--- a/rgToolFactory.xml	Sat Jun 02 20:02:11 2012 +1000
+++ b/rgToolFactory.xml	Sat Jun 02 21:08:57 2012 +1000
@@ -5,10 +5,13 @@
      rgToolFactory.py --bad_user $__user_email__
   #else:
     rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 
-     --tool_name "$tool_name"  --input_tab "$input1" 
+     --tool_name "$tool_name"  
     #if $make_HTML.value=="yes" or $factory.make_Tool=="yes":
       --output_dir "$html_file.files_path" --output_html "$html_file"
     #end if
+    #if $input1.value != 'None':
+       --input_tab "$input1"
+    #end if
     #if $make_HTML.value=="yes":
     --make_HTML "yes"
     #end if
@@ -78,21 +81,24 @@
 <configfile name="runme">
 ${dynScript}
 </configfile>
+
+<configfile name="helpme">
 #if $factory.make_Tool == "yes":
-<configfile name="helpme">
 $factory.help_text
+#end if
 </configfile>
-#end if
-
 </configfiles>
 <help>
 **What it does**
 This tool enables a user to paste and submit an arbitrary R/python/perl script to run in Galaxy.
-This is (extremely) insecure.
+This is (extremely) insecure. However, once you get the script working on some test data, you can generate a complete ready to run
+Galaxy tool by setting the "Make tool" option to Yes. The resulting tarball will be ready to install
+It will run like as securely as any other Galaxy tool - unlike this one used to generate it.
 
 **Restrictions**
 This tool will ONLY work if your user id has been added to the local copy's list of permitted users.
-Ask your friendly Galaxy administrator to edit this tool's source for you if you need this.
+It should only ever be used on a private, personal Galaxy instance and you should edit this tool's source so your local login
+is authorised to use it - == it will not run otherwise ==
 
 **Note to system administrators**
 Under no circumstances should you allow any user to use this tool unless you really, really trust them to do
@@ -122,6 +128,16 @@
  outp = t(inp)
  write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
 
+A more complex example takes no input file but generates a random heatmap pdf - you must make sure the option to create an HTML output file is
+turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page::
+
+ foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
+ bar = as.matrix(foo)
+ pdf( "heattest.pdf" )
+ heatmap(bar,main='Random Heatmap')
+ dev.off()
+
+
 </help>
 
 </tool>