diff mda_heatmap_gen.xml @ 34:58437af2d675 draft

Uploaded

--- a/mda_heatmap_gen.xml	Tue Dec 05 14:57:34 2017 -0500
+++ b/mda_heatmap_gen.xml	Thu Feb 08 14:45:46 2018 -0500
@@ -1,8 +1,10 @@
 <?xml version="1.0" encoding="UTF-8" ?>
-<tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.1.1">
-  <description>Create Clustered Heat Maps</description>
-<!-- <command interpreter="python" detect_errors="aggressive">$__tool_directory__/mda_heatmap_gen.py  'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' 0 0 labels labels 'None'-->
-   <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh  "standard" "Heat_Map_$hmname" "$hmdesc" '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__/' 0 0 labels labels 'None'
+<tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.3">
+   <requirements>
+     <requirement type="package" version="3.4.1">r-base</requirement> 
+   </requirements>
+   <description>Create Clustered Heat Maps</description>
+   <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh  "standard" "Heat_Map_$hmname" "$hmdesc" '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__;$__tool_data_path__/' 0 0 labels labels 'None'
     #for $op in $operations
        ${op.class_name}
        ${op.repeatinput.file_name}
@@ -15,8 +17,33 @@
 	</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="20" type="text" value="Heat_Map_name"  label="Heat Map Name" help="Short Name for heat map (no spaces)."/>
+    <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"/>
+<!--            <add value="string.letters"/>
+                <add value="string.digits"/>
+                <add value="-"/>
+                <add value="_"/>
+-->
+            	<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="_"/>
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
+                <remove value=" "/> 
+              </valid>
+           </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>
@@ -93,17 +120,17 @@
         </when>
     </conditional>
     <repeat name="operations" title="Covariate Bars">
-        <param name="class_name" size="20" type="text" value="" label="Covariate Name" help="Label for the covariate to display in the heat map.">
-           <sanitizer invalid_char="_">
-              <valid initial="none">
-                <add preset="string.letters"/>
-                <add preset="string.digits"/>
+        <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>
-              <mapping initial="none">
-              </mapping>
            </sanitizer>
         </param>
-        <param name="repeatinput" type="data" format="text" label="Covariate File" help="Tab delimited text file with row or column label and covariate value on each line."/>
+        <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.">
 	  <option value="row_categorical" >Row Categorical</option>
 	  <option value="row_continuous" >Row Continuous</option>