comparison toolfactory/rgToolFactory2.py @ 38:a30536c100bf draft

Updated history outputs

37:099047ee7094

# rgToolFactory.py
# see https://github.com/fubar2/toolfactory
#
# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
#

import tempfile
import time

import galaxyxml.tool as gxt
import galaxyxml.tool.parameters as gxtp
import lxml

foo = lxml.__name__   # fug you, flake8. Say my name! Please accept the PR, Helena!

progname = os.path.split(sys.argv[0])[1]
myversion = "V2.1 July 2020"
verbose = True
debug = True
toolFactoryURL = "https://github.com/fubar2/toolfactory"
ourdelim = "~~~"

# --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label~~~$input_help"
IPATHPOS = 0
ICLPOS = 1
IFMTPOS = 2
ILABPOS = 3
IHELPOS = 4
IOCLPOS = 5
# --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL
ONAMEPOS = 0
OFMTPOS = 1
OCLPOS = 2
OOCLPOS = 3

# --additional_parameters="$i.param_name~~~$i.param_value~~~$i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL"
ANAMEPOS = 0
AVALPOS = 1
ALABPOS = 2
AHELPPOS = 3
ATYPEPOS = 4
ACLPOS = 5
AOCLPOS = 6


def timenow():
    """return current time as a string
    """
    return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))

    """
    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

            "argparse",
            "positional",
        ], 'Parameter passing in 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.xmlfile = "%s.xml" % self.tool_name
        if self.args.interpreter_name:
            exe = "$runMe"
        else:
            exe = self.args.exe_package
        assert (

            self.clsimple()
        else:
            clsuffix = []
            xclsuffix = []
            for i, p in enumerate(self.infiles):
                appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS]]
                clsuffix.append(appendme)
                xclsuffix.append([p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS]])
                # print('##infile i=%d, appendme=%s' % (i,appendme))
            for i, p in enumerate(self.outfiles):
                if p[OOCLPOS] == "STDOUT":
                    self.lastclredirect = [">", p[ONAMEPOS]]
                    self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
                    # print('##outfiles i=%d lastclredirect = %s' % (i,self.lastclredirect))
                else:
                    appendme = [p[OOCLPOS], p[OCLPOS], p[ONAMEPOS]]
                    clsuffix.append(appendme)
                    xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS]])
                    # print('##outfiles i=%d' % i,'appendme',appendme)
            for p in self.addpar:
                appendme = [p[AOCLPOS], p[ACLPOS], p[AVALPOS]]
                clsuffix.append(appendme)
                xclsuffix.append([p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS]])
                # print('##adpar %d' % i,'appendme=',appendme)
            clsuffix.sort()
            xclsuffix.sort()
            self.xclsuffix = xclsuffix
            self.clsuffix = clsuffix
            if self.args.parampass == "positional":

        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.args.interpreter_name)
        )
        tscript = open(self.sfile, "w")
        tscript.write(self.script)
        tscript.close()
        self.indentedScript = "  %s" % "\n".join([" %s" % html_escape(x) for x in rx])
        self.escapedScript = "%s" % "\n".join([" %s" % html_escape(x) for x in rx])
        art = "%s.%s" % (self.tool_name, self.args.interpreter_name)
        artifact = open(art, "wb")
        artifact.write(bytes(self.script, "utf8"))
        artifact.close()
        aCL(self.args.interpreter_name)

        aXCL("$%s" % self.outfiles[0][ONAMEPOS])

    def clpositional(self):
        # inputs in order then params
        aCL = self.cl.append
        for (o_v, k, v) in self.clsuffix:
            if " " in v:
                aCL("%s" % v)
            else:
                aCL(v)
        aXCL = self.xmlcl.append
        for (o_v, k, v) in self.xclsuffix:
            aXCL(v)
        if self.lastxclredirect:
            aXCL(self.lastxclredirect[0])
            aXCL(self.lastxclredirect[1])

        """ argparse style
        """
        aCL = self.cl.append
        aXCL = self.xmlcl.append
        # inputs then params in argparse named form
        for (o_v, k, v) in self.xclsuffix:
            if len(k.strip()) == 1:
                k = "-%s" % k
            else:
                k = "--%s" % k
            aXCL(k)
            aXCL(v)
        for (o_v, k, v) in self.clsuffix:
            if len(k.strip()) == 1:
                k = "-%s" % k
            else:
                k = "--%s" % k
            aCL(k)
            aCL(v)

                    aparm.command_line_override = "> $%s" % newcl
                else:
                    aparm.positional = int(oldcl)
                    aparm.command_line_override = "$%s" % newcl
            self.toutputs.append(aparm)
            tp = gxtp.TestOutput(name=newcl, value="%s_sample" % newcl, format=newfmt)
            self.testparam.append(tp)
        for p in self.infiles:
            newname = p[ICLPOS]
            newfmt = p[IFMTPOS]
            ndash = self.getNdash(newname)

            aninput.positional = self.is_positional
            self.tinputs.append(aninput)
            tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
            self.testparam.append(tparm)
        for p in self.addpar:
            newname, newval, newlabel, newhelp, newtype, newcl, oldcl = p
            if not len(newlabel) > 0:
                newlabel = newname
            ndash = self.getNdash(newname)
            if newtype == "text":
                aparm = gxtp.TextParam(

        newfmt = self.outfiles[0][OFMTPOS]
        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, format=newfmt)
        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...
        """
        self.tool.command_line_override = self.xmlcl
        if self.args.interpreter_name:
            self.tool.interpreter = self.interp
        if self.args.help_text:
            helptext = open(self.args.help_text, "r").readlines()
            helptext = [html_escape(x) for x in helptext]
            self.tool.help = "".join([x for x in helptext])
        else:

        requirements = gxtp.Requirements()

        if self.args.interpreter_name:
            if self.args.interpreter_name == "python":
                requirements.append(
                    gxtp.Requirement("package", "python", self.args.interpreter_version)
                )
            elif self.args.interpreter_name not in ["bash", "sh"]:
                requirements.append(
                    gxtp.Requirement(
                        "package",

                )
        else:
            if self.args.exe_package and self.args.parampass != "system":
                requirements.append(
                    gxtp.Requirement(
                        "package", self.args.exe_package, self.args.exe_package_version
                    )
                )
        self.tool.requirements = requirements
        if self.args.parampass == "0":
            self.doXMLNoparam()
        else:
            self.doXMLParam()
        self.tool.outputs = self.toutputs
        self.tool.inputs = self.tinputs
        if self.args.runmode not in ["Executable", "system"]:
            configfiles = gxtp.Configfiles()
            configfiles.append(gxtp.Configfile(name="runMe", text=self.script))

        self.tool.add_comment("Source in git at: %s" % (toolFactoryURL))
        self.tool.add_comment(
            "Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573"
        )
        exml = self.tool.export()
        xf = open(self.xmlfile, "w")
        xf.write(exml)
        xf.write("\n")
        xf.close()
        # ready for the tarball

        NOTE names for test inputs and outputs are munged here so must
        correspond to actual input and output names used on the generated cl
        """
        retval = self.run()
        if retval:
            sys.stderr.write("## Run failed. Cannot build yet. Please fix and retry")
            sys.exit(1)
        tdir = "tfout"
        if not os.path.exists(tdir):
            os.mkdir(tdir)
        self.makeXML()

                shutil.copyfile(pth, dest)
                dest = os.path.join(tdir, p[OCLPOS])
                shutil.copyfile(pth, dest)

        if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0:
            shutil.copyfile(self.tlog, os.path.join(testdir, "test1_log.txt"))
        if self.args.runmode not in ["Executable", "system"]:
            stname = os.path.join(tdir, "%s" % (self.sfile))
            if not os.path.exists(stname):
                shutil.copyfile(self.sfile, stname)
        xtname = os.path.join(tdir, self.xmlfile)
        if not os.path.exists(xtname):
            shutil.copyfile(self.xmlfile, xtname)
        tarpath = "toolfactory_%s.tgz" % self.tool_name
        tf = tarfile.open(tarpath, "w:gz")
        tf.add(name=tdir, arcname=self.tool_name)
        tf.close()
        shutil.copyfile(tarpath, self.args.new_tool)
        return retval

    def run(self):
        """
        Some devteam tools have this defensive stderr read so I'm keeping with the faith

        scl = " ".join(self.cl)
        err = None
        if self.args.parampass != "0":
            ste = open(self.elog, "wb")
            if self.lastclredirect:
                sto = open(self.lastclredirect[1], "wb")  # is name of an output file
            else:
                sto = open(self.tlog, "wb")
                sto.write(
                    bytes(
                        "## Executing Toolfactory generated command line = %s\n" % scl,
                        "utf8",
                    )
                )
            sto.flush()
            p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)

    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 configuration file'
        % (args.bad_user, args.bad_user)
    )
    assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
    assert (
        args.interpreter_name or args.exe_package
    ), "## Tool Factory wrapper expects an interpreter or an executable package"
    assert args.exe_package or (
        len(args.script_path) > 0 and os.path.isfile(args.script_path)
    ), "## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable"
    args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files]
    # remove quotes we need to deal with spaces in CL params
    for i, x in enumerate(args.additional_parameters):
        args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
    r = ScriptRunner(args)
    if args.make_Tool:
        retcode = r.makeTooltar()
    else:
        retcode = r.run()

38:a30536c100bf

#!/usr/bin/env python
# rgToolFactory.py
# see https://github.com/fubar2/toolfactory
#
# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
#

import tempfile
import time

import galaxyxml.tool as gxt
import galaxyxml.tool.parameters as gxtp

import lxml

myversion = "V2.1 July 2020"
verbose = True
debug = True
toolFactoryURL = "https://github.com/fubar2/toolfactory"
ourdelim = "~~~"

# --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label
# ~~~$input_help"
IPATHPOS = 0
ICLPOS = 1
IFMTPOS = 2
ILABPOS = 3
IHELPOS = 4
IOCLPOS = 5

# --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL
ONAMEPOS = 0
OFMTPOS = 1
OCLPOS = 2
OOCLPOS = 3

# --additional_parameters="$i.param_name~~~$i.param_value~~~
# $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
ANAMEPOS = 0
AVALPOS = 1
ALABPOS = 2
AHELPPOS = 3
ATYPEPOS = 4
ACLPOS = 5
AOVERPOS = 6
AOCLPOS = 7


foo = len(lxml.__version__)
# fug you, flake8. Say my name!

def timenow():
    """return current time as a string
    """
    return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))

    """
    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

            "argparse",
            "positional",
        ], 'Parameter passing in 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
        if self.args.interpreter_name:
            exe = "$runMe"
        else:
            exe = self.args.exe_package
        assert (

            self.clsimple()
        else:
            clsuffix = []
            xclsuffix = []
            for i, p in enumerate(self.infiles):
                if p[IOCLPOS] == "STDIN":
                    appendme = [
                        p[IOCLPOS],
                        p[ICLPOS],
                        p[IPATHPOS],
                        "< %s" % p[IPATHPOS],
                    ]
                    xappendme = [
                        p[IOCLPOS],
                        p[ICLPOS],
                        p[IPATHPOS],
                        "< $%s" % p[ICLPOS],
                    ]
                else:
                    appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
                    xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
                clsuffix.append(appendme)
                xclsuffix.append(xappendme)
                # print('##infile i=%d, appendme=%s' % (i,appendme))
            for i, p in enumerate(self.outfiles):
                if p[OOCLPOS] == "STDOUT":
                    self.lastclredirect = [">", p[ONAMEPOS]]
                    self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
                else:
                    clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
                    xclsuffix.append(
                        [p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""]
                    )
            for p in self.addpar:
                clsuffix.append(
                    [p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]]
                )
                xclsuffix.append(
                    [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
                )
            clsuffix.sort()
            xclsuffix.sort()
            self.xclsuffix = xclsuffix
            self.clsuffix = clsuffix
            if self.args.parampass == "positional":

        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.args.interpreter_name)
        )
        tscript = open(self.sfile, "w")
        tscript.write(self.script)
        tscript.close()
        self.indentedScript = "  %s" % "\n".join(
            [" %s" % html_escape(x) for x in rx]
        )
        self.escapedScript = "%s" % "\n".join(
            [" %s" % html_escape(x) for x in rx]
        )
        art = "%s.%s" % (self.tool_name, self.args.interpreter_name)
        artifact = open(art, "wb")
        artifact.write(bytes(self.script, "utf8"))
        artifact.close()
        aCL(self.args.interpreter_name)

        aXCL("$%s" % self.outfiles[0][ONAMEPOS])

    def clpositional(self):
        # inputs in order then params
        aCL = self.cl.append
        for (o_v, k, v, koverride) in self.clsuffix:
            if " " in v:
                aCL("%s" % v)
            else:
                aCL(v)
        aXCL = self.xmlcl.append
        for (o_v, k, v, koverride) in self.xclsuffix:
            aXCL(v)
        if self.lastxclredirect:
            aXCL(self.lastxclredirect[0])
            aXCL(self.lastxclredirect[1])

        """ argparse style
        """
        aCL = self.cl.append
        aXCL = self.xmlcl.append
        # inputs then params in argparse named form
        for (o_v, k, v, koverride) in self.xclsuffix:
            if koverride > "":
                k = koverride
            elif len(k.strip()) == 1:
                k = "-%s" % k
            else:
                k = "--%s" % k
            aXCL(k)
            aXCL(v)
        for (o_v, 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)

                    aparm.command_line_override = "> $%s" % newcl
                else:
                    aparm.positional = int(oldcl)
                    aparm.command_line_override = "$%s" % newcl
            self.toutputs.append(aparm)
            tp = gxtp.TestOutput(
                name=newcl, value="%s_sample" % newcl, format=newfmt
            )
            self.testparam.append(tp)
        for p in self.infiles:
            newname = p[ICLPOS]
            newfmt = p[IFMTPOS]
            ndash = self.getNdash(newname)

            aninput.positional = self.is_positional
            self.tinputs.append(aninput)
            tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
            self.testparam.append(tparm)
        for p in self.addpar:
            newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
            if not len(newlabel) > 0:
                newlabel = newname
            ndash = self.getNdash(newname)
            if newtype == "text":
                aparm = gxtp.TextParam(

        newfmt = self.outfiles[0][OFMTPOS]
        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, format=newfmt
        )
        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...
        """
        self.tool.command_line_override = self.xmlcl
        if self.args.interpreter_name:
            self.tool.interpreter = self.args.interpreter_name
        if self.args.help_text:
            helptext = open(self.args.help_text, "r").readlines()
            helptext = [html_escape(x) for x in helptext]
            self.tool.help = "".join([x for x in helptext])
        else:

        requirements = gxtp.Requirements()

        if self.args.interpreter_name:
            if self.args.interpreter_name == "python":
                requirements.append(
                    gxtp.Requirement(
                        "package", "python", self.args.interpreter_version
                    )
                )
            elif self.args.interpreter_name not in ["bash", "sh"]:
                requirements.append(
                    gxtp.Requirement(
                        "package",

                )
        else:
            if self.args.exe_package and self.args.parampass != "system":
                requirements.append(
                    gxtp.Requirement(
                        "package",
                        self.args.exe_package,
                        self.args.exe_package_version,
                    )
                )
        self.tool.requirements = requirements
        if self.args.parampass == "0":
            self.doNoXMLparam()
        else:
            self.doXMLparam()
        self.tool.outputs = self.toutputs
        self.tool.inputs = self.tinputs
        if self.args.runmode not in ["Executable", "system"]:
            configfiles = gxtp.Configfiles()
            configfiles.append(gxtp.Configfile(name="runMe", text=self.script))

        self.tool.add_comment("Source in git at: %s" % (toolFactoryURL))
        self.tool.add_comment(
            "Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573"
        )
        exml = self.tool.export()
        xf = open('%s.xml' % self.tool_name, "w")
        xf.write(exml)
        xf.write("\n")
        xf.close()
        # ready for the tarball

        NOTE names for test inputs and outputs are munged here so must
        correspond to actual input and output names used on the generated cl
        """
        retval = self.run()
        if retval:
            sys.stderr.write(
                "## Run failed. Cannot build yet. Please fix and retry"
            )
            sys.exit(1)
        tdir = "tfout"
        if not os.path.exists(tdir):
            os.mkdir(tdir)
        self.makeXML()

                shutil.copyfile(pth, dest)
                dest = os.path.join(tdir, p[OCLPOS])
                shutil.copyfile(pth, dest)

        if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0:
            shutil.copyfile(self.tlog, os.path.join(testdir, "test1_log_outfiletxt"))
        if self.args.runmode not in ["Executable", "system"]:
            stname = os.path.join(tdir, "%s" % (self.sfile))
            if not os.path.exists(stname):
                shutil.copyfile(self.sfile, stname)
        xreal = '%s.xml' % self.tool_name
        xout = os.path.join(tdir,xreal)
        shutil.copyfile(xreal, xout)
        tarpath = "toolfactory_%s.tgz" % self.tool_name
        tf = tarfile.open(tarpath, "w:gz")
        tf.add(name=tdir, arcname=self.tool_name)
        tf.close()
        shutil.copyfile(tarpath, self.args.new_tool)
        shutil.copyfile(xreal,"tool_xml.txt")
        repdir = "TF_run_report_tempdir"
        if not os.path.exists(repdir):
            os.mkdir(repdir)
        repoutnames = [x[OCLPOS] for x in self.outfiles]
        with os.scandir('.') as outs:
            for entry in outs:
                if entry.name.endswith('.tgz') or not entry.is_file():
                    continue
                if entry.name in repoutnames:
                    shutil.copyfile(entry.name,os.path.join(repdir,entry.name))
                elif entry.name == "%s.xml" % self.tool_name:
                    shutil.copyfile(entry.name,os.path.join(repdir,"new_tool_xml"))
        return retval

    def run(self):
        """
        Some devteam tools have this defensive stderr read so I'm keeping with the faith

        scl = " ".join(self.cl)
        err = None
        if self.args.parampass != "0":
            ste = open(self.elog, "wb")
            if self.lastclredirect:
                sto = open(
                    self.lastclredirect[1], "wb"
                )  # is name of an output file
            else:
                sto = open(self.tlog, "wb")
                sto.write(
                    bytes(
                        "## Executing Toolfactory generated command line = %s\n"
                        % scl,
                        "utf8",
                    )
                )
            sto.flush()
            p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)

    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 configuration file'
        % (args.bad_user, args.bad_user)
    )
    assert (
        args.tool_name
    ), "## Tool Factory expects a tool name - eg --tool_name=DESeq"
    assert (
        args.interpreter_name or args.exe_package
    ), "## Tool Factory wrapper expects an interpreter or an executable package"
    assert args.exe_package or (
        len(args.script_path) > 0 and os.path.isfile(args.script_path)
    ), "## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable"
    args.input_files = [
        x.replace('"', "").replace("'", "") for x in args.input_files
    ]
    # remove quotes we need to deal with spaces in CL params
    for i, x in enumerate(args.additional_parameters):
        args.additional_parameters[i] = args.additional_parameters[i].replace(
            '"', ""
        )
    r = ScriptRunner(args)
    if args.make_Tool:
        retcode = r.makeTooltar()
    else:
        retcode = r.run()