# HG changeset patch
# User insilico-bob
# Date 1580243539 18000
# Node ID 8acca16f3921af8bd6c26d9bd45d9c3d4231f23e
# Parent  8f8ab332a05078219e95caec1e4f0378dbbc252a
Uploaded

diff -r 8f8ab332a050 -r 8acca16f3921 GalaxyMapGen.jar
Binary file GalaxyMapGen.jar has changed
diff -r 8f8ab332a050 -r 8acca16f3921 heatmap.sh
--- a/heatmap.sh	Thu Jun 20 11:39:46 2019 -0400
+++ b/heatmap.sh	Tue Jan 28 15:32:19 2020 -0500
@@ -42,11 +42,17 @@
 	if [ $ctr -gt 1 ]
 	then
 		currParm=$(cut -d'|' -f1 <<< $i)
-		if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ]
+		if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "chm_name" ]
 		then
 			#Parse pipe-delimited parameter parameter
 			parmJson=$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 <<< $i)
@@ -108,7 +114,11 @@
 	then
 		classIter=$((classIter+1))
 		#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 <<< $i)'"'
+		className=$(cut -d'|' -f3 <<< $i)
+		if [[ -z "$className" ]]; then
+		   className="covar"$classIter
+		fi
+		classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$className'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'"'
 		classCat=$(cut -d'|' -f7 <<< $i)
 		classColorType=$(cut -d'_' -f2 <<< $classCat)
 		classJson=$classJson','
@@ -135,8 +145,11 @@
   if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
   then
     echo "";
-    echo "Note: This error can occur when there is no variation in a row or column.  Try a different distance measure or remove rows/columns without variation.";
-    echo "This error may also be caused when a covariate file has inadvertently been selected as an Input Matrix.  Check your Input Matrix entry.";
+    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
diff -r 8f8ab332a050 -r 8acca16f3921 mda_heatmap_gen.xml
--- a/mda_heatmap_gen.xml	Thu Jun 20 11:39:46 2019 -0400
+++ b/mda_heatmap_gen.xml	Tue Jan 28 15:32:19 2020 -0500
@@ -19,28 +19,20 @@
 	</stdio>
   <inputs>
     <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."  />
-    <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"/>
+    <param name="hmname" size="40" type="text" value="Heat_Map_name"  label="Heat Map Name" help="Short Name for heat map (no spaces)." optional="false"/>
+	    <sanitizer>
+        	<valid initial="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"/>
-                <add value="string.letters"/>
-                <add value="string.digits"/>
-                <add value="-"/>
-                <add value="_"/>
+	    </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 initial="string.printable">
             	<remove value="&quot;"/>
             	<remove value="&apos;"/>
-                <remove value=" "/> 
               </valid>
-           </sanitizer>
+	    </sanitizer>
     <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>
@@ -117,15 +109,13 @@
         </when>
     </conditional>
     <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"/>
+        <param name="class_name" size="25" type="text" value="" label="Covariate Name" optional="false" help="Covariate heat map display label.">
+	    <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="cat" type="select" label="Axis Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values.">
diff -r 8f8ab332a050 -r 8acca16f3921 mda_heatmap_viz.zip
Binary file mda_heatmap_viz.zip has changed