--- a/toolfactory_docker/rgToolFactory2.py	Tue Jan 05 00:35:40 2021 +0000
+++ b/toolfactory_docker/rgToolFactory2.py	Thu Jan 07 23:34:14 2021 +0000
@@ -19,13 +19,6 @@
 # calling venv. Hilarity ensues.
 
 
-# # expects tarball as first, html out as second parameter
-# cp $1 foo.tar.gz
-# tar -xvzf foo.tar.gz
-# TOOLNAME=`find . -name "*.xml"`
-# echo "*****TOOLNAME = $TOOLNAME"
-# planemo test  --test_output $2 $TOOLNAME
-
 import argparse
 import copy
 import logging
@@ -133,17 +126,6 @@
     return "".join([cheetah_escape_table.get(c, c) for c in text])
 
 
-def html_unescape(text):
-    """Revert entities within text. Multiple character targets so use replace"""
-    t = text.replace("&", "&")
-    t = t.replace(">", ">")
-    t = t.replace("&lt;", "<")
-    t = t.replace("\\$", "$")
-    t = t.replace("&#36;", "$")
-    t = t.replace("&#35;", "#")
-    return t
-
-
 def parse_citations(citations_text):
     """"""
     citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
@@ -462,7 +444,6 @@
                     tp = gxtp.TestOutput(
                         name=newname,
                         value="%s_sample" % newname,
-                        format=newfmt,
                         compare=c,
                         lines_diff=ld,
                     )
@@ -479,7 +460,6 @@
                     tp = gxtp.TestOutput(
                         name=newname,
                         value="%s_sample" % newname,
-                        format=newfmt,
                         compare=c,
                         delta=delta,
                         delta_frac=delta_frac,
@@ -591,7 +571,7 @@
             anout.positional = self.is_positional
             self.toutputs.append(anout)
             tp = gxtp.TestOutput(
-                name=newname, value="%s_sample" % newname, format=newfmt
+                name=newname, value="%s_sample" % newname,
             )
             self.testparam.append(tp)
 
@@ -605,28 +585,34 @@
             self.newtool.command_override = self.command_override  # config file
         else:
             self.newtool.command_override = self.xmlcl
+        cite = gxtp.Citations()
+        acite = gxtp.Citation(type="doi", value="10.1093/bioinformatics/bts573")
+        cite.append(acite)
+        self.newtool.citations = cite
+        safertext = ""
         if self.args.help_text:
             helptext = open(self.args.help_text, "r").readlines()
             safertext = "\n".join([cheetah_escape(x) for x in helptext])
-            if self.args.script_path:
-                scr = [x for x in self.spacedScript if x.strip() > ""]
-                scr.insert(0, "\n------\n\n\nScript::\n")
-                if len(scr) > 300:
-                    scr = (
-                        scr[:100]
-                        + ["    >300 lines - stuff deleted", "    ......"]
-                        + scr[-100:]
-                    )
-                scr.append("\n")
-                safertext = safertext + "\n".join(scr)
-            self.newtool.help = safertext
-        else:
-            self.newtool.help = (
-                "Please ask the tool author (%s) for help \
-              as none was supplied at tool generation\n"
+        if len(safertext.strip()) == 0:
+            safertext = (
+                "Ask the tool author (%s) to rebuild with help text please\n"
                 % (self.args.user_email)
             )
-        self.newtool.version_command = None  # do not want
+        if self.args.script_path:
+            if len(safertext) > 0:
+                safertext = safertext + "\n\n------\n"  # transition allowed!
+            scr = [x for x in self.spacedScript if x.strip() > ""]
+            scr.insert(0, "\n\nScript::\n")
+            if len(scr) > 300:
+                scr = (
+                    scr[:100]
+                    + ["    >300 lines - stuff deleted", "    ......"]
+                    + scr[-100:]
+                )
+            scr.append("\n")
+            safertext = safertext + "\n".join(scr)
+        self.newtool.help = safertext
+        self.newtool.version_command = f'echo "{self.args.tool_version}"'
         requirements = gxtp.Requirements()
         if self.args.packages:
             for d in self.args.packages.split(","):
@@ -640,7 +626,7 @@
                 requirements.append(
                     gxtp.Requirement("package", packg.strip(), ver.strip())
                 )
-        self.newtool.requirements = requirements
+            self.newtool.requirements = requirements
         if self.args.parampass == "0":
             self.doNoXMLparam()
         else:
@@ -664,9 +650,6 @@
             % (self.args.user_email, timenow())
         )
         self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
-        self.newtool.add_comment(
-            "Cite: Creating re-usable tools from scripts doi:10.1093/bioinformatics/bts573"
-        )
         exml0 = self.newtool.export()
         exml = exml0.replace(FAKEEXE, "")  # temporary work around until PR accepted
         if (
@@ -683,6 +666,7 @@
         xf.close()
         # ready for the tarball
 
+
     def run(self):
         """
         generate test outputs by running a command line