation tools to fix invalid data.";
+    echo "   2. There is no variation in a row or column in the matrix.  Try a different distance measure or remove rows/columns without variation using Matrix Manipulation tools.";
+    echo "   3. A covariate file has inadvertently been selected as an Input Matrix.  Check your Input Matrix entry.";
   fi
   exit $rc;
 fi
--- a/mda_advanced_heatmap_gen.xml	Thu Jun 20 11:36:53 2019 -0400
+++ b/mda_advanced_heatmap_gen.xml	Tue Jan 28 15:33:09 2020 -0500
@@ -26,14 +26,12 @@
     <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"/>
+	    <sanitizer>
+        	<valid initial="string.printable">
             	<remove value="&quot;"/>
             	<remove value="&apos;"/>
-                <remove value=" "/> 
               </valid>
-           </sanitizer>
+	    </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>
@@ -73,23 +71,19 @@
 	    </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"/>
+	    <sanitizer>
+        	<valid initial="string.printable">
             	<remove value="&quot;"/>
             	<remove value="&apos;"/>
-                <remove value=" "/> 
               </valid>
-           </sanitizer>
+	    </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"/>
+	    <sanitizer>
+        	<valid initial="string.printable">
             	<remove value="&quot;"/>
             	<remove value="&apos;"/>
-                <remove value=" "/> 
               </valid>
-           </sanitizer>
+	    </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>
@@ -183,6 +177,8 @@
 			    <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"/>
+	  		    <param name="rowDendroShow" type="text" size="0" hidden="true"   value="ALL"/>
+	  		    <param name="rowDendroHeight" 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>
@@ -200,6 +196,8 @@
 			    <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"/>
+	  		    <param name="rowDendroShow" type="text" size="0" hidden="true"   value="ALL"/>
+	  		    <param name="rowDendroHeight" 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>
@@ -318,6 +316,8 @@
 		    <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"/>
+  		    <param name="columnDendroShow" type="text" size="0" hidden="true"   value="ALL"/>
+  		    <param name="columnDendroHeight" 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>
@@ -335,6 +335,8 @@
 		    <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"/>
+  		    <param name="columnDendroShow" type="text" size="0" hidden="true"   value="ALL"/>
+  		    <param name="columnDendroHeight" 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>
@@ -373,17 +375,22 @@
     </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"/>
+	    <sanitizer>
+        	<valid initial="string.printable">
             	<remove value="&quot;"/>
             	<remove value="&apos;"/>
-                <remove value=" "/> 
               </valid>
-           </sanitizer>
+	    </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.">
+		    <sanitizer>
+	        	<valid initial="string.digits">
+	            	<remove value="&quot;"/>
+	            	<remove value="&apos;"/>
+	              </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>
@@ -459,24 +466,20 @@
      </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"/>
+	    <sanitizer>
+        	<valid initial="string.printable">
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
               </valid>
-              <mapping initial="">
-              </mapping>
-           </sanitizer>
+	    </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"/>
+	    <sanitizer>
+        	<valid initial="string.printable">
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
               </valid>
-              <mapping initial="">
-              </mapping>
-           </sanitizer>
+	    </sanitizer>
         </param>
     </repeat>       
   </inputs>
Binary file mda_heatmap_viz.zip has changed