changeset 0:fc50a3f507ab draft

Need a new repo - old tool_factory_2 is broken
author fubar
date Sat, 10 Apr 2021 02:16:35 +0000
parents
children 48458b0369aa
files toolfactory/LICENSE toolfactory/README.md toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml toolfactory/test-data/input1_sample toolfactory/test-data/output2_sample toolfactory/test-data/pyrevpos.python toolfactory/test-data/test1_log.txt toolfactory/test-data/toolfactory_pyrevpos_tgz_sample
diffstat 9 files changed, 2812 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/LICENSE	Sat Apr 10 02:16:35 2021 +0000
@@ -0,0 +1,504 @@
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+That's all there is to it!
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/README.md	Sat Apr 10 02:16:35 2021 +0000
@@ -0,0 +1,211 @@
+**Breaking news! Docker container is recommended as at August 2020**
+
+A Docker container can be built - see the docker directory.
+It is highly recommended for isolation. It also has an integrated toolshed to allow installation of new tools back 
+into the Galaxy being used to generate them. 
+
+Built from quay.io/bgruening/galaxy:20.05 but updates the
+Galaxy code to the dev branch - it seems to work fine with updated bioblend>=0.14
+with planemo and the right version of gxformat2 needed by the ToolFactory (TF).
+
+The runclean.sh script run from the docker subdirectory of your local clone of this repository
+should create a container (eventually) and serve it at localhost:8080 with a toolshed at
+localhost:9009.
+
+Once it's up, please restart Galaxy in the container with 
+```docker exec [container name] supervisorctl restart galaxy: ```
+Jobs just do not seem to run properly otherwise and the next steps won't work!
+
+The generated container includes a workflow and 2 sample data sets for the workflow
+
+Load the workflow. Adjust the inputs for each as labelled. The perl example counts GC in phiX.fasta. 
+The python scripts use the rgToolFactory.py as their input - any text file will work but I like the
+recursion. The BWA example has some mitochondrial reads and reference. Run the workflow and watch.
+This should fill the history with some sample tools you can rerun and play with.
+Note that each new tool will have been tested using Planemo. In the workflow, in Galaxy.
+Extremely cool to watch.
+
+*WARNING* 
+
+ Install this tool on a throw-away private Galaxy or Docker container ONLY
+ Please NEVER on a public or production instance
+
+*Short Story*
+
+Galaxy is easily extended to new applications by adding a new tool. Each new scientific computational package added as
+a tool to Galaxy requires some special instructions to be written. This is sometimes termed "wrapping" the package
+because the instructions tell Galaxy how to run the package as a new Galaxy tool. Any tool in a Galaxy is 
+readily available to all the users through a consistent and easy to use interface.
+
+Most Galaxy tool wrappers have been manually prepared by skilled programmers, many using Planemo because it 
+automates much of the basic boilerplate and makes the process much easier. The ToolFactory (TF) 
+uses Planemo under the hood for many functions, but hides the command
+line complexities from the TF user. 
+
+*More Explanation*
+
+The TF is an unusual Galaxy tool, designed to allow a skilled user to make new Galaxy tools. 
+It appears in Galaxy just like any other tool but outputs include new Galaxy tools generated
+using instructions provided by the user and the results of Planemo lint and tool testing using
+small sample inputs provided by the TF user. The small samples become tests built in to the new tool.
+
+It offers a familiar Galaxy form driven way to define how the user of the new tool will 
+choose input data from their history, and what parameters the new tool user will be able to adjust.
+The TF user must know, or be able to read, enough about the tool to be able to define the details of
+the new Galaxy interface and the ToolFactory offers little guidance on that other than some examples.
+
+Tools always depend on other things. Most tools in Galaxy depend on third party
+scientific packages, so TF tools usually have one or more dependencies. These can be
+scientific packages such as BWA or scripting languages such as Python and are
+usually managed by Conda. If the new tool relies on a system utility such as bash or awk 
+where the importance of version control on reproducibility is low, these can be used without 
+Conda management - but remember the potential risks of unmanaged dependencies on computational
+reproducibility.
+
+The TF user can optionally supply a working script where scripting is
+required and the chosen dependency is a scripting language such as Python or a system
+scripting executable such as bash. Whatever the language, the script must correctly parse the command line
+arguments it receives at tool execution, as they are defined by the TF user. The
+text of that script is "baked in" to the new tool and will be executed each time
+the new tool is run. It is highly recommended that scripts and their command lines be developed
+and tested until proven to work before the TF is invoked. Galaxy as a software development
+environment is actually possible, but not recommended being somewhat clumsy and inefficient.
+
+Tools nearly always take one or more data sets from the user's history as input. TF tools
+allow the TF user to define what Galaxy datatypes the tool end user will be able to choose and what 
+names or positions will be used to pass them on a command line to the package or script.
+
+Tools often have various parameter settings. The TF allows the TF user to define how each
+parameter will appear on the tool form to the end user, and what names or positions will be
+used to pass them on the command line to the package. At present, parameters are limited to
+simple text and number fields. Pull requests for other kinds of parameters that galaxyxml
+can handle are welcomed.
+
+Best practice Galaxy tools have one or more automated tests. These should use small sample data sets and
+specific parameter settings so when the tool is tested, the outputs can be compared with their expected
+values. The TF will automatically create a test for the new tool. It will use the sample data sets 
+chosen by the TF user when they built the new tool.
+
+The TF works by exposing *unrestricted* and therefore extremely dangerous scripting
+to all designated administrators of the host Galaxy server, allowing them to
+run scripts in R, python, sh and perl. For this reason, a Docker container is
+available to help manage the associated risks.
+
+*Scripting uses*
+
+To use a scripting language to create a new tool, you must first prepared and properly test a script. Use small sample
+data sets for testing. When the script is working correctly, upload the small sample datasets
+into a new history, start configuring a new ToolFactory tool, and paste the script into the script text box on the TF form.
+
+*Outputs*
+
+Once the script runs sucessfully, a new Galaxy tool that runs your script
+can be generated. Select the "generate" option and supply some help text and
+names. The new tool will be generated in the form of a new Galaxy datatype
+*tgz* - as the name suggests, it's an archive ready to upload to a
+Galaxy ToolShed as a new tool repository.
+
+It is also possible to run a tool to generate test outputs, then test it
+using planemo. A toolshed is built in to the Docker container and configured
+so a tool can be tested, sent to that toolshed, then installed in the Galaxy
+where the TF is running.
+
+If the tool requires a command or test XML override, then planemo is 
+needed to generate test outputs to make a complete tool, rerun to test 
+and if required upload to the local toolshed and install in the Galaxy 
+where the TF is running.
+
+Once it's in a ToolShed, it can be installed into any local Galaxy server
+from the server administrative interface.
+
+Once the new tool is installed, local users can run it - each time, the 
+package and/or script that was supplied when it was built will be executed with the input chosen
+from the user's history, together with user supplied parameters. In other words, the tools you generate with the
+ToolFactory run just like any other Galaxy tool.
+
+TF generated tools work as normal workflow components.
+
+
+*Limitations*
+
+The TF is flexible enough to generate wrappers for many common scientific packages
+but the inbuilt automation will not cope with all possible situations. Users can
+supply overrides for two tool XML segments - tests and command and the BWA
+example in the supplied samples workflow illustrates their use.  
+
+*Installation*
+
+The Docker container is the best way to use the TF because it is preconfigured
+to automate new tool testing and has a built in local toolshed where each new tool
+is uploaded. If you grab the docker container, it should just work. 
+
+If you build the container, there are some things to watch out for. Let it run for 10 minutes
+or so once you build it - check with top until conda has finished fussing. Once everything quietens
+down, find the container with
+```docker ps```
+and use
+```docker exec [containername] supervisorctl restart galaxy:```
+That colon is not a typographical mistake.
+Not restarting after first boot seems to leave the job/worflow system confused and the workflow
+just will not run properly until Galaxy has restarted.
+
+Login as admin@galaxy.org with password "password". Feel free to change it once you are logged in. 
+There should be a companion toolshed at localhost:9090. The history should have some sample data for
+the workflow.
+
+Run the workflow and make sure the right dataset is selected for each of the input files. Most of the 
+examples use text files so should run, but the bwa example needs the right ones to work properly.
+
+When the workflow is finished, you will have half a dozen examples to rerun and play with. They have also 
+all been tested and installed so you should find them in your tool menu under "Generated Tools"
+
+It is easy to install without Docker, but you will need to make some 
+configuration changes (TODO write a configuration). You can install it most conveniently using the
+administrative "Search and browse tool sheds" link. Find the Galaxy Main
+toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
+repository in the Tool Maker section. Open it and review the code and select the option to install it.
+
+Otherwise, if not already there pending an accepted PR,
+please add:
+<datatype extension="tgz" type="galaxy.datatypes.binary:Binary"
+mimetype="multipart/x-gzip" subclass="True" />
+to your local data_types_conf.xml.
+
+
+*Restricted execution*
+
+The tool factory tool itself will then be usable ONLY by admin users -
+people with IDs in admin_users. **Yes, that's right. ONLY
+admin_users can run this tool** Think about it for a moment. If allowed to
+run any arbitrary script on your Galaxy server, the only thing that would
+impede a miscreant bent on destroying all your Galaxy data would probably
+be lack of appropriate technical skills.
+
+**Generated tool Security**
+
+Once you install a generated tool, it's just
+another tool - assuming the script is safe. They just run normally and their
+user cannot do anything unusually insecure but please, practice safe toolshed.
+Read the code before you install any tool. Especially this one - it is really scary.
+
+**Send Code**
+
+Pull requests and suggestions welcome as git issues please?
+
+**Attribution**
+
+Creating re-usable tools from scripts: The Galaxy Tool Factory
+Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
+Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
+
+http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
+
+**Licensing**
+
+Copyright Ross Lazarus 2010
+ross lazarus at g mail period com
+
+All rights reserved.
+
+Licensed under the LGPL
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/rgToolFactory2.py	Sat Apr 10 02:16:35 2021 +0000
@@ -0,0 +1,1139 @@
+# replace with shebang for biocontainer
+# see https://github.com/fubar2/toolfactory
+#
+# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
+#
+# all rights reserved
+# Licensed under the LGPL
+# suggestions for improvement and bug fixes welcome at
+# https://github.com/fubar2/toolfactory
+#
+# July 2020: BCC was fun and I feel like rip van winkle after 5 years.
+# Decided to
+# 1. Fix the toolfactory so it works - done for simplest case
+# 2. Fix planemo so the toolfactory function works
+# 3. Rewrite bits using galaxyxml functions where that makes sense - done
+
+import argparse
+import copy
+import json
+import logging
+import os
+import re
+import shlex
+import shutil
+import subprocess
+import sys
+import tarfile
+import tempfile
+import time
+
+import galaxyxml.tool as gxt
+import galaxyxml.tool.parameters as gxtp
+import lxml
+import yaml
+from bioblend import ConnectionError
+from bioblend import toolshed
+
+myversion = "V2.2 February 2021"
+verbose = True
+debug = True
+toolFactoryURL = "https://github.com/fubar2/toolfactory"
+foo = len(lxml.__version__)
+FAKEEXE = "~~~REMOVE~~~ME~~~"
+# need this until a PR/version bump to fix galaxyxml prepending the exe even
+# with override.
+
+
+def timenow():
+    """return current time as a string"""
+    return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
+
+
+cheetah_escape_table = {"$": "\\$", "#": "\\#"}
+
+
+def cheetah_escape(text):
+    """Produce entities within text."""
+    return "".join([cheetah_escape_table.get(c, c) for c in text])
+
+
+def parse_citations(citations_text):
+    """"""
+    citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
+    citation_tuples = []
+    for citation in citations:
+        if citation.startswith("doi"):
+            citation_tuples.append(("doi", citation[len("doi") :].strip()))
+        else:
+            citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
+    return citation_tuples
+
+
+class ScriptRunner:
+    """Wrapper for an arbitrary script
+    uses galaxyxml
+
+    """
+
+    def __init__(self, args=None):
+        """
+        prepare command line cl for running the tool here
+        and prepare elements needed for galaxyxml tool generation
+        """
+        self.ourcwd = os.getcwd()
+        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
+        self.lastxclredirect = None
+        self.cl = []
+        self.xmlcl = []
+        self.is_positional = self.args.parampass == "positional"
+        if 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(), ]
+            else:
+                self.executeme = None
+        aCL = self.cl.append
+        aXCL = self.xmlcl.append
+        assert args.parampass in [
+            "0",
+            "argparse",
+            "positional",
+        ], 'args.parampass must be "0","positional" or "argparse"'
+        self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
+        self.tool_id = self.tool_name
+        self.newtool = gxt.Tool(
+            self.tool_name,
+            self.tool_id,
+            self.args.tool_version,
+            self.args.tool_desc,
+            FAKEEXE,
+        )
+        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")
+        if not os.path.exists(self.tooloutdir):
+            os.mkdir(self.tooloutdir)
+        if not os.path.exists(self.testdir):
+            os.mkdir(self.testdir)
+        if not os.path.exists(self.repdir):
+            os.mkdir(self.repdir)
+        self.tinputs = gxtp.Inputs()
+        self.toutputs = gxtp.Outputs()
+        self.testparam = []
+        if self.args.script_path:
+            self.prepScript()
+        if self.args.command_override:
+            scos = open(self.args.command_override, "r").readlines()
+            self.command_override = [x.rstrip() for x in scos]
+        else:
+            self.command_override = None
+        if self.args.test_override:
+            stos = open(self.args.test_override, "r").readlines()
+            self.test_override = [x.rstrip() for x in stos]
+        else:
+            self.test_override = None
+        if self.args.script_path:
+            for ex in self.executeme:
+                aCL(ex)
+                aXCL(ex)
+            aCL(self.sfile)
+            aXCL("$runme")
+        else:
+            for ex in self.executeme:
+                aCL(ex)
+                aXCL(ex)
+
+        self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
+        self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
+        if self.args.parampass == "0":
+            self.clsimple()
+        else:
+            if self.args.parampass == "positional":
+                self.prepclpos()
+                self.clpositional()
+            else:
+                self.prepargp()
+                self.clargparse()
+        if self.args.cl_suffix:  # DIY CL end
+            clp = shlex.split(self.args.cl_suffix)
+            for c in clp:
+                aCL(c)
+                aXCL(c)
+
+    def clsimple(self):
+        """no parameters or repeats - uses < and > for i/o"""
+        aCL = self.cl.append
+        aXCL = self.xmlcl.append
+        if len(self.infiles) > 0:
+            aCL("<")
+            aCL(self.infiles[0]["infilename"])
+            aXCL("<")
+            aXCL("$%s" % self.infiles[0]["infilename"])
+        if len(self.outfiles) > 0:
+            aCL(">")
+            aCL(self.outfiles[0]["name"])
+            aXCL(">")
+            aXCL("$%s" % self.outfiles[0]["name"])
+
+    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 = [">", "$%s" % p["name"]]
+            else:
+                clsuffix.append([p["name"], p["name"], ""])
+                xclsuffix.append([p["name"], "$%s" % p["name"], ""])
+        for p in self.addpar:
+            nam = p["name"]
+            rep = p["repeat"] == "1"
+            if rep:
+                over = f" #for $rep in $R_{nam}:\n--{nam} $rep.{nam}\n#end for"
+            else:
+                over = p["override"]
+            clsuffix.append([p["CL"], nam, over])
+            xclsuffix.append([p["CL"], nam, over])
+        for p in self.selpar:
+            clsuffix.append([p["CL"], p["name"], p["override"]])
+            xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
+        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:
+            nam = p["name"]
+            rep = p["repeat"] == "1"  # repeats make NO sense
+            if rep:
+                print(f'### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!')
+            over = p["override"]
+            clsuffix.append([p["CL"], nam, over])
+            xclsuffix.append([p["CL"], '"$%s"' % nam, over])
+        for p in self.selpar:
+            clsuffix.append([p["CL"], p["name"], p["override"]])
+            xclsuffix.append([p["CL"], '"$%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()
+        rx = [x.rstrip() for x in rx]
+        rxcheck = [x.strip() for x in rx if x.strip() > ""]
+        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[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[0])
+        artifact = open(art, "wb")
+        artifact.write(bytes("\n".join(self.escapedScript), "utf8"))
+        artifact.close()
+
+    def cleanuppar(self):
+        """ positional parameters are complicated by their numeric ordinal"""
+        if self.args.parampass == "positional":
+            for i, p in enumerate(self.infiles):
+                assert (
+                    p["CL"].isdigit() or p["CL"].strip().upper() == "STDIN"
+                ), "Positional parameters must be ordinal integers - got %s for %s" % (
+                    p["CL"],
+                    p["label"],
+                )
+            for i, p in enumerate(self.outfiles):
+                assert (
+                    p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT"
+                ), "Positional parameters must be ordinal integers - got %s for %s" % (
+                    p["CL"],
+                    p["name"],
+                )
+            for i, p in enumerate(self.addpar):
+                assert p[
+                    "CL"
+                ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
+                    p["CL"],
+                    p["name"],
+                )
+        for i, p in enumerate(self.infiles):
+            infp = copy.copy(p)
+            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["origCL"] = p["CL"]  # keep copy
+            self.outfiles[i] = p
+        for i, p in enumerate(self.addpar):
+            p["origCL"] = p["CL"]
+            self.addpar[i] = p
+
+    def clpositional(self):
+        # inputs in order then params
+        aCL = self.cl.append
+        for (k, v, koverride) in self.clsuffix:
+            if " " in v:
+                aCL("%s" % v)
+            else:
+                aCL(v)
+        aXCL = self.xmlcl.append
+        for (k, v, koverride) in self.xclsuffix:
+            aXCL(v)
+        if self.lastxclredirect:
+            aXCL(self.lastxclredirect[0])
+            aXCL(self.lastxclredirect[1])
+
+    def clargparse(self):
+        """argparse style"""
+        aCL = self.cl.append
+        aXCL = self.xmlcl.append
+        # inputs then params in argparse named form
+
+        for (k, v, koverride) in self.xclsuffix:
+            if koverride > "":
+                k = koverride
+                aXCL(k)
+            else:
+                if len(k.strip()) == 1:
+                    k = "-%s" % k
+                else:
+                    k = "--%s" % k
+                aXCL(k)
+                aXCL(v)
+        for (k, v, koverride) in self.clsuffix:
+            if koverride > "":
+                k = koverride
+            elif len(k.strip()) == 1:
+                k = "-%s" % k
+            else:
+                k = "--%s" % k
+            aCL(k)
+            aCL(v)
+        if self.lastxclredirect:
+            aXCL(self.lastxclredirect[0])
+            aXCL(self.lastxclredirect[1])
+
+    def getNdash(self, newname):
+        if self.is_positional:
+            ndash = 0
+        else:
+            ndash = 2
+            if len(newname) < 2:
+                ndash = 1
+        return ndash
+
+    def doXMLparam(self):
+        """flake8 made me do this..."""
+        for p in self.outfiles:
+            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(
+                name=newname, format=newfmt, num_dashes=ndash, label=newname
+            )
+            aparm.positional = self.is_positional
+            if self.is_positional:
+                if oldcl.upper() == "STDOUT":
+                    aparm.positional = 9999999
+                    aparm.command_line_override = "> $%s" % newname
+                else:
+                    aparm.positional = int(oldcl)
+                    aparm.command_line_override = "$%s" % newname
+            self.toutputs.append(aparm)
+            ld = None
+            if test.strip() > "":
+                if test.startswith("diff"):
+                    c = "diff"
+                    ld = 0
+                    if test.split(":")[1].isdigit:
+                        ld = int(test.split(":")[1])
+                    tp = gxtp.TestOutput(
+                        name=newname,
+                        value="%s_sample" % newname,
+                        compare=c,
+                        lines_diff=ld,
+                    )
+                elif test.startswith("sim_size"):
+                    c = "sim_size"
+                    tn = test.split(":")[1].strip()
+                    if tn > "":
+                        if "." in tn:
+                            delta = None
+                            delta_frac = min(1.0, float(tn))
+                        else:
+                            delta = int(tn)
+                            delta_frac = None
+                    tp = gxtp.TestOutput(
+                        name=newname,
+                        value="%s_sample" % newname,
+                        compare=c,
+                        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["infilename"]
+            newfmt = p["format"]
+            ndash = self.getNdash(newname)
+            reps = p.get("repeat", 0) == 1
+            if not len(p["label"]) > 0:
+                alab = p["CL"]
+            else:
+                alab = p["label"]
+            aninput = gxtp.DataParam(
+                newname,
+                optional=False,
+                label=alab,
+                help=p["help"],
+                format=newfmt,
+                multiple=False,
+                num_dashes=ndash,
+            )
+            aninput.positional = self.is_positional
+            if self.is_positional:
+                if p["origCL"].upper() == "STDIN":
+                    aninput.positional = 9999998
+                    aninput.command_line_override = "> $%s" % newname
+                else:
+                    aninput.positional = int(p["origCL"])
+                    aninput.command_line_override = "$%s" % newname
+            if reps:
+                repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {alab} as needed")
+                repe.append(aninput)
+                self.tinputs.append(repe)
+                tparm = gxtp.TestRepeat(name=f"R_{newname}")
+                tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname)
+                tparm.append(tparm2)
+                self.testparam.append(tparm)
+            else:
+                self.tinputs.append(aninput)
+                tparm = gxtp.TestParam(newname, value="%s_sample" % newname)
+                self.testparam.append(tparm)
+        for p in self.addpar:
+            newname = p["name"]
+            newval = p["value"]
+            newlabel = p["label"]
+            newhelp = p["help"]
+            newtype = p["type"]
+            newcl = p["CL"]
+            oldcl = p["origCL"]
+            reps = p["repeat"] == "1"
+            if not len(newlabel) > 0:
+                newlabel = newname
+            ndash = self.getNdash(newname)
+            if newtype == "text":
+                aparm = gxtp.TextParam(
+                    newname,
+                    label=newlabel,
+                    help=newhelp,
+                    value=newval,
+                    num_dashes=ndash,
+                )
+            elif newtype == "integer":
+                aparm = gxtp.IntegerParam(
+                    newname,
+                    label=newlabel,
+                    help=newhelp,
+                    value=newval,
+                    num_dashes=ndash,
+                )
+            elif newtype == "float":
+                aparm = gxtp.FloatParam(
+                    newname,
+                    label=newlabel,
+                    help=newhelp,
+                    value=newval,
+                    num_dashes=ndash,
+                )
+            elif newtype == "boolean":
+                aparm = gxtp.BooleanParam(
+                    newname,
+                    label=newlabel,
+                    help=newhelp,
+                    value=newval,
+                    num_dashes=ndash,
+                )
+            else:
+                raise ValueError(
+                    'Unrecognised parameter type "%s" for\
+                 additional parameter %s in makeXML'
+                    % (newtype, newname)
+                )
+            aparm.positional = self.is_positional
+            if self.is_positional:
+                aparm.positional = int(oldcl)
+            if reps:
+                repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {newlabel} as needed")
+                repe.append(aparm)
+                self.tinputs.append(repe)
+                tparm = gxtp.TestRepeat(name=f"R_{newname}")
+                tparm2 = gxtp.TestParam(newname, value=newval)
+                tparm.append(tparm2)
+                self.testparam.append(tparm)
+            else:
+                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)
+            try:
+                tparm = gxtp.TestOutputCollection(newname)  # broken until PR merged.
+                self.testparam.append(tparm)
+            except Exception:
+                print("#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!")
+
+    def doNoXMLparam(self):
+        """filter style package - stdin to stdout"""
+        if len(self.infiles) > 0:
+            alab = self.infiles[0]["label"]
+            if len(alab) == 0:
+                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]["infilename"]
+            aninput = gxtp.DataParam(
+                newname,
+                optional=False,
+                label=alab,
+                help=self.infiles[0]["help"],
+                format=self.infiles[0]["format"],
+                multiple=False,
+                num_dashes=0,
+            )
+            aninput.command_line_override = "< $%s" % newname
+            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]["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)
+            self.testparam.append(tp)
+
+    def makeXML(self):
+        """
+        Create a Galaxy xml tool wrapper for the new script
+        Uses galaxyhtml
+        Hmmm. How to get the command line into correct order...
+        """
+        if self.command_override:
+            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 len(safertext.strip()) == 0:
+            safertext = (
+                "Ask the tool author (%s) to rebuild with help text please\n"
+                % (self.args.user_email)
+            )
+        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(","):
+                ver = ""
+                d = d.replace("==", ":")
+                d = d.replace("=", ":")
+                if ":" in d:
+                    packg, ver = d.split(":")
+                else:
+                    packg = d
+                requirements.append(
+                    gxtp.Requirement("package", packg.strip(), ver.strip())
+                )
+            self.newtool.requirements = requirements
+        if self.args.parampass == "0":
+            self.doNoXMLparam()
+        else:
+            self.doXMLparam()
+        self.newtool.outputs = self.toutputs
+        self.newtool.inputs = self.tinputs
+        if self.args.script_path:
+            configfiles = gxtp.Configfiles()
+            configfiles.append(
+                gxtp.Configfile(name="runme", text="\n".join(self.escapedScript))
+            )
+            self.newtool.configfiles = configfiles
+        tests = gxtp.Tests()
+        test_a = gxtp.Test()
+        for tp in self.testparam:
+            test_a.append(tp)
+        tests.append(test_a)
+        self.newtool.tests = tests
+        self.newtool.add_comment(
+            "Created by %s at %s using the Galaxy Tool Factory."
+            % (self.args.user_email, timenow())
+        )
+        self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
+        exml0 = self.newtool.export()
+        exml = exml0.replace(FAKEEXE, "")  # temporary work around until PR accepted
+        if (
+            self.test_override
+        ):  # 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, "\n".join(self.test_override), part2)
+            exml = fixed
+        # exml = exml.replace('range="1:"', 'range="1000:"')
+        xf = open("%s.xml" % self.tool_name, "w")
+        xf.write(exml)
+        xf.write("\n")
+        xf.close()
+        # ready for the tarball
+
+    def run(self):
+        """
+        generate test outputs by running a command line
+        won't work if command or test override in play - planemo is the
+        easiest way to generate test outputs for that case so is
+        automagically selected
+        """
+        scl = " ".join(self.cl)
+        err = None
+        if self.args.parampass != "0":
+            if os.path.exists(self.elog):
+                ste = open(self.elog, "a")
+            else:
+                ste = open(self.elog, "w")
+            if self.lastclredirect:
+                sto = open(self.lastclredirect[1], "wb")  # is name of an output file
+            else:
+                if os.path.exists(self.tlog):
+                    sto = open(self.tlog, "a")
+                else:
+                    sto = open(self.tlog, "w")
+                sto.write(
+                    "## Executing Toolfactory generated command line = %s\n" % scl
+                )
+            sto.flush()
+            subp = subprocess.run(
+                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]["name"], "rb")
+            else:
+                sti = sys.stdin
+            if len(self.outfiles) > 0:
+                sto = open(self.outfiles[0]["name"], "wb")
+            else:
+                sto = sys.stdout
+            subp = subprocess.run(
+                self.cl, shell=False, stdout=sto, stdin=sti
+            )
+            sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
+            retval = subp.returncode
+            sto.close()
+            sti.close()
+        if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
+            os.unlink(self.tlog)
+        if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
+            os.unlink(self.elog)
+        if retval != 0 and err:  # problem
+            sys.stderr.write(err)
+        logging.debug("run done")
+        return retval
+
+    def shedLoad(self):
+        """
+        use bioblend to create new repository
+        or update existing
+
+        """
+        if os.path.exists(self.tlog):
+            sto = open(self.tlog, "a")
+        else:
+            sto = open(self.tlog, "w")
+
+        ts = toolshed.ToolShedInstance(
+            url=self.args.toolshed_url,
+            key=self.args.toolshed_api_key,
+            verify=False,
+        )
+        repos = ts.repositories.get_repositories()
+        rnames = [x.get("name", "?") for x in repos]
+        rids = [x.get("id", "?") for x in repos]
+        tfcat = "ToolFactory generated tools"
+        if self.tool_name not in rnames:
+            tscat = ts.categories.get_categories()
+            cnames = [x.get("name", "?").strip() for x in tscat]
+            cids = [x.get("id", "?") for x in tscat]
+            catID = None
+            if tfcat.strip() in cnames:
+                ci = cnames.index(tfcat)
+                catID = cids[ci]
+            res = ts.repositories.create_repository(
+                name=self.args.tool_name,
+                synopsis="Synopsis:%s" % self.args.tool_desc,
+                description=self.args.tool_desc,
+                type="unrestricted",
+                remote_repository_url=self.args.toolshed_url,
+                homepage_url=None,
+                category_ids=catID,
+            )
+            tid = res.get("id", None)
+            sto.write(f"#create_repository {self.args.tool_name} tid={tid} res={res}\n")
+        else:
+            i = rnames.index(self.tool_name)
+            tid = rids[i]
+        try:
+            res = ts.repositories.update_repository(
+                id=tid, tar_ball_path=self.newtarpath, commit_message=None
+            )
+            sto.write(f"#update res id {id} ={res}\n")
+        except ConnectionError:
+            sto.write(
+                "####### Is the toolshed running and the API key correct? Bioblend shed upload failed\n"
+            )
+        sto.close()
+
+    def eph_galaxy_load(self):
+        """
+        use ephemeris to load the new tool from the local toolshed after planemo uploads it
+        """
+        if os.path.exists(self.tlog):
+            tout = open(self.tlog, "a")
+        else:
+            tout = open(self.tlog, "w")
+        cll = [
+            "shed-tools",
+            "install",
+            "-g",
+            self.args.galaxy_url,
+            "--latest",
+            "-a",
+            self.args.galaxy_api_key,
+            "--name",
+            self.tool_name,
+            "--owner",
+            "fubar",
+            "--toolshed",
+            self.args.toolshed_url,
+            "--section_label",
+            "ToolFactory",
+        ]
+        tout.write("running\n%s\n" % " ".join(cll))
+        subp = subprocess.run(
+            cll,
+            cwd=self.ourcwd,
+            shell=False,
+            stderr=tout,
+            stdout=tout,
+        )
+        tout.write(
+            "installed %s - got retcode %d\n" % (self.tool_name, subp.returncode)
+        )
+        tout.close()
+        return subp.returncode
+
+    def writeShedyml(self):
+        """for planemo"""
+        yuser = self.args.user_email.split("@")[0]
+        yfname = os.path.join(self.tooloutdir, ".shed.yml")
+        yamlf = open(yfname, "w")
+        odict = {
+            "name": self.tool_name,
+            "owner": yuser,
+            "type": "unrestricted",
+            "description": self.args.tool_desc,
+            "synopsis": self.args.tool_desc,
+            "category": "TF Generated Tools",
+        }
+        yaml.dump(odict, yamlf, allow_unicode=True)
+        yamlf.close()
+
+    def makeTool(self):
+        """write xmls and input samples into place"""
+        if self.args.parampass == 0:
+            self.doNoXMLparam()
+        else:
+            self.makeXML()
+        if self.args.script_path:
+            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["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, report_fail=False):
+        """move outputs into test-data and prepare the tarball"""
+        excludeme = "_planemo_test_report.html"
+
+        def exclude_function(tarinfo):
+            filename = tarinfo.name
+            return None if filename.endswith(excludeme) else tarinfo
+
+        if os.path.exists(self.tlog):
+            tout = open(self.tlog, "a")
+        else:
+            tout = open(self.tlog, "w")
+        for p in self.outfiles:
+            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):
+                if os.path.isfile(src):
+                    shutil.copyfile(src, tdest)
+                    dest = os.path.join(self.repdir, "%s.sample" % (oname))
+                    shutil.copyfile(src, dest)
+                else:
+                    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,
+            arcname=self.tool_name,
+            filter=exclude_function,
+        )
+        tf.close()
+        shutil.copyfile(self.newtarpath, self.args.new_tool)
+
+    def moveRunOutputs(self):
+        """need to move planemo or run outputs into toolfactory collection"""
+        with os.scandir(self.tooloutdir) as outs:
+            for entry in outs:
+                if not entry.is_file():
+                    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.tooloutdir, 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_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
+        supplied test outputs are sent to repdir for display
+        """
+        xreal = "%s.xml" % self.tool_name
+        tool_test_path = os.path.join(
+            self.repdir, f"{self.tool_name}_planemo_test_report.html"
+        )
+        if os.path.exists(self.tlog):
+            tout = open(self.tlog, "a")
+        else:
+            tout = open(self.tlog, "w")
+        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
+
+
+def main():
+    """
+    This is a Galaxy wrapper.
+    It expects to be called by a special purpose tool.xml
+
+    """
+    parser = argparse.ArgumentParser()
+    a = parser.add_argument
+    a("--script_path", default=None)
+    a("--history_test", default=None)
+    a("--cl_suffix", default=None)
+    a("--sysexe", default=None)
+    a("--packages", default=None)
+    a("--tool_name", default="newtool")
+    a("--tool_dir", default=None)
+    a("--input_files", default=[], action="append")
+    a("--output_files", default=[], action="append")
+    a("--user_email", default="Unknown")
+    a("--bad_user", default=None)
+    a("--make_Tool", default="runonly")
+    a("--help_text", default=None)
+    a("--tool_desc", default=None)
+    a("--tool_version", default=None)
+    a("--citations", default=None)
+    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")
+    a("--new_tool", default="new_tool")
+    a("--galaxy_url", default="http://localhost:8080")
+    a("--toolshed_url", default="http://localhost:9009")
+    # make sure this is identical to tool_sheds_conf.xml
+    # localhost != 127.0.0.1 so validation fails
+    a("--toolshed_api_key", default="fakekey")
+    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 \
+admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file'
+        % (args.bad_user, args.bad_user)
+    )
+    assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
+    assert (
+        args.sysexe or args.packages
+    ), "## Tool Factory wrapper expects an interpreter \
+or an executable package in --sysexe or --packages"
+    r = ScriptRunner(args)
+    r.writeShedyml()
+    r.makeTool()
+    if args.make_Tool == "generate":
+        r.run()
+        r.moveRunOutputs()
+        r.makeToolTar()
+    else:
+        # r.planemo_test(genoutputs=True)  # this fails :( - see PR
+        # r.moveRunOutputs()
+        # r.makeToolTar(report_fail=False)
+        r.planemo_test_once()
+        r.moveRunOutputs()
+        r.makeToolTar(report_fail=True)
+        if args.make_Tool == "gentestinstall":
+            r.shedLoad()
+            r.eph_galaxy_load()
+
+
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/rgToolFactory2.xml	Sat Apr 10 02:16:35 2021 +0000
@@ -0,0 +1,613 @@
+<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"/>
+            <param name="tool_desc" label="Tool Synopsis" type="text" value=""
+             help="Supply a brief tool description for the Galaxy tool menu entry" />
+            <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
+            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" />
+                    <mapping initial="none"/>
+                </sanitizer>
+            </param>
+            <repeat name="citations" title="Citation">
+                <conditional name="citation_type">
+                    <param name="type" type="select" display="radio" label="Citation Type">
+                        <option value="doi">DOI</option>
+                        <option value="bibtex">BibTeX</option>
+                    </param>
+                    <when value="doi">
+                        <param name="doi" label="DOI" type="text" value=""
+                        help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) to be cited when this tool is used in published research." />
+                    </when>
+                    <when value="bibtex">
+                        <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" />
+                                <mapping initial="none"/>
+                            </sanitizer>
+                        </param>
+                    </when>
+                </conditional>
+            </repeat>
+     </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 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" 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">
+               <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
+                <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" >
+            </param>
+            <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 wanted - script/executable must parse these."/>
+        </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" >
+                   <add value="_" />
+                </valid>
+              </sanitizer>
+            </param>
+            <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
+              help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
+               <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
+                <column name="value" index="0"/>
+               </options>
+            </param>
+            <param name="history_CL" type="text"  label="Positional: ordinal integer. Use STDOUT if '>' required. Otherwise ignored if argparse because name is used"
+              help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/>
+            <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="Hides 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! Script MUST create and fill a directory with the same name and the tool test MUST be overwritten - see the plotter example for hints">
+              <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">
+     <section name="addparam" title="Executable or script settings passed on the command line other than I/O files" expanded="true">
+        <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?"
+             help="If no, users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
+            <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 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="">
+              <valid initial="string.ascii_letters,string.digits"/>
+              <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 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>
+          <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">
+          </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"
+              help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
+          <param name="param_repeat" type="boolean" checked="False" truevalue="1"  falsevalue="0" label="Allow user to repeat this as many times as needed." />
+        </repeat>
+        </section>
+     </xml>
+  </macros>
+
+<requirements>
+   <requirement type="package" version="0.4.13">galaxyxml</requirement>
+   <requirement type="package" version="0.14.0">bioblend</requirement>
+   <requirement type="package" version="0.10.6">ephemeris</requirement>
+   <requirement type="package" version="0.74.3">planemo</requirement>
+</requirements>
+
+  <command ><![CDATA[
+#import os
+#set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
+#if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
+python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
+ #else:
+python3 $__tool_directory__/rgToolFactory2.py
+    #if len(str($cl_suffix)) > 0:
+--cl_suffix "$cl_suffix"
+    #end if
+    #if $cover.commover == "yes":
+       #if len(str($cover.command_override)) > 10:
+--command_override "$commandoverride"
+       #end if
+       #if len(str($cover.test_override)) > 10:
+--test_override "$testoverride"
+       #end if
+    #end if
+--packages "$deps.packages"
+   #if $deps.usescript.choosescript == "yes":
+--script_path "$runme"
+--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"
+--tool_version "$make.makeMode.tool_version"
+--help_text "$helpme"
+--new_tool "$new_tool"
+--toolshed_api_key "$make.makeMode.toolshed_apikey"
+--galaxy_api_key "$make.makeMode.galaxy_apikey"
+--toolshed_url "$make.makeMode.toolshed_url"
+--galaxy_url "$make.makeMode.galaxy_url"
+   #end if
+   #if $io_param.ppass.parampass != '0':
+     #if str($io_param.ppass.addparam.edit_params) == "yes":
+--edit_additional_parameters
+     #end if
+     #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": "$apar.param_CLprefixed", "repeat": "$apar.param_repeat"}'
+       #end if
+     #end for
+   #end if
+     #for $intab in $io_param.ppass.io.history_inputs:
+--input_files '{"name": "$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 $io_param.ppass.io.history_outputs:
+--output_files '{"name": "$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 "$__tool_directory__"
+ #end if
+]]></command>
+ <configfiles>
+  <configfile name="runme">
+$deps.usescript.dynScript
+ </configfile>
+ <configfile name="commandoverride">
+#if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1:
+$cover.command_override
+#end if
+ </configfile>
+ <configfile name="testoverride">
+#if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1:
+$cover.test_override
+#end if
+ </configfile>
+ <configfile name="helpme">
+    #if $make.makeMode.make_Tool != "runonly":
+${make.makeMode.help_text}
+    #else
+$tool_name help goes here
+    #end if
+ </configfile>
+ <configfile name="citeme">
+#if $make.makeMode.make_Tool != "runonly":
+    #for $citation in $make.makeMode.citations:
+        #if $citation.citation_type.type == "bibtex":
+            **ENTRY**bibtex
+            ${citation.citation_type.bibtex}
+        #else
+            **ENTRY**doi
+            ${citation.citation_type.doi}
+        #end if
+    #end for
+#end if
+ </configfile>
+  </configfiles>
+  <inputs>
+   <param name="tool_name" type="text" value="tool1"   label="New tool ID and title for outputs"
+         help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only">
+        <sanitizer invalid_char="">
+            <valid initial="string.ascii_lowercase,string.digits">
+                <add value="_"/>
+            </valid>
+        </sanitizer>
+    </param>
+
+    <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"
+     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"
+        help = "For script interpreters like Python or bash, parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them">
+            <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>
+            <option value="yes" selected="true">Yes, a script is ready to be pasted below</option>
+        </param>
+        <when value="no">
+            <param name="dynScript" type="hidden"  value="" />
+            <param name="scriptrunner" type="hidden"  value="" />
+        </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. 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"/>
+                 <mapping initial="none"/>
+              </sanitizer>
+             </param>
+        </when>
+    </conditional>
+    </section>
+    <section name="io_param" title="Data file input, output and settings forming the executable or script command line" expanded="true">
+    <conditional name="ppass">
+        <param name="parampass"  type="select" display="radio" label="Command line parameter passing method to use">
+            <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option>
+            <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option>
+            <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option>
+        </param>
+        <when value="argparse">
+            <expand macro="io" />
+            <expand macro="additparam" />
+        </when>
+        <when value="positional">
+            <expand macro="io" />
+            <expand macro="additparam" />
+        </when>
+        <when value="0">
+             <expand macro="io"/>
+        </when>
+    </conditional>
+    </section>
+    <param name="cl_suffix" 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">
+            <sanitizer>
+                 <valid initial="string.printable" />
+                 <mapping initial="none"/>
+            </sanitizer>
+    </param>
+    <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">
+            <option value="no" selected="true">No. Use automatically generated command/test XML </option>
+            <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option>
+        </param>
+        <when value="no">
+            <param name="command_override" type="hidden"  value="" />
+            <param name="test_override" type="hidden"  value="" />
+        </when>
+        <when value="yes">
+            <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"/>
+                 <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" />
+                 <mapping initial="none"/>
+              </sanitizer>
+            </param>
+        </when>
+    </conditional>
+     <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true">
+    <conditional name="makeMode">
+        <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. The TF Docker container is recommended for local installation"
+          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 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>
+           <param name="toolshed_apikey" value="" type="hidden"  ></param>
+           <param name="galaxy_url" value="" type="hidden"  ></param>
+           <param name="toolshed_url" value="" type="hidden"  ></param>
+            <expand macro="tool_metadata" />
+        </when>
+       <when value="gentest">
+           <param name="galaxy_apikey" value="" type="hidden"  ></param>
+           <param name="toolshed_apikey" value="" type="hidden"  ></param>
+           <param name="galaxy_url" value="" type="hidden"  ></param>
+           <param name="toolshed_url" value="" type="hidden"  ></param>
+            <expand macro="tool_metadata" />
+        </when>
+       <when value="gentestinstall">
+            <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" />
+                 <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" />
+                 <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" />
+                 <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" />
+                 <mapping initial="none"/>
+              </sanitizer>
+            </param>
+            <expand macro="tool_metadata" />
+        </when>
+    </conditional>
+    </section>
+  </inputs>
+  <outputs>
+
+    <data format="toolshed.gz" name="new_tool" label="${tool_name}_toolshed.gz" >
+        <filter>makeMode['make_Tool'] != "runonly"</filter>
+    </data>
+
+  <collection name="TF_run_report" type="list" label="${tool_name} outputs">
+      <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
+  </collection>
+  </outputs>
+<tests>
+<test>
+    <param name="user_email" value="admin@galaxy.org"/>
+    <param name="input_files" value="input1_sample" />
+    <param name="input_CL" value="1" />
+    <param name="input_formats" value="txt" />
+    <param name="input_label" value="input" />
+    <param name="input_help" value="help" />
+    <param name="tool_name" value="pyrevpos" />
+    <param name="parampass" value="positional" />
+    <param name="make_Tool" value="gentest" />
+    <param name="tool_version" value="0.01" />
+    <param name="tool_desc" value="positional reverse" />
+    <param name="help_text" value="help text goes here" />
+    <param name="packages" value="python"/>
+    <param name="history_name" value="output2" />
+    <param name="history_format" value="txt" />
+    <param name="history_CL" value="2" />
+    <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/>
+    <param name="choosescript" value="yes" />
+    <param name="script_path" value="$runme"/>
+    <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
+</test>
+</tests>
+<help>
+
+.. class:: warningmark
+
+**Details and attribution**
+(see GTF_)
+
+**Local Admins ONLY**
+Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
+
+**If you find a bug**
+Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_
+
+**What it does**
+This tool optionally generates normal workflow compatible first class Galaxy tools
+
+Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form.
+Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user.
+Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example.
+
+Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime.
+These can be editable by the downstream user or baked in.
+
+When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical
+set of outputs - these are used to construct a test for the new tool.
+
+If tool generation is required, a new tarball compatible with any Galaxy toolshed is created.
+It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or
+installed into any toolshed from where it can be installed into your Galaxy.
+
+
+.. class:: warningmark
+
+**Note to system administrators**
+This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
+Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
+
+.. class:: warningmark
+
+**Use on public servers**  is STRONGLY discouraged for obvious reasons
+
+The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation.
+We recommend that you follow the good code hygiene practices associated with safe toolshed practices.
+
+Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing:
+
+::
+
+    # reverse order of text by row
+    import sys
+    inp = sys.argv[1]
+    outp = sys.argv[2]
+    i = open(inp,'r').readlines()
+    o = open(outp,'w')
+    for row in i:
+      rs = row.rstrip()
+      rs = list(rs)
+      rs.reverse()
+      o.write(''.join(rs))
+      o.write('\n')
+    o.close()
+
+With argparse style parameters:
+
+::
+
+    # reverse order of text by row
+    import argparse
+    parser = argparse.ArgumentParser()
+    a = parser.add_argument
+    a('--infile',default='')
+    a('--outfile',default=None)
+    args = parser.parse_args()
+    inp = args.infile
+    outp = args.outfile
+    i = open(inp,'r').readlines()
+    o = open(outp,'w')
+    for row in i:
+      rs = row.rstrip()
+      rs = list(rs)
+      rs.reverse()
+      o.write(''.join(rs))
+      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_
+
+*Licensing*
+
+Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
+All rights reserved.
+Licensed under the LGPL_
+
+.. _LGPL: http://www.gnu.org/copyleft/lesser.html
+.. _GTF:  https://github.com/fubar2/toolfactory
+.. _Paper: https://academic.oup.com/bioinformatics/article/28/23/3139/192853
+
+
+</help>
+<citations>
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
+</citations>
+</tool>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/input1_sample	Sat Apr 10 02:16:35 2021 +0000
@@ -0,0 +1,166 @@
+*WARNING before you start*
+
+ Install this tool on a private Galaxy ONLY
+ Please NEVER on a public or production instance
+ 
+Updated august 2014 by John Chilton adding citation support
+
+Updated august 8 2014 to fix bugs reported by Marius van den Beek
+
+Please cite the resource at
+http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
+if you use this tool in your published work.
+
+**Short Story**
+
+This is an unusual Galaxy tool capable of generating new Galaxy tools.
+It works by exposing *unrestricted* and therefore extremely dangerous scripting
+to all designated administrators of the host Galaxy server, allowing them to
+run scripts in R, python, sh and perl over multiple selected input data sets,
+writing a single new data set as output.
+
+*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*
+
+It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.
+
+
+**Automated generation of new Galaxy tools for installation into any Galaxy**
+
+A test is generated using small sample test data inputs and parameter settings you supply.
+Once the test case outputs have been produced, they can be used to build a
+new Galaxy tool. The supplied script or executable is baked as a requirement
+into a new, ordinary Galaxy tool, fully workflow compatible out of the box.
+Generated tools are installed via a tool shed by an administrator
+and work exactly like all other Galaxy tools for your users.
+
+**More Detail**
+
+To use the ToolFactory, you should have prepared a script to paste into a
+text box, or have a package in mind and a small test input example ready to select from your history
+to test your new script.
+
+```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me
+
+There is an example in each scripting language on the Tool Factory form. You
+can just cut and paste these to try it out - remember to select the right
+interpreter please. You'll also need to create a small test data set using
+the Galaxy history add new data tool.
+
+If the script fails somehow, use the "redo" button on the tool output in
+your history to recreate the form complete with broken script. Fix the bug
+and execute again. Rinse, wash, repeat.
+
+Once the script runs sucessfully, a new Galaxy tool that runs your script
+can be generated. Select the "generate" option and supply some help text and
+names. The new tool will be generated in the form of a new Galaxy datatype
+*toolshed.gz* - as the name suggests, it's an archive ready to upload to a
+Galaxy ToolShed as a new tool repository.
+
+Once it's in a ToolShed, it can be installed into any local Galaxy server
+from the server administrative interface.
+
+Once the new tool is installed, local users can run it - each time, the script
+that was supplied when it was built will be executed with the input chosen
+from the user's history. In other words, the tools you generate with the
+ToolFactory run just like any other Galaxy tool,but run your script every time.
+
+Tool factory tools are perfect for workflow components. One input, one output,
+no variables.
+
+*To fully and safely exploit the awesome power* of this tool,
+Galaxy and the ToolShed, you should be a developer installing this
+tool on a private/personal/scratch local instance where you are an
+admin_user. Then, if you break it, you get to keep all the pieces see
+https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+**Installation**
+This is a Galaxy tool. You can install it most conveniently using the
+administrative "Search and browse tool sheds" link. Find the Galaxy Main
+toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
+repository. Open it and review the code and select the option to install it.
+
+If you can't get the tool that way, the xml and py files here need to be
+copied into a new tools
+subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry
+pointing to the xml
+file - something like::
+
+  <section name="Tool building tools" id="toolbuilders">
+    <tool file="toolfactory/rgToolFactory.xml"/>
+  </section>
+
+If not already there,
+please add:
+<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary"
+mimetype="multipart/x-gzip" subclass="True" />
+to your local data_types_conf.xml.
+
+
+**Restricted execution**
+
+The tool factory tool itself will then be usable ONLY by admin users -
+people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY
+admin_users can run this tool** Think about it for a moment. If allowed to
+run any arbitrary script on your Galaxy server, the only thing that would
+impede a miscreant bent on destroying all your Galaxy data would probably
+be lack of appropriate technical skills.
+
+**What it does** 
+
+This is a tool factory for simple scripts in python, R and
+perl currently. Functional tests are automatically generated. How cool is that.
+
+LIMITED to simple scripts that read one input from the history. Optionally can
+write one new history dataset, and optionally collect any number of outputs
+into links on an autogenerated HTML index page for the user to navigate -
+useful if the script writes images and output files - pdf outputs are shown
+as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and
+imagemagik need to be available.
+
+Generated tools can be edited and enhanced like any Galaxy tool, so start
+small and build up since a generated script gets you a serious leg up to a
+more complex one.
+
+**What you do**
+
+You paste and run your script, you fix the syntax errors and
+eventually it runs. You can use the redo button and edit the script before
+trying to rerun it as you debug - it works pretty well.
+
+Once the script works on some test data, you can generate a toolshed compatible
+gzip file containing your script ready to run as an ordinary Galaxy tool in
+a repository on your local toolshed. That means safe and largely automated
+installation in any production Galaxy configured to use your toolshed.
+
+**Generated tool Security**
+
+Once you install a generated tool, it's just
+another tool - assuming the script is safe. They just run normally and their
+user cannot do anything unusually insecure but please, practice safe toolshed.
+Read the code before you install any tool. Especially this one - it is really scary.
+
+**Send Code**
+
+Patches and suggestions welcome as bitbucket issues please?
+
+**Attribution**
+
+Creating re-usable tools from scripts: The Galaxy Tool Factory
+Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
+Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
+
+http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
+
+**Licensing**
+
+Copyright Ross Lazarus 2010
+ross lazarus at g mail period com
+
+All rights reserved.
+
+Licensed under the LGPL
+
+**Obligatory screenshot**
+
+http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/output2_sample	Sat Apr 10 02:16:35 2021 +0000
@@ -0,0 +1,165 @@
+*trats uoy erofeb GNINRAW*
+
+YLNO yxalaG etavirp a no loot siht llatsnI 
+ecnatsni noitcudorp ro cilbup a no REVEN esaelP 
+
+troppus noitatic gnidda notlihC nhoJ yb 4102 tsugua detadpU
+
+keeB ned nav suiraM yb detroper sgub xif ot 4102 8 tsugua detadpU
+
+ta ecruoser eht etic esaelP
+fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth
+.krow dehsilbup ruoy ni loot siht esu uoy fi
+
+**yrotS trohS**
+
+.sloot yxalaG wen gnitareneg fo elbapac loot yxalaG lausunu na si sihT
+gnitpircs suoregnad ylemertxe erofereht dna *detcirtsernu* gnisopxe yb skrow tI
+ot meht gniwolla ,revres yxalaG tsoh eht fo srotartsinimda detangised lla ot
+,stes atad tupni detceles elpitlum revo lrep dna hs ,nohtyp ,R ni stpircs nur
+.tuptuo sa tes atad wen elgnis a gnitirw
+
+*sretemarap elyts esrapgra ro lanoitisop htiw elbatucexe yna ro tpircs hsab/lrep/nohtyp/r gnikrow a evah uoY*
+
+.loot yxalaG a gnisu ,setunim ni loot yxalaG yranidro na otni denrut eb nac tI
+
+
+**yxalaG yna otni noitallatsni rof sloot yxalaG wen fo noitareneg detamotuA**
+
+.ylppus uoy sgnittes retemarap dna stupni atad tset elpmas llams gnisu detareneg si tset A
+a dliub ot desu eb nac yeht ,decudorp neeb evah stuptuo esac tset eht ecnO
+tnemeriuqer a sa dekab si elbatucexe ro tpircs deilppus ehT .loot yxalaG wen
+.xob eht fo tuo elbitapmoc wolfkrow ylluf ,loot yxalaG yranidro ,wen a otni
+rotartsinimda na yb dehs loot a aiv dellatsni era sloot detareneG
+.sresu ruoy rof sloot yxalaG rehto lla ekil yltcaxe krow dna
+
+**liateD eroM**
+
+a otni etsap ot tpircs a deraperp evah dluohs uoy ,yrotcaFlooT eht esu oT
+yrotsih ruoy morf tceles ot ydaer elpmaxe tupni tset llams a dna dnim ni egakcap a evah ro ,xob txet
+.tpircs wen ruoy tset ot
+
+em rof skrow ```atad-tset/yrotcafloot/srekam_loot/sloot/yxalag/~ atad_tset-- yxalag/~ toor_yxalag-- lmx.2yrotcaFlooTgr tset omenalp```
+
+uoY .mrof yrotcaF looT eht no egaugnal gnitpircs hcae ni elpmaxe na si erehT
+thgir eht tceles ot rebmemer - tuo ti yrt ot eseht etsap dna tuc tsuj nac
+gnisu tes atad tset llams a etaerc ot deen osla ll'uoY .esaelp reterpretni
+.loot atad wen dda yrotsih yxalaG eht
+
+ni tuptuo loot eht no nottub "oder" eht esu ,wohemos sliaf tpircs eht fI
+gub eht xiF .tpircs nekorb htiw etelpmoc mrof eht etaercer ot yrotsih ruoy
+.taeper ,hsaw ,esniR .niaga etucexe dna
+
+tpircs ruoy snur taht loot yxalaG wen a ,yllufssecus snur tpircs eht ecnO
+dna txet pleh emos ylppus dna noitpo "etareneg" eht tceleS .detareneg eb nac
+epytatad yxalaG wen a fo mrof eht ni detareneg eb lliw loot wen ehT .seman
+a ot daolpu ot ydaer evihcra na s'ti ,stseggus eman eht sa - *zg.dehsloot*
+.yrotisoper loot wen a sa dehSlooT yxalaG
+
+revres yxalaG lacol yna otni dellatsni eb nac ti ,dehSlooT a ni s'ti ecnO
+.ecafretni evitartsinimda revres eht morf
+
+tpircs eht ,emit hcae - ti nur nac sresu lacol ,dellatsni si loot wen eht ecnO
+nesohc tupni eht htiw detucexe eb lliw tliub saw ti nehw deilppus saw taht
+eht htiw etareneg uoy sloot eht ,sdrow rehto nI .yrotsih s'resu eht morf
+.emit yreve tpircs ruoy nur tub,loot yxalaG rehto yna ekil tsuj nur yrotcaFlooT
+
+,tuptuo eno ,tupni enO .stnenopmoc wolfkrow rof tcefrep era sloot yrotcaf looT
+.selbairav on
+
+,loot siht fo *rewop emosewa eht tiolpxe ylefas dna ylluf oT*
+siht gnillatsni repoleved a eb dluohs uoy ,dehSlooT eht dna yxalaG
+na era uoy erehw ecnatsni lacol hctarcs/lanosrep/etavirp a no loot
+ees seceip eht lla peek ot teg uoy ,ti kaerb uoy fi ,nehT .resu_nimda
+emoH/ikiw/yrotcaflootyxalag/rabuf/gro.tekcubtib//:sptth
+
+**noitallatsnI**
+eht gnisu yltneinevnoc tsom ti llatsni nac uoY .loot yxalaG a si sihT
+niaM yxalaG eht dniF .knil "sdehs loot esworb dna hcraeS" evitartsinimda
+yrotcafloot eht rof hcraes dna /ude.usp.xb.2g.dehsloot//:sptth ta dehsloot
+.ti llatsni ot noitpo eht tceles dna edoc eht weiver dna ti nepO .yrotisoper
+
+eb ot deen ereh selif yp dna lmx eht ,yaw taht loot eht teg t'nac uoy fI
+sloot wen a otni deipoc
+yrtne wen a sdeen lmx.fnoc_loot ruoY yrotcafloot/sloot sa hcus yrotceridbus
+lmx eht ot gnitniop
+::ekil gnihtemos - elif
+
+>"sredliubloot"=di "sloot gnidliub looT"=eman noitces<  
+>/"lmx.yrotcaFlooTgr/yrotcafloot"=elif loot<    
+>noitces/<  
+
+,ereht ydaerla ton fI
+:dda esaelp
+"yraniB:yranib.sepytatad.yxalag"=epyt "zg.dehsloot"=noisnetxe epytatad<
+>/ "eurT"=ssalcbus "pizg-x/trapitlum"=epytemim
+.lmx.fnoc_sepyt_atad lacol ruoy ot
+
+
+**noitucexe detcirtseR**
+
+- sresu nimda yb YLNO elbasu eb neht lliw flesti loot yrotcaf loot ehT
+YLNO .thgir s'taht ,seY** ini.igsw_esrevinu ni sresu_nimda ni sDI htiw elpoep
+ot dewolla fI .tnemom a rof ti tuoba knihT **loot siht nur nac sresu_nimda
+dluow taht gniht ylno eht ,revres yxalaG ruoy no tpircs yrartibra yna nur
+ylbaborp dluow atad yxalaG ruoy lla gniyortsed no tneb tnaercsim a edepmi
+.slliks lacinhcet etairporppa fo kcal eb
+
+**seod ti tahW**
+
+dna R ,nohtyp ni stpircs elpmis rof yrotcaf loot a si sihT
+.taht si looc woH .detareneg yllacitamotua era stset lanoitcnuF .yltnerruc lrep
+
+nac yllanoitpO .yrotsih eht morf tupni eno daer taht stpircs elpmis ot DETIMIL
+stuptuo fo rebmun yna tcelloc yllanoitpo dna ,tesatad yrotsih wen eno etirw
+- etagivan ot resu eht rof egap xedni LMTH detarenegotua na no sknil otni
+nwohs era stuptuo fdp - selif tuptuo dna segami setirw tpircs eht fi lufesu
+dna taht os tpircstsohg htiw knurhs era s'fdp detaolb s'R dna slianbmuht sa
+.elbaliava eb ot deen kigamegami
+
+trats os ,loot yxalaG yna ekil decnahne dna detide eb nac sloot detareneG
+a ot pu gel suoires a uoy steg tpircs detareneg a ecnis pu dliub dna llams
+.eno xelpmoc erom
+
+**od uoy tahW**
+
+dna srorre xatnys eht xif uoy ,tpircs ruoy nur dna etsap uoY
+erofeb tpircs eht tide dna nottub oder eht esu nac uoY .snur ti yllautneve
+.llew ytterp skrow ti - gubed uoy sa ti nurer ot gniyrt
+
+elbitapmoc dehsloot a etareneg nac uoy ,atad tset emos no skrow tpircs eht ecnO
+ni loot yxalaG yranidro na sa nur ot ydaer tpircs ruoy gniniatnoc elif pizg
+detamotua ylegral dna efas snaem tahT .dehsloot lacol ruoy no yrotisoper a
+.dehsloot ruoy esu ot derugifnoc yxalaG noitcudorp yna ni noitallatsni
+
+**ytiruceS loot detareneG**
+
+tsuj s'ti ,loot detareneg a llatsni uoy ecnO
+rieht dna yllamron nur tsuj yehT .efas si tpircs eht gnimussa - loot rehtona
+.dehsloot efas ecitcarp ,esaelp tub erucesni yllausunu gnihtyna od tonnac resu
+.yracs yllaer si ti - eno siht yllaicepsE .loot yna llatsni uoy erofeb edoc eht daeR
+
+**edoC dneS**
+
+?esaelp seussi tekcubtib sa emoclew snoitseggus dna sehctaP
+
+**noitubirttA**
+
+yrotcaF looT yxalaG ehT :stpircs morf sloot elbasu-er gnitaerC
+maeT yxalaG ehT ;nnameiZ kraM ;ipsaK ynotnA ;surazaL ssoR
+375stb/scitamrofnioib/3901.01 :iod ;2102 scitamrofnioiB
+
+fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth
+
+**gnisneciL**
+
+0102 surazaL ssoR thgirypoC
+moc doirep liam g ta surazal ssor
+
+.devreser sthgir llA
+
+LPGL eht rednu desneciL
+
+**tohsneercs yrotagilbO**
+
+gnp.looTtpircScimanyd/segami/989ef2308adf/crs/rekamlootyxalag/rabuf/gro.tekcubtib//:ptth
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/pyrevpos.python	Sat Apr 10 02:16:35 2021 +0000
@@ -0,0 +1,13 @@
+# reverse order of text by row
+import sys
+inp = sys.argv[1]
+outp = sys.argv[2]
+i = open(inp,'r').readlines()
+o = open(outp,'w')
+for row in i:
+   rs = row.rstrip()
+   rs = list(rs)
+   rs.reverse()
+   o.write(''.join(rs))
+o.close() 
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/test1_log.txt	Sat Apr 10 02:16:35 2021 +0000
@@ -0,0 +1,1 @@
+## Executing Toolfactory generated command line = python /tmp/pyrevposq5dmcdy1.python /tmp/tmpqrksf8sd/files/5/b/9/dataset_5b952a86-87df-44ad-a415-ea549f3f0cee.dat output2
Binary file toolfactory/test-data/toolfactory_pyrevpos_tgz_sample has changed