# HG changeset patch
# User fubar
# Date 1616750998 0
# Node ID def0f754ee1b963bb40d24f34f4bf289b0c59bc5
# Parent  2dbb412af425c2abdc9395888782977dc93739a4
Uploaded

diff -r 2dbb412af425 -r def0f754ee1b toolfactory/rgToolFactory2.py
--- a/toolfactory/rgToolFactory2.py	Fri Mar 26 09:27:55 2021 +0000
+++ b/toolfactory/rgToolFactory2.py	Fri Mar 26 09:29:58 2021 +0000
@@ -16,6 +16,7 @@
 
 import argparse
 import copy
+import json
 import logging
 import os
 import re
@@ -36,44 +37,11 @@
 
 import yaml
 
-myversion = "V2.1 July 2020"
+
+myversion = "V2.2 February 2021"
 verbose = True
 debug = True
 toolFactoryURL = "https://github.com/fubar2/toolfactory"
-ourdelim = "~~~"
-
-# --input_files="$intab.input_files~~~$intab.input_CL~~~
-# $intab.input_formats# ~~~$intab.input_label
-# ~~~$intab.input_help"
-IPATHPOS = 0
-ICLPOS = 1
-IFMTPOS = 2
-ILABPOS = 3
-IHELPOS = 4
-IOCLPOS = 5
-
-# --output_files "$otab.history_name~~~$otab.history_format~~~
-# $otab.history_CL~~~$otab.history_test"
-ONAMEPOS = 0
-OFMTPOS = 1
-OCLPOS = 2
-OTESTPOS = 3
-OOCLPOS = 4
-
-
-# --additional_parameters="$i.param_name~~~$i.param_value~~~
-# $i.param_label~~~$i.param_help~~~$i.param_type
-# ~~~$i.CL~~~i$.param_CLoverride"
-ANAMEPOS = 0
-AVALPOS = 1
-ALABPOS = 2
-AHELPPOS = 3
-ATYPEPOS = 4
-ACLPOS = 5
-AOVERPOS = 6
-AOCLPOS = 7
-
-
 foo = len(lxml.__version__)
 # fug you, flake8. Say my name!
 FAKEEXE = "~~~REMOVE~~~ME~~~"
@@ -86,32 +54,9 @@
     return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
 
 
-def quote_non_numeric(s):
-    """return a prequoted string for non-numerics
-    useful for perl and Rscript parameter passing?
-    """
-    try:
-        _ = float(s)
-        return s
-    except ValueError:
-        return '"%s"' % s
-
-
-html_escape_table = {
-    "&": "&",
-    ">": ">",
-    "<": "&lt;",
-    "#": "&#35;",
-    "$": "&#36;",
-}
 cheetah_escape_table = {"$": "\\$", "#": "\\#"}
 
 
-def html_escape(text):
-    """Produce entities within text."""
-    return "".join([html_escape_table.get(c, c) for c in text])
-
-
 def cheetah_escape(text):
     """Produce entities within text."""
     return "".join([cheetah_escape_table.get(c, c) for c in text])
@@ -141,10 +86,48 @@
         and prepare elements needed for galaxyxml tool generation
         """
         self.ourcwd = os.getcwd()
-        self.ourenv = copy.deepcopy(os.environ)
-        self.infiles = [x.split(ourdelim) for x in args.input_files]
-        self.outfiles = [x.split(ourdelim) for x in args.output_files]
-        self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
+        self.collections = []
+        if len(args.collection) > 0:
+            try:
+                self.collections = [
+                    json.loads(x) for x in args.collection if len(x.strip()) > 1
+                ]
+            except Exception:
+                print(
+                    f"--collections parameter {str(args.collection)} is malformed - should be a dictionary"
+                )
+        try:
+            self.infiles = [
+                json.loads(x) for x in args.input_files if len(x.strip()) > 1
+            ]
+        except Exception:
+            print(
+                f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary"
+            )
+        try:
+            self.outfiles = [
+                json.loads(x) for x in args.output_files if len(x.strip()) > 1
+            ]
+        except Exception:
+            print(
+                f"--output_files parameter {args.output_files} is malformed - should be a dictionary"
+            )
+        try:
+            self.addpar = [
+                json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1
+            ]
+        except Exception:
+            print(
+                f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary"
+            )
+        try:
+            self.selpar = [
+                json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1
+            ]
+        except Exception:
+            print(
+                f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary"
+            )
         self.args = args
         self.cleanuppar()
         self.lastclredirect = None
@@ -153,10 +136,13 @@
         self.xmlcl = []
         self.is_positional = self.args.parampass == "positional"
         if self.args.sysexe:
-            self.executeme = self.args.sysexe
+            if ' ' in self.args.sysexe:
+                self.executeme = self.args.sysexe.split(' ')
+            else:
+                self.executeme = [self.args.sysexe, ]
         else:
             if self.args.packages:
-                self.executeme = self.args.packages.split(",")[0].split(":")[0].strip()
+                self.executeme = [self.args.packages.split(",")[0].split(":")[0].strip(), ]
             else:
                 self.executeme = None
         aCL = self.cl.append
@@ -175,7 +161,7 @@
             self.args.tool_desc,
             FAKEEXE,
         )
-        self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
+        self.newtarpath = "%s_toolshed.gz" % self.tool_name
         self.tooloutdir = "./tfout"
         self.repdir = "./TF_run_report_tempdir"
         self.testdir = os.path.join(self.tooloutdir, "test-data")
@@ -200,67 +186,122 @@
             self.test_override = [x.rstrip() for x in stos]
         else:
             self.test_override = None
-        if self.args.cl_prefix:  # DIY CL start
+        if self.args.script_path:
+            for ex in self.executeme:
+                aCL(ex)
+                aXCL(ex)
+            aCL(self.sfile)
+            aXCL("$runme")
+        else:
+            aCL(self.executeme[0])
+            aXCL(self.executeme[0])
+        self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
+        self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
+        if self.args.parampass == "0":
+            self.clsimple()
+        else:
+            if self.args.parampass == "positional":
+                self.prepclpos()
+                self.clpositional()
+            else:
+                self.prepargp()
+                self.clargparse()
+        if self.args.cl_prefix:  # DIY CL end - misnamed!
             clp = self.args.cl_prefix.split(" ")
             for c in clp:
                 aCL(c)
                 aXCL(c)
-        else:
-            if self.args.script_path:
-                aCL(self.executeme)
-                aCL(self.sfile)
-                aXCL(self.executeme)
-                aXCL("$runme")
-            else:
-                aCL(self.executeme)
-                aXCL(self.executeme)
-        self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
-        self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
+
+    def clsimple(self):
+        """no parameters - uses < and > for i/o"""
+        aCL = self.cl.append
+        aXCL = self.xmlcl.append
+        if len(self.infiles) > 0:
+            aCL("<")
+            aCL(self.infiles[0]["infilename"])
+            aXCL("<")
+            aXCL("$%s" % self.infiles[0]["infilename"])
+        if len(self.outfiles) > 0:
+            aCL(">")
+            aCL(self.outfiles[0]["name"])
+            aXCL(">")
+            aXCL("$%s" % self.outfiles[0]["name"])
 
-        if self.args.parampass == "0":
-            self.clsimple()
-        else:
-            clsuffix = []
-            xclsuffix = []
-            for i, p in enumerate(self.infiles):
-                if p[IOCLPOS].upper() == "STDIN":
-                    appendme = [
-                        p[ICLPOS],
-                        p[ICLPOS],
-                        p[IPATHPOS],
-                        "< %s" % p[IPATHPOS],
-                    ]
-                    xappendme = [
-                        p[ICLPOS],
-                        p[ICLPOS],
-                        p[IPATHPOS],
-                        "< $%s" % p[ICLPOS],
-                    ]
-                else:
-                    appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
-                    xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
-                clsuffix.append(appendme)
-                xclsuffix.append(xappendme)
-            for i, p in enumerate(self.outfiles):
-                if p[OOCLPOS] == "STDOUT":
-                    self.lastclredirect = [">", p[ONAMEPOS]]
-                    self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
-                else:
-                    clsuffix.append([p[OCLPOS], p[ONAMEPOS], p[ONAMEPOS], ""])
-                    xclsuffix.append([p[OCLPOS], p[ONAMEPOS], "$%s" % p[ONAMEPOS], ""])
-            for p in self.addpar:
-                clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]])
-                xclsuffix.append(
-                    [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
-                )
-            clsuffix.sort()
-            xclsuffix.sort()
-            self.xclsuffix = xclsuffix
-            self.clsuffix = clsuffix
-            if self.args.parampass == "positional":
-                self.clpositional()
+    def prepargp(self):
+        clsuffix = []
+        xclsuffix = []
+        for i, p in enumerate(self.infiles):
+            if p["origCL"].strip().upper() == "STDIN":
+                appendme = [
+                    p["infilename"],
+                    p["infilename"],
+                    "< %s" % p["infilename"],
+                ]
+                xappendme = [
+                    p["infilename"],
+                    p["infilename"],
+                    "< $%s" % p["infilename"],
+                ]
+            else:
+                appendme = [p["CL"], p["CL"], ""]
+                xappendme = [p["CL"], "$%s" % p["CL"], ""]
+            clsuffix.append(appendme)
+            xclsuffix.append(xappendme)
+        for i, p in enumerate(self.outfiles):
+            if p["origCL"].strip().upper() == "STDOUT":
+                self.lastclredirect = [">", p["name"]]
+                self.lastxclredirect = [">", "$%s" % p["name"]]
             else:
-                self.clargparse()
+                clsuffix.append([p["name"], p["name"], ""])
+                xclsuffix.append([p["name"], "$%s" % p["name"], ""])
+        for p in self.addpar:
+            clsuffix.append([p["CL"], p["name"], p["override"]])
+            xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
+        for p in self.selpar:
+            clsuffix.append([p["CL"], p["name"], p["override"]])
+            xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
+        clsuffix.sort()
+        xclsuffix.sort()
+        self.xclsuffix = xclsuffix
+        self.clsuffix = clsuffix
+
+    def prepclpos(self):
+        clsuffix = []
+        xclsuffix = []
+        for i, p in enumerate(self.infiles):
+            if p["origCL"].strip().upper() == "STDIN":
+                appendme = [
+                    "999",
+                    p["infilename"],
+                    "< $%s" % p["infilename"],
+                ]
+                xappendme = [
+                    "999",
+                    p["infilename"],
+                    "< $%s" % p["infilename"],
+                ]
+            else:
+                appendme = [p["CL"], p["infilename"], ""]
+                xappendme = [p["CL"], "$%s" % p["infilename"], ""]
+            clsuffix.append(appendme)
+            xclsuffix.append(xappendme)
+        for i, p in enumerate(self.outfiles):
+            if p["origCL"].strip().upper() == "STDOUT":
+                self.lastclredirect = [">", p["name"]]
+                self.lastxclredirect = [">", "$%s" % p["name"]]
+            else:
+                clsuffix.append([p["CL"], p["name"], ""])
+                xclsuffix.append([p["CL"], "$%s" % p["name"], ""])
+        for p in self.addpar:
+            clsuffix.append([p["CL"], p["name"], p["override"]])
+            xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
+        for p in self.selpar:
+            clsuffix.append([p["CL"], p["name"], p["override"]])
+            xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
+        clsuffix.sort()
+        xclsuffix.sort()
+        self.xclsuffix = xclsuffix
+        self.clsuffix = clsuffix
 
     def prepScript(self):
         rx = open(self.args.script_path, "r").readlines()
@@ -269,14 +310,14 @@
         assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
         self.script = "\n".join(rx)
         fhandle, self.sfile = tempfile.mkstemp(
-            prefix=self.tool_name, suffix="_%s" % (self.executeme)
+            prefix=self.tool_name, suffix="_%s" % (self.executeme[0])
         )
         tscript = open(self.sfile, "w")
         tscript.write(self.script)
         tscript.close()
         self.escapedScript = [cheetah_escape(x) for x in rx]
         self.spacedScript = [f"    {x}" for x in rx if x.strip() > ""]
-        art = "%s.%s" % (self.tool_name, self.executeme)
+        art = "%s.%s" % (self.tool_name, self.executeme[0])
         artifact = open(art, "wb")
         artifact.write(bytes("\n".join(self.escapedScript), "utf8"))
         artifact.close()
@@ -286,78 +327,50 @@
         if self.args.parampass == "positional":
             for i, p in enumerate(self.infiles):
                 assert (
-                    p[ICLPOS].isdigit() or p[ICLPOS].strip().upper() == "STDIN"
+                    p["CL"].isdigit() or p["CL"].strip().upper() == "STDIN"
                 ), "Positional parameters must be ordinal integers - got %s for %s" % (
-                    p[ICLPOS],
-                    p[ILABPOS],
+                    p["CL"],
+                    p["label"],
                 )
             for i, p in enumerate(self.outfiles):
                 assert (
-                    p[OCLPOS].isdigit() or p[OCLPOS].strip().upper() == "STDOUT"
+                    p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT"
                 ), "Positional parameters must be ordinal integers - got %s for %s" % (
-                    p[OCLPOS],
-                    p[ONAMEPOS],
+                    p["CL"],
+                    p["name"],
                 )
             for i, p in enumerate(self.addpar):
                 assert p[
-                    ACLPOS
+                    "CL"
                 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
-                    p[ACLPOS],
-                    p[ANAMEPOS],
+                    p["CL"],
+                    p["name"],
                 )
         for i, p in enumerate(self.infiles):
             infp = copy.copy(p)
-            icl = infp[ICLPOS]
-            infp.append(icl)
-            if (
-                infp[ICLPOS].isdigit()
-                or self.args.parampass == "0"
-                or infp[ICLPOS].strip().upper() == "STDOUT"
-            ):
-                scl = "input%d" % (i + 1)
-                infp[ICLPOS] = scl
+            infp["origCL"] = infp["CL"]
+            if self.args.parampass in ["positional", "0"]:
+                infp["infilename"] = infp["label"].replace(" ", "_")
+            else:
+                infp["infilename"] = infp["CL"]
             self.infiles[i] = infp
         for i, p in enumerate(self.outfiles):
-            p.append(p[OCLPOS])  # keep copy
-            if (p[OOCLPOS].isdigit() and self.args.parampass != "positional") or p[
-                OOCLPOS
-            ].strip().upper() == "STDOUT":
-                scl = p[ONAMEPOS]
-                p[OCLPOS] = scl
+            p["origCL"] = p["CL"]  # keep copy
             self.outfiles[i] = p
         for i, p in enumerate(self.addpar):
-            p.append(p[ACLPOS])
-            if p[ACLPOS].isdigit():
-                scl = "param%s" % p[ACLPOS]
-                p[ACLPOS] = scl
+            p["origCL"] = p["CL"]
             self.addpar[i] = p
 
-    def clsimple(self):
-        """no parameters - uses < and > for i/o"""
-        aCL = self.cl.append
-        aXCL = self.xmlcl.append
-
-        if len(self.infiles) > 0:
-            aCL("<")
-            aCL(self.infiles[0][IPATHPOS])
-            aXCL("<")
-            aXCL("$%s" % self.infiles[0][ICLPOS])
-        if len(self.outfiles) > 0:
-            aCL(">")
-            aCL(self.outfiles[0][OCLPOS])
-            aXCL(">")
-            aXCL("$%s" % self.outfiles[0][ONAMEPOS])
-
     def clpositional(self):
         # inputs in order then params
         aCL = self.cl.append
-        for (o_v, k, v, koverride) in self.clsuffix:
+        for (k, v, koverride) in self.clsuffix:
             if " " in v:
                 aCL("%s" % v)
             else:
                 aCL(v)
         aXCL = self.xmlcl.append
-        for (o_v, k, v, koverride) in self.xclsuffix:
+        for (k, v, koverride) in self.xclsuffix:
             aXCL(v)
         if self.lastxclredirect:
             aXCL(self.lastxclredirect[0])
@@ -369,7 +382,7 @@
         aXCL = self.xmlcl.append
         # inputs then params in argparse named form
 
-        for (o_v, k, v, koverride) in self.xclsuffix:
+        for (k, v, koverride) in self.xclsuffix:
             if koverride > "":
                 k = koverride
             elif len(k.strip()) == 1:
@@ -378,7 +391,7 @@
                 k = "--%s" % k
             aXCL(k)
             aXCL(v)
-        for (o_v, k, v, koverride) in self.clsuffix:
+        for (k, v, koverride) in self.clsuffix:
             if koverride > "":
                 k = koverride
             elif len(k.strip()) == 1:
@@ -400,8 +413,11 @@
     def doXMLparam(self):
         """flake8 made me do this..."""
         for p in self.outfiles:
-            # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
-            newname, newfmt, newcl, test, oldcl = p
+            newname = p["name"]
+            newfmt = p["format"]
+            newcl = p["CL"]
+            test = p["test"]
+            oldcl = p["origCL"]
             test = test.strip()
             ndash = self.getNdash(newcl)
             aparm = gxtp.OutputData(
@@ -446,39 +462,50 @@
                         delta=delta,
                         delta_frac=delta_frac,
                     )
+                else:
+                    c = test
+                    tp = gxtp.TestOutput(
+                        name=newname,
+                        value="%s_sample" % newname,
+                        compare=c,
+                    )
                 self.testparam.append(tp)
         for p in self.infiles:
-            newname = p[ICLPOS]
-            newfmt = p[IFMTPOS]
+            newname = p["infilename"]
+            newfmt = p["format"]
             ndash = self.getNdash(newname)
-            if not len(p[ILABPOS]) > 0:
-                alab = p[ICLPOS]
+            if not len(p["label"]) > 0:
+                alab = p["CL"]
             else:
-                alab = p[ILABPOS]
+                alab = p["label"]
             aninput = gxtp.DataParam(
                 newname,
                 optional=False,
                 label=alab,
-                help=p[IHELPOS],
+                help=p["help"],
                 format=newfmt,
                 multiple=False,
                 num_dashes=ndash,
             )
             aninput.positional = self.is_positional
+            if self.is_positional:
+                if p["origCL"].upper() == "STDIN":
+                    aparm.positional = 9999998
+                    aparm.command_line_override = "> $%s" % newname
+                else:
+                    aparm.positional = int(p["origCL"])
+                    aparm.command_line_override = "$%s" % newname
             self.tinputs.append(aninput)
             tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
             self.testparam.append(tparm)
         for p in self.addpar:
-            (
-                newname,
-                newval,
-                newlabel,
-                newhelp,
-                newtype,
-                newcl,
-                override,
-                oldcl,
-            ) = p
+            newname = p["name"]
+            newval = p["value"]
+            newlabel = p["label"]
+            newhelp = p["help"]
+            newtype = p["type"]
+            newcl = p["CL"]
+            oldcl = p["origCL"]
             if not len(newlabel) > 0:
                 newlabel = newname
             ndash = self.getNdash(newname)
@@ -506,6 +533,14 @@
                     value=newval,
                     num_dashes=ndash,
                 )
+            elif newtype == "boolean":
+                aparm = gxtp.BooleanParam(
+                    newname,
+                    label=newname,
+                    help=newhelp,
+                    value=newval,
+                    num_dashes=ndash,
+                )
             else:
                 raise ValueError(
                     'Unrecognised parameter type "%s" for\
@@ -518,43 +553,90 @@
             self.tinputs.append(aparm)
             tparm = gxtp.TestParam(newname, value=newval)
             self.testparam.append(tparm)
+        for p in self.selpar:
+            newname = p["name"]
+            newval = p["value"]
+            newlabel = p["label"]
+            newhelp = p["help"]
+            newtype = p["type"]
+            newcl = p["CL"]
+            if not len(newlabel) > 0:
+                newlabel = newname
+            ndash = self.getNdash(newname)
+            if newtype == "selecttext":
+                newtext = p["texts"]
+                aparm = gxtp.SelectParam(
+                    newname,
+                    label=newlabel,
+                    help=newhelp,
+                    num_dashes=ndash,
+                )
+                for i in range(len(newval)):
+                    anopt = gxtp.SelectOption(
+                        value=newval[i],
+                        text=newtext[i],
+                    )
+                    aparm.append(anopt)
+                aparm.positional = self.is_positional
+                if self.is_positional:
+                    aparm.positional = int(newcl)
+                self.tinputs.append(aparm)
+                tparm = gxtp.TestParam(newname, value=newval)
+                self.testparam.append(tparm)
+            else:
+                raise ValueError(
+                    'Unrecognised parameter type "%s" for\
+                 selecttext parameter %s in makeXML'
+                    % (newtype, newname)
+                )
+        for p in self.collections:
+            newkind = p["kind"]
+            newname = p["name"]
+            newlabel = p["label"]
+            newdisc = p["discover"]
+            collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind)
+            disc = gxtp.DiscoverDatasets(
+                pattern=newdisc, directory=f"{newname}", visible="false"
+            )
+            collect.append(disc)
+            self.toutputs.append(collect)
+            tparm = gxtp.TestOutput(newname, ftype="pdf")
+            self.testparam.append(tparm)
 
     def doNoXMLparam(self):
         """filter style package - stdin to stdout"""
         if len(self.infiles) > 0:
-            alab = self.infiles[0][ILABPOS]
+            alab = self.infiles[0]["label"]
             if len(alab) == 0:
-                alab = self.infiles[0][ICLPOS]
+                alab = self.infiles[0]["infilename"]
             max1s = (
                 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
                 % str(self.infiles)
             )
             assert len(self.infiles) == 1, max1s
-            newname = self.infiles[0][ICLPOS]
+            newname = self.infiles[0]["infilename"]
             aninput = gxtp.DataParam(
                 newname,
                 optional=False,
                 label=alab,
-                help=self.infiles[0][IHELPOS],
-                format=self.infiles[0][IFMTPOS],
+                help=self.infiles[0]["help"],
+                format=self.infiles[0]["format"],
                 multiple=False,
                 num_dashes=0,
             )
             aninput.command_line_override = "< $%s" % newname
-            aninput.positional = self.is_positional
+            aninput.positional = True
             self.tinputs.append(aninput)
             tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
             self.testparam.append(tp)
         if len(self.outfiles) > 0:
-            newname = self.outfiles[0][OCLPOS]
-            newfmt = self.outfiles[0][OFMTPOS]
+            newname = self.outfiles[0]["name"]
+            newfmt = self.outfiles[0]["format"]
             anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
             anout.command_line_override = "> $%s" % newname
             anout.positional = self.is_positional
             self.toutputs.append(anout)
-            tp = gxtp.TestOutput(
-                name=newname, value="%s_sample" % newname
-            )
+            tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname)
             self.testparam.append(tp)
 
     def makeXML(self):
@@ -639,7 +721,7 @@
         ):  # cannot do this inside galaxyxml as it expects lxml objects for tests
             part1 = exml.split("<tests>")[0]
             part2 = exml.split("</tests>")[1]
-            fixed = "%s\n%s\n%s" % (part1, self.test_override, part2)
+            fixed = "%s\n%s\n%s" % (part1, "\n".join(self.test_override), part2)
             exml = fixed
         # exml = exml.replace('range="1:"', 'range="1000:"')
         xf = open("%s.xml" % self.tool_name, "w")
@@ -674,22 +756,22 @@
                 )
             sto.flush()
             subp = subprocess.run(
-                self.cl, env=self.ourenv, shell=False, stdout=sto, stderr=ste
+                self.cl, shell=False, stdout=sto, stderr=ste
             )
             sto.close()
             ste.close()
             retval = subp.returncode
         else:  # work around special case - stdin and write to stdout
             if len(self.infiles) > 0:
-                sti = open(self.infiles[0][IPATHPOS], "rb")
+                sti = open(self.infiles[0]["name"], "rb")
             else:
                 sti = sys.stdin
             if len(self.outfiles) > 0:
-                sto = open(self.outfiles[0][ONAMEPOS], "wb")
+                sto = open(self.outfiles[0]["name"], "wb")
             else:
                 sto = sys.stdout
             subp = subprocess.run(
-                self.cl, env=self.ourenv, shell=False, stdout=sto, stdin=sti
+                self.cl, shell=False, stdout=sto, stdin=sti
             )
             sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
             retval = subp.returncode
@@ -785,7 +867,6 @@
         tout.write("running\n%s\n" % " ".join(cll))
         subp = subprocess.run(
             cll,
-            env=self.ourenv,
             cwd=self.ourcwd,
             shell=False,
             stderr=tout,
@@ -815,20 +896,25 @@
 
     def makeTool(self):
         """write xmls and input samples into place"""
-        self.makeXML()
+        if self.args.parampass == 0:
+            self.doNoXMLparam()
+        else:
+            self.makeXML()
         if self.args.script_path:
-            stname = os.path.join(self.tooloutdir, "%s" % (self.sfile))
+            stname = os.path.join(self.tooloutdir, self.sfile)
             if not os.path.exists(stname):
                 shutil.copyfile(self.sfile, stname)
         xreal = "%s.xml" % self.tool_name
         xout = os.path.join(self.tooloutdir, xreal)
         shutil.copyfile(xreal, xout)
         for p in self.infiles:
-            pth = p[IPATHPOS]
-            dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
+            pth = p["name"]
+            dest = os.path.join(self.testdir, "%s_sample" % p["infilename"])
+            shutil.copyfile(pth, dest)
+            dest = os.path.join(self.repdir, "%s_sample" % p["infilename"])
             shutil.copyfile(pth, dest)
 
-    def makeToolTar(self):
+    def makeToolTar(self, report_fail=False):
         """move outputs into test-data and prepare the tarball"""
         excludeme = "_planemo_test_report.html"
 
@@ -841,19 +927,20 @@
         else:
             tout = open(self.tlog, "w")
         for p in self.outfiles:
-            oname = p[ONAMEPOS]
+            oname = p["name"]
             tdest = os.path.join(self.testdir, "%s_sample" % oname)
+            src = os.path.join(self.testdir, oname)
             if not os.path.isfile(tdest):
-                src = os.path.join(self.testdir, oname)
                 if os.path.isfile(src):
                     shutil.copyfile(src, tdest)
                     dest = os.path.join(self.repdir, "%s.sample" % (oname))
                     shutil.copyfile(src, dest)
                 else:
-                    tout.write(
-                        "###Output file %s not found in testdir %s. This is normal during the first Planemo run that generates test outputs"
-                        % (tdest, self.testdir)
-                    )
+                    if report_fail:
+                        tout.write(
+                            "###Tool may have failed - output file %s not found in testdir after planemo run %s."
+                            % (tdest, self.testdir)
+                        )
         tf = tarfile.open(self.newtarpath, "w:gz")
         tf.add(
             name=self.tooloutdir,
@@ -870,33 +957,41 @@
                 if not entry.is_file():
                     continue
                 if "." in entry.name:
-                    nayme, ext = os.path.splitext(entry.name)
-                    if ext in [".yml", ".xml", ".json", ".yaml"]:
-                        ext = f"{ext}.txt"
+                    _, ext = os.path.splitext(entry.name)
+                    if ext in [".tgz", ".json"]:
+                        continue
+                    if ext in [".yml", ".xml", ".yaml"]:
+                        newname = f"{entry.name.replace('.','_')}.txt"
+                    else:
+                        newname = entry.name
                 else:
-                    ext = ".txt"
-                ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
-                dest = os.path.join(self.repdir, ofn)
+                    newname = f"{entry.name}.txt"
+                dest = os.path.join(self.repdir, newname)
                 src = os.path.join(self.tooloutdir, entry.name)
                 shutil.copyfile(src, dest)
-        with os.scandir(self.testdir) as outs:
-            for entry in outs:
-                if (
-                    (not entry.is_file())
-                    or entry.name.endswith("_sample")
-                    or entry.name.endswith("_planemo_test_report.html")
-                ):
-                    continue
-                if "." in entry.name:
-                    nayme, ext = os.path.splitext(entry.name)
-                else:
-                    ext = ".txt"
-                newname = f"{entry.name}{ext}"
-                dest = os.path.join(self.repdir, newname)
-                src = os.path.join(self.testdir, entry.name)
-                shutil.copyfile(src, dest)
+        if self.args.include_tests:
+            with os.scandir(self.testdir) as outs:
+                for entry in outs:
+                    if (not entry.is_file()) or entry.name.endswith(
+                        "_planemo_test_report.html"
+                    ):
+                        continue
+                    if "." in entry.name:
+                        _, ext = os.path.splitext(entry.name)
+                        if ext in [".tgz", ".json"]:
+                            continue
+                        if ext in [".yml", ".xml", ".yaml"]:
+                            newname = f"{entry.name.replace('.','_')}.txt"
+                        else:
+                            newname = entry.name
+                    else:
+                        newname = f"{entry.name}.txt"
+                    dest = os.path.join(self.repdir, newname)
+                    src = os.path.join(self.testdir, entry.name)
+                    shutil.copyfile(src, dest)
 
-    def planemo_test(self, genoutputs=True):
+
+    def planemo_test_once(self):
         """planemo is a requirement so is available for testing but needs a
         different call if in the biocontainer - see above
         and for generating test outputs if command or test overrides are
@@ -910,51 +1005,26 @@
             tout = open(self.tlog, "a")
         else:
             tout = open(self.tlog, "w")
-        if genoutputs:
-            dummy, tfile = tempfile.mkstemp()
-            cll = [
-                "planemo",
-                "test",
-                "--test_data",
-                os.path.abspath(self.testdir),
-                "--test_output",
-                os.path.abspath(tool_test_path),
-                "--skip_venv",
-                "--galaxy_root",
-                self.args.galaxy_root,
-                "--update_test_data",
-                os.path.abspath(xreal),
-            ]
-            p = subprocess.run(
-                cll,
-                env=self.ourenv,
-                shell=False,
-                cwd=self.tooloutdir,
-                stderr=dummy,
-                stdout=dummy,
-            )
-
-        else:
-            cll = [
-                "planemo",
-                "test",
-                "--test_data",
-                os.path.abspath(self.testdir),
-                "--test_output",
-                os.path.abspath(tool_test_path),
-                "--skip_venv",
-                "--galaxy_root",
-                self.args.galaxy_root,
-                os.path.abspath(xreal),
-            ]
-            p = subprocess.run(
-                cll,
-                shell=False,
-                env=self.ourenv,
-                cwd=self.tooloutdir,
-                stderr=tout,
-                stdout=tout,
-            )
+        cll = [
+            "planemo",
+            "test",
+            "--conda_auto_init",
+            "--test_data",
+            os.path.abspath(self.testdir),
+            "--test_output",
+            os.path.abspath(tool_test_path),
+            "--galaxy_root",
+            self.args.galaxy_root,
+            "--update_test_data",
+            os.path.abspath(xreal),
+        ]
+        p = subprocess.run(
+            cll,
+            shell=False,
+            cwd=self.tooloutdir,
+            stderr=tout,
+            stdout=tout,
+        )
         tout.close()
         return p.returncode
 
@@ -986,6 +1056,7 @@
     a("--command_override", default=None)
     a("--test_override", default=None)
     a("--additional_parameters", action="append", default=[])
+    a("--selecttext_parameters", action="append", default=[])
     a("--edit_additional_parameters", action="store_true", default=False)
     a("--parampass", default="positional")
     a("--tfout", default="./tfout")
@@ -998,6 +1069,8 @@
     a("--galaxy_api_key", default="fakekey")
     a("--galaxy_root", default="/galaxy-central")
     a("--galaxy_venv", default="/galaxy_venv")
+    a("--collection", action="append", default=[])
+    a("--include_tests", default=False, action="store_true")
     args = parser.parse_args()
     assert not args.bad_user, (
         'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \
@@ -1009,25 +1082,20 @@
         args.sysexe or args.packages
     ), "## Tool Factory wrapper expects an interpreter \
 or an executable package in --sysexe or --packages"
-    args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files]
-    # remove quotes we need to deal with spaces in CL params
-    for i, x in enumerate(args.additional_parameters):
-        args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
     r = ScriptRunner(args)
     r.writeShedyml()
     r.makeTool()
     if args.make_Tool == "generate":
-        retcode = r.run()
+        r.run()
         r.moveRunOutputs()
         r.makeToolTar()
     else:
-        retcode = r.planemo_test(genoutputs=True)  # this fails :( - see PR
+        # r.planemo_test(genoutputs=True)  # this fails :( - see PR
+        # r.moveRunOutputs()
+        # r.makeToolTar(report_fail=False)
+        r.planemo_test_once()
         r.moveRunOutputs()
-        r.makeToolTar()
-        retcode = r.planemo_test(genoutputs=False)
-        r.moveRunOutputs()
-        r.makeToolTar()
-        print(f"second planemo_test returned {retcode}")
+        r.makeToolTar(report_fail=True)
         if args.make_Tool == "gentestinstall":
             r.shedLoad()
             r.eph_galaxy_load()
diff -r 2dbb412af425 -r def0f754ee1b toolfactory/rgToolFactory2.xml
--- a/toolfactory/rgToolFactory2.xml	Fri Mar 26 09:27:55 2021 +0000
+++ b/toolfactory/rgToolFactory2.xml	Fri Mar 26 09:29:58 2021 +0000
@@ -1,6 +1,32 @@
 <tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" >
   <description>Scripts into tools v2.0</description>
   <macros>
+      <xml name="singleText">
+            <param name="param_value" type="text" value="" label="Enter this parameter's default text value">
+          </param>
+      </xml>
+      <xml name="singleInt">
+            <param name="param_value" type="integer" value="" label="Enter this parameter's default integer value" >
+          </param>
+      </xml>
+      <xml name="singleFloat">
+            <param name="param_value" type="float" value="" label="Enter this parameter's default value">
+          </param>
+      </xml>
+     <xml name="singleBoolean">
+            <param name="param_value" type="boolean" value="" label="Enter this parameter's default value" />
+            <param name="truevalue" type="text" value="True" label="Command line value to emit when True" />
+            <param name="falsevalue" type="boolean" value="True" label="Command line value to emit when False" />
+      </xml>
+      <xml name="selectText">
+          <repeat name="selectTexts" title="Add each option to be presented in a text select box" min="2" default="2"
+             help="Each text added here will also have  a value to be emitted on the command line when the text is chosen">
+            <param name="select_text" type="text" value="" label="Enter the explanatory text the user will see for this choice" >
+          </param>
+          <param name="select_value" type="text" value="" label="Enter the value for the command line when the user selects this option">
+          </param>
+          </repeat>
+      </xml>
      <xml name="tool_metadata">
          <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
             help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
@@ -10,8 +36,7 @@
             value="**What it Does**"
              help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
                 <sanitizer>
-                    <valid initial="string.printable">
-                    </valid>
+                    <valid initial="string.printable" />
                     <mapping initial="none"/>
                 </sanitizer>
             </param>
@@ -29,8 +54,7 @@
                         <param name="bibtex" label="BibTex" type="text" area="true"
                             help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
                             <sanitizer>
-                                <valid initial="string.printable">
-                                </valid>
+                                <valid initial="string.printable" />
                                 <mapping initial="none"/>
                             </sanitizer>
                         </param>
@@ -40,9 +64,9 @@
      </xml>
      <xml name="io">
      <section name="io" title="Input and output files" expanded="true">
-        <repeat name="history_inputs" title="zero or more input data files to pass as parameters to the executable."
+        <repeat name="history_inputs" title="zero or more input data files to pass on the command line to the executable."
              help="USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool">
-            <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false"
+            <param name="input_files" type="data" format="data" label="Select an input file from your history" multiple="false"
                help=""/>
             <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
               help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
@@ -50,32 +74,23 @@
                 <column name="value" index="0"/>
                </options>
             </param>
-            <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative"
-             help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" >
-            <sanitizer invalid_char="">
-              <valid initial="string.printable"> <remove value='~~~'/> </valid>
-              <mapping initial="none"/>
-            </sanitizer>
+            <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" >
             </param>
-            <param name="input_help" type="text" value="" label="This will become help text on the form."
-             help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation">
-            <sanitizer invalid_char="">
-              <valid initial="string.printable"> <remove value='~~~'/> </valid>
-              <mapping initial="none"/>
-            </sanitizer>
+            <param name="input_help" type="text" value="" label="This will become help text on the form." >
             </param>
             <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
               help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value="">
             </param>
+            <param name="input_repeat" type="boolean" checked="False" truevalue="1"  falsevalue="0" label="Allow user to repeat this input as many times as needed." />
         </repeat>
         <repeat name="history_outputs" title="one or more new history items output by the executable to appear in the user history after the tool runs"
              help="The name will become a history item for users of the new tool you are making containing one of it's outputs">
             <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false"
               help="No spaces! Argparse will also use this name as --[name]">
               <sanitizer invalid_char="_">
-                <valid initial="string.ascii_letters,string.digits">
+                <valid initial="string.ascii_letters,string.digits" >
                    <add value="_" />
-                 </valid>
+                </valid>
               </sanitizer>
             </param>
             <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
@@ -89,6 +104,26 @@
             <param name="history_test" type="text"  label="Test pass decision criterion for this output compared to test generation"
               help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/>
         </repeat>
+        <repeat name="collection_outputs" title="zero or more new history collections to appear in the user history after the tool runs"
+             help="A collection contains outputs not needed for downstream tools such as images and intermediate reports" default="0">
+            <param name="name" type="text" label="Name for new collection with all outputs not individually passed to history outputs"
+              help="No spaces! ">
+              <sanitizer invalid_char="_">
+                <valid initial="string.ascii_letters,string.digits" >
+                   <add value="_" />
+                </valid>
+              </sanitizer>
+            </param>
+            <param name="kind" type="select" multiple="false" label="Select the kind of collection for this output"
+              help="">
+                <option value="list" selected="true">List</option>
+                <option value="paired">Paired</option>
+                <option value="list:paired">List of paired</option>
+            </param>
+            <param name="label" type="text"  label="Label for this collection" help="" value=""/>
+            <param name="discover" type="text"  label="Discover datasets expression" help="__name_and_ext__ should catch all filenames with extensions" value="__name_and_ext__"/>
+        </repeat>
+
         </section>
      </xml>
      <xml name="additparam">
@@ -98,8 +133,7 @@
             <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
             <option value="no">No - use the fixed values for all additional parameters - no user editing</option>
         </param>
-
-        <repeat name="additional_parameters" title="zero or more settings to be set by the tool user and passed on the command line"
+        <repeat name="additional_parameters" title="zero or more command line settings for the user to pass to the executable"
              help="See examples below to see how these can be parsed by scripts in the various languages">
           <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!">
             <sanitizer invalid_char="">
@@ -107,35 +141,37 @@
               <mapping initial="none"/>
             </sanitizer>
           </param>
+          <conditional name="ap_type">
           <param name="param_type" type="select" label="Select the type for this parameter">
-            <option value="text" selected="true">text</option>
-            <option value="integer">integer</option>
-            <option value="float">float</option>
-          </param>
-          <param name="param_value" type="text" value="" label="Enter this parameter's default value"
-            help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" >
-            <sanitizer invalid_char="">
-              <valid initial="string.printable"> <remove value='~~~'/> </valid>
-              <mapping initial="none"/>
-            </sanitizer>
+            <option value="text" selected="true">Text string</option>
+            <option value="integer">Integer</option>
+            <option value="float">Float</option>
+            <option value="boolean">Boolean</option>
+            <option value="selecttext">Select text string</option>
           </param>
-          <param name="param_label" type="text" value="" label="Enter this parameter's label for the form"
-             help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" >
-            <sanitizer invalid_char="">
-              <valid initial="string.printable"> <remove value='~~~'/> </valid>
-              <mapping initial="none"/>
-            </sanitizer>
+          <when value = "text">
+              <expand macro="singleText" />
+          </when>
+          <when value = "integer">
+              <expand macro="singleInt" />
+          </when>
+          <when value = "float">
+              <expand macro="singleFloat" />
+          </when>
+          <when value = "boolean">
+              <expand macro="singleBoolean" />
+          </when>
+          <when value = "selecttext">
+              <expand macro="selectText" />
+          </when>
+          </conditional>
+          <param name="param_label" type="text" value="" label="Enter this parameter's label for the form">
           </param>
-          <param name="param_help" type="text" value="" label="Help for this parameter"
-             help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" >
-            <sanitizer invalid_char="">
-              <valid initial="string.printable"> <remove value='~~~'/> </valid>
-              <mapping initial="none"/>
-            </sanitizer>
+          <param name="param_help" type="text" value="" label="Help for this parameter">
           </param>
           <param name="param_CL" type="text" label="Positional ordinal | argparse argument name"
               help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value="" />
-          <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ~~--foo if needed"
+          <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed"
               help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
         </repeat>
         </section>
@@ -146,7 +182,7 @@
    <requirement type="package" version="0.4.12">galaxyxml</requirement>
    <requirement type="package" version="0.14.0">bioblend</requirement>
    <requirement type="package" version="0.10.6">ephemeris</requirement>
-   <requirement type="package" version="0.74.1">planemo</requirement>
+   <requirement type="package" version="0.74.3">planemo</requirement>
 </requirements>
 
   <command ><![CDATA[
@@ -173,6 +209,7 @@
 --sysexe "$deps.usescript.scriptrunner"
     #end if
 --tool_name "$tool_name"  --user_email "$__user_email__" --citations "$citeme"  --parampass "$io_param.ppass.parampass"
+
    #if str($make.makeMode.make_Tool)!="runonly":
 --make_Tool "$make.makeMode.make_Tool"
 --tool_desc "$make.makeMode.tool_desc"
@@ -188,15 +225,40 @@
      #if str($io_param.ppass.addparam.edit_params) == "yes":
 --edit_additional_parameters
      #end if
-     #for apar in $io_param.ppass.addparam.additional_parameters:
---additional_parameters "$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed"
+     #for $apar in $io_param.ppass.addparam.additional_parameters:
+        #if $apar.ap_type.param_type=="selecttext":
+--selecttext_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help",
+"type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [
+         #for $i,$st in enumerate($apar.ap_type.selectTexts):
+           "$st.select_value"
+           #if ($i < (len($apar.ap_type.selectTexts)-1)):
+           ,
+           #end if
+         #end for
+         ], "texts": [
+         #for $i,$st in enumerate($apar.ap_type.selectTexts):
+         "$st.select_text"
+          #if ($i < (len($apar.ap_type.selectTexts)-1)):
+           ,
+           #end if
+
+         #end for
+         ]
+         }'
+       #else:
+--additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help",
+"type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed" }'
+       #end if
      #end for
    #end if
      #for $intab in $io_param.ppass.io.history_inputs:
---input_files "$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help"
+--input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label", "help": "$intab.input_help", "repeat": "$intab.input_repeat"}'
      #end for
      #for $otab in $io_param.ppass.io.history_outputs:
---output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
+--output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"}'
+     #end for
+     #for $collect in $io_param.ppass.io.collection_outputs:
+--collection '{"name": "$collect.name", "kind": "$collect.kind", "discover": "$collect.discover", "label": "$collect.label"}'
      #end for
 --galaxy_root "$__root_dir__"
 --tool_dir "$__tool_directory__"
@@ -250,7 +312,7 @@
     <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true">
 
     <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes"
-    optional="false" help="Use =[ver] or :[ver] for specific version - 'bwa=0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported"  />
+     help="Use =[ver] or :[ver] for specific version - 'bwa=0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported"  />
 
     <conditional name="usescript">
         <param name="choosescript" type="select" display="radio" label="Supply a script for a dependency (e.g. python/R/bash) or a system executable such as Bash"
@@ -264,18 +326,12 @@
         </when>
         <when value="yes">
             <param name="scriptrunner" type="text" value=""   label="Interpreter for the script - eg bash or python. Can be one of the dependencies named above or a system executable"
-             help="Scripts are interpreted by the executable named here. Use bash for bash scripts, or a conda dependency such as R or Python for those scripts">
-            <sanitizer invalid_char="">
-                <valid initial="string.ascii_letters,string.digits">
-                    <add value="_"/>
-                </valid>
-            </sanitizer>
+              help="Scripts are interpreted by the executable named here. For conda r-base, 'Rscript --vanilla' or for conda planemo, 'planemo test' for example">
             </param>
             <param name="dynScript" type="text" area="True" value="" label="Script for executable above to interpret. It can be one of the Conda dependency names "
              help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below">
               <sanitizer>
-                 <valid initial="string.printable">
-                 </valid>
+                 <valid initial="string.printable"/>
                  <mapping initial="none"/>
               </sanitizer>
              </param>
@@ -302,8 +358,8 @@
         </when>
     </conditional>
     </section>
-    <param name="cl_prefix" type="text" value="" label="Prefix for generated command line. Prepends generated i/o and parameter CL. Use override below to replace completely"
-            help="Text will replace generated executable/script elements. Sometimes required before i/o and parameters in the generated command line." />
+    <param name="cl_prefix" type="text" value="" label="Suffix for generated command line. Useful for bash post processing. Use override below to replace completely"
+            help="';' separated bash commands can be used here for post processing - added at end of autogenerated command line" />
     <conditional name="cover">
         <param name="commover" type="select" display="radio" label="Add Human wrought code to override the generated XML command and/or test section - DIY"
         help = "For arbitrary and artfull command lines. All i/o and parameters must be passed. Choose No unless needed. Not for the faint of heart">
@@ -318,16 +374,14 @@
             <param name="command_override" type="text" area="True" value="" label="Optional. Human wrought command element override XML/template - e.g. for bwa"
              help="For arbitrary and artfull command lines. All i/o and parameters must be passed. Leave blank unless needed. Not for the faint of heart">
               <sanitizer>
-                 <valid initial="string.printable">
-                 </valid>
+                 <valid initial="string.printable"/>
                  <mapping initial="none"/>
               </sanitizer>
              </param>
             <param name="test_override" type="text" area="True" value="" label="Optional. Human wrought test element override XML/template - e.g. for bwa"
              help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart">
               <sanitizer>
-                 <valid initial="string.printable">
-                 </valid>
+                 <valid initial="string.printable" />
                  <mapping initial="none"/>
               </sanitizer>
             </param>
@@ -339,7 +393,7 @@
           help="Installation in this Galaxy is optional" >
         <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
         <option value="gentest" selected="true">Test with planemo after generating.</option>
-        <option value="gentestinstall">Install in Galaxy after generation and testing. URLs and matching API keys are required for this step! </option>
+        <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option>
         </param>
        <when value="generate">
            <param name="galaxy_apikey" value="" type="hidden"  ></param>
@@ -359,32 +413,28 @@
             <param name="galaxy_url" type="text" value="http://localhost:8080" label="URL for the Galaxy server where the new tool should be installed"
              help="Default is localhost">
               <sanitizer>
-                 <valid initial="string.printable">
-                 </valid>
+                 <valid initial="string.printable" />
                  <mapping initial="none"/>
               </sanitizer>
             </param>
           <param name="galaxy_apikey" type="text" value="fakekey" label="API key for the Galaxy to install the new tool"
              help="Cut and paste from the admin user properties screen">
               <sanitizer>
-                 <valid initial="string.ascii_letters,string.digits">
-                 </valid>
+                 <valid initial="string.ascii_letters,string.digits" />
                  <mapping initial="none"/>
               </sanitizer>
             </param>
            <param name="toolshed_url" type="text" value="http://localhost:9009" label="URL for the Toolshed where the new tool should be installed"
              help="Default value is localhost:9009">
               <sanitizer>
-                 <valid initial="string.printable">
-                 </valid>
+                 <valid initial="string.printable" />
                  <mapping initial="none"/>
               </sanitizer>
             </param>
            <param name="toolshed_apikey" type="text" value="fakekey" label="API key for the local toolshed to use when installing the tool"
              help="Cut and paste from the admin user properties screen">
               <sanitizer>
-                 <valid initial="string.ascii_letters,string.digits">
-                 </valid>
+                 <valid initial="string.ascii_letters,string.digits" />
                  <mapping initial="none"/>
               </sanitizer>
             </param>
@@ -395,7 +445,7 @@
   </inputs>
   <outputs>
 
-    <data format="tgz" name="new_tool" label="${tool_name}_toolshed.tgz" >
+    <data format="toolshed.gz" name="new_tool" label="${tool_name}_toolshed.gz" >
         <filter>makeMode['make_Tool'] != "runonly"</filter>
     </data>
 
@@ -413,7 +463,7 @@
     <param name="input_help" value="help" />
     <param name="tool_name" value="pyrevpos" />
     <param name="parampass" value="positional" />
-    <param name="make_Tool" value="generate" />
+    <param name="make_Tool" value="gentest" />
     <param name="tool_version" value="0.01" />
     <param name="tool_desc" value="positional reverse" />
     <param name="help_text" value="help text goes here" />
@@ -512,6 +562,27 @@
       o.write('\n')
     o.close()
 
+R script to draw some plots - use a collection.
+
+::
+
+
+     \# note this script takes NO input because it generates random data
+    dir.create('plots')
+    for (i in 1:10) {
+        foo = runif(100)
+        bar = rnorm(100)
+        bar = foo + 0.05*bar
+        pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_'))
+        plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6)
+        dev.off()
+        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(paste('plots/yet',i,"anotherheatmap.pdf",sep='_'))
+        heatmap(bar,main='Random Heatmap')
+        dev.off()
+    }
+
 
 
 Paper_
@@ -524,7 +595,7 @@
 
 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
 .. _GTF:  https://github.com/fubar2/toolfactory
-.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573
+.. _Paper: https://academic.oup.com/bioinformatics/article/28/23/3139/192853
 
 
 </help>