--- a/rgToolFactory2.py	Sun Jan 11 22:01:27 2015 -0500
+++ b/rgToolFactory2.py	Sun Jan 11 23:03:00 2015 -0500
@@ -190,15 +190,15 @@
         self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
         self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
         self.xmlfile = '%s.xml' % self.toolname
-        s = open(self.opts.script_path,'r').readlines()
-        s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
-        self.script = '\n'.join(s)
+        rx = open(self.opts.script_path,'r').readlines()
+        rx = [x.rstrip() for x in rx] # remove pesky dos line endings if needed
+        self.script = '\n'.join(rx)
         fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
         tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
         tscript.write(self.script)
         tscript.close()
-        self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
-        self.escapedScript = '\n'.join([html_escape(x) for x in s])
+        self.indentedScript = "<![CDATA[%s]]>" % '\n'.join([' %s' % x for x in rx]) # for restructured text in help
+        self.escapedScript = "<![CDATA[%s]]>" % self.script)
         self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
         if opts.output_dir: # may not want these complexities 
             self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/savedeps.xml	Sun Jan 11 23:03:00 2015 -0500
@@ -0,0 +1,18 @@
+x
+xmlgoeshereBiocGenerics_0.8.0.tar.gz?raw=true</package>
+xmlgoeshereIRanges_1.20.7.tar.gz?raw=true</package>
+xmlgoeshereXVector_0.2.0.tar.gz?raw=true</package>
+xmlgoeshereGenomicRanges_1.14.4.tar.gz?raw=true</package>
+xmlgoeshereRcpp_0.11.3.tar.gz?raw=true</package>
+xmlgoeshereRcppArmadillo_0.4.600.0.tar.gz?raw=true</package>
+xmlgoesherelocfit_1.5-9.1.tar.gz?raw=true</package>
+xmlgoeshereBiobase_2.22.0.tar.gz?raw=true</package>
+xmlgoeshereDBI_0.3.1.tar.gz?raw=true</package>
+xmlgoeshereRSQLite_1.0.0.tar.gz?raw=true</package>
+xmlgoeshereAnnotationDbi_1.24.0.tar.gz?raw=true</package>
+xmlgoesherextable_1.7-4.tar.gz?raw=true</package>
+xmlgoeshereXML_3.98-1.1.tar.gz?raw=true</package>
+xmlgoeshereannotate_1.40.1.tar.gz?raw=true</package>
+xmlgoesheregenefilter_1.44.0.tar.gz?raw=true</package>
+xmlgoeshereRColorBrewer_1.1-2.tar.gz?raw=true</package>
+xmlgoeshereDESeq2_1.2.10.tar.gz?raw=true</package>