comparison toolfactory/rgToolFactory2.py @ 50:bf432f4486c7 draft

Uploaded

49:35a912ce0c83

# essential problem is to create two command lines - one for the tool xml and a different
# one to run the executable with the supplied test data and settings
# Be simpler to write the tool, then run it with planemo and soak up the test outputs.



import argparse
import logging
import os
import re
import shutil

myversion = "V2.1 July 2020"
verbose = True
debug = True
toolFactoryURL = "https://github.com/fubar2/toolfactory"
ourdelim = "~~~"
ALOT = 10000000 # srsly. command or test overrides use read() so just in case
STDIOXML = """<stdio>
<exit_code range="100:" level="debug" description="shite happens" />
</stdio>"""

# --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label

            "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.tool = gxt.Tool(
            self.args.tool_name,
            self.tool_id,
            self.args.tool_version,
            self.args.tool_desc,
            FAKEEXE, 
        )
        if self.args.script_path:
            self.tool.interpreter = self.executeme
        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 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.cl_prefix: # DIY CL start
            clp = self.args.cl_prefix.split(" ")
            for c in clp:
                aCL(c)
                aXCL(c)
        else:
            if self.args.runmode == "Executable":
                if self.args.script_path:
                    aCL(self.executeme)
                    aCL(self.sfile)
                    aXCL("$runme")
                else:
                    aCL(self.executeme)  # this little CL will just run
                    aXCL(self.executeme)
            else:
                if self.args.script_path:
                    aCL(self.executeme)
                    aCL(self.sfile)
                    aXCL("$runme")
                else:
                    aCL(self.executeme)  # this little CL will just run
                    aXCL(self.executeme)
        self.elog = os.path.join(self.repdir,"%s_error_log.txt" % self.tool_name)
        self.tlog = os.path.join(self.repdir,"%s_runner_log.txt" % self.tool_name)

        if self.args.parampass == "0":
            self.clsimple()
        else:
            clsuffix = []

                    aparm.positional = int(oldcl)
                    aparm.command_line_override = "$%s" % newcl
            self.toutputs.append(aparm)
            usetest = None
            ld = None
            if test > '':
                if test.startswith('diff'):
                    usetest = 'diff'
                    if test.split(':')[1].isdigit:
                        ld = int(test.split(':')[1])
                else:
                    usetest = test
            tp = gxtp.TestOutput(name=newcl, value="%s_sample" % newcl, format=newfmt,
                compare=usetest, lines_diff=ld, delta=None,)
            self.testparam.append(tp)
        for p in self.infiles:
            newname = p[ICLPOS]
            newfmt = p[IFMTPOS]
            ndash = self.getNdash(newname)

        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.tool.command_line_override = self.command_override # config file
        else:
            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:
            self.tool.help = (
                "Please ask the tool author (%s) for help \
              as none was supplied at tool generation\n"
                % (self.args.user_email)
            )
        self.tool.version_command = None  # do not want
        requirements = gxtp.Requirements()
        if self.args.packages:
            for d in self.args.packages.split(","):
                if ":" in d:
                    packg, ver = d.split(":")
                else:
                    packg = d
                    ver = ""
                requirements.append(gxtp.Requirement("package", packg.strip(), ver.strip()))
        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.script_path
        ):
            configfiles = gxtp.Configfiles()
            configfiles.append(gxtp.Configfile(name="runme", text=self.script))
            self.tool.configfiles = configfiles
        tests = gxtp.Tests()
        test_a = gxtp.Test()
        for tp in self.testparam:
            test_a.append(tp)
        tests.append(test_a)
        self.tool.tests = tests
        self.tool.add_comment(
            "Created by %s at %s using the Galaxy Tool Factory."
            % (self.args.user_email, timenow())
        )
        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"
        )
        exml0 = self.tool.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,self.test_override,part2)
            exml = fixed
        xf = open("%s.xml" % self.tool_name, "w")
        xf.write(exml)
        xf.write("\n")
        xf.close()
        # ready for the tarball

    def makeTool(self):
        """write xmls and samples into place
        """
        self.makeXML()
        if self.args.script_path:
            stname = os.path.join(self.tooloutdir, "%s" % (self.sfile))
            if not os.path.exists(stname):
                shutil.copyfile(self.sfile, stname)
        xreal = "%s.xml" % self.tool_name
        xout = os.path.join(self.tooloutdir, xreal)
        shutil.copyfile(xreal, xout)
        for p in self.infiles:
            pth = p[IPATHPOS]
            dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
            shutil.copyfile(pth, dest)

    def makeToolTar(self):
        self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
        tf = tarfile.open(self.newtarpath, "w:gz")
        tf.add(name=self.tooloutdir, arcname=self.tool_name)
        tf.close()
        shutil.copyfile(self.newtarpath, self.args.new_tool)
        if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0:
            shutil.copyfile(
                self.tlog, os.path.join(self.tooloutdir, "test1_log_outfiletxt")
            )

    def moveRunOutputs(self):
        """need to move files into toolfactory collection after any run - planemo or not
        """
        for p in self.outfiles:
            naym = p[ONAMEPOS]
            src = os.path.join(self.tooloutdir,naym)
            if os.path.isfile(src):
                dest = os.path.join(self.testdir, "%s_sample" % naym)
                shutil.copyfile(naym, dest)
            else:
                print('### problem - output file %s not found in tooloutdir %s' % (src,self.tooloutdir))
        with os.scandir(self.tooloutdir) as outs:
            for entry in outs:
                if not entry.is_file() or entry.name.startswith('.'):
                    continue
                if "." in entry.name:
                    nayme,ext = os.path.splitext(entry.name) 
                else:
                    ext = ".txt"
                ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
                dest = os.path.join(self.repdir, ofn)
                src = os.path.join(self.tooloutdir,entry.name)
                shutil.copyfile(src, dest)

    def run(self):
        """

        """
        s = "run cl=%s" % str(self.cl)

        logging.debug(s)
        scl = " ".join(self.cl)
        err = None
        if self.args.parampass != "0":
            ste = open(self.elog, "wb")

        """
        planemo shed_create --shed_target testtoolshed
        planemo shed_update --check_diff --shed_target testtoolshed
        """
        if os.path.exists(self.tlog):
            tout = open(self.tlog,'a')
        else:
            tout = open(self.tlog,'w')
        cll = ["planemo", "shed_create", "--shed_target", "local"]
        try:
            p = subprocess.run(cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr = tout)
        except:
            pass
        if p.returncode != 0:
            print("Repository %s exists" % self.args.tool_name)
        else:

            "--shed_key",
            self.args.toolshed_api_key,
            "--tar",
            self.newtarpath,
        ]
        print("Run", " ".join(cll))
        p = subprocess.run(cll, shell=False)
        print("Ran", " ".join(cll), "got", p.returncode)
        tout.close()
        return p.returncode

    def planemo_test(self, genoutputs=True):
        """planemo is a requirement so is available
        """
        xreal = "%s.xml" % self.tool_name
        if os.path.exists(self.tlog):
            tout = open(self.tlog,'a')
        else:
            tout = open(self.tlog,'w')
        if genoutputs:
            cll = [
                "planemo",
                "test",
                "--galaxy_root",
                self.args.galaxy_root,
                "--update_test_data",
                xreal,
            ]
        else:
            cll = ["planemo", "test", "--galaxy_root", self.args.galaxy_root, xreal]
        try:
            p = subprocess.run(cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout)
        except:
            pass
        tout.close()
        return p.returncode

    def eph_galaxy_load(self):
        """
        """
        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,

            print("installed %s" % self.args.tool_name)
        tout.close()
        return p.returncode

    def writeShedyml(self):
        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,
        }
        yaml.dump(odict, yamlf, allow_unicode=True)
        yamlf.close()


    def install_load(self):
        _ = self.planemo_test(genoutputs=True)
        testres = self.planemo_test(genoutputs=False)
        if testres == 0:
            if self.args.make_Tool == "install":
                self.planemo_shedload()
                self.eph_galaxy_load()
        else:
            os.stderr.write(
                "Planemo test failed - tool %s was not installed" % self.args.tool_name
            )

def main():
    """
    This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
    <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath"

    a("--parampass", default="positional")
    a("--tfout", default="./tfout")
    a("--new_tool", default="new_tool")
    a("--runmode", default=None)
    a("--galaxy_url", default="http://localhost:8080")
    a("--galaxy_api_key", default="fbdd3c2eecd191e88939fffc02eeeaf8")
    a("--toolshed_url", default="http://localhost:9009")
    a("--toolshed_api_key", default="d46e5ed0e242ed52c6e1f506b5d7f9f7")
    a("--galaxy_root", default="/home/ross/galaxy")

    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)

    for i, x in enumerate(args.additional_parameters):
        args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
    r = ScriptRunner(args)
    r.writeShedyml()
    r.makeTool()
    if args.make_Tool == "runonly":
        retcode = r.run()
        if retcode:
            sys.stderr.write(
                "## Run failed with return code %d. Cannot build yet. Please fix and retry"
                % retcode
            )
            sys.exit(1)
        else:
            r.moveRunOutputs()
    elif args.make_Tool in ["gentestinstall", "generate", "gentest"]:
        retcode = r.run()
        if retcode:
            sys.stderr.write(
                "## Run failed with return code %d. Cannot build yet. Please fix and retry"
                % retcode
            )
            sys.exit(1)
        r.moveRunOutputs()
        r.makeToolTar()
        if args.make_Tool in ["gentestinstall","gentest"]:
            r.planemo_test(genoutputs=False)
            r.moveRunOutputs()
            r.planemo_shedload()
            r.eph_galaxy_load()
    else:
        retcode = r.planemo_test(genoutputs=True)  # this fails :(
        r.moveRunOutputs()
        r.makeToolTar()
        retcode = r.planemo_test(genoutputs=False)
        r.moveRunOutputs()
        if args.make_Tool == "planemotestinstall":
            r.planemo_shedload()            
            r.eph_galaxy_load()
        # if retcode:
        # sys.exit(retcode)  # indicate failure to job runner


if __name__ == "__main__":
    main()

50:bf432f4486c7

# essential problem is to create two command lines - one for the tool xml and a different
# one to run the executable with the supplied test data and settings
# Be simpler to write the tool, then run it with planemo and soak up the test outputs.


import argparse
import logging
import os
import re
import shutil

myversion = "V2.1 July 2020"
verbose = True
debug = True
toolFactoryURL = "https://github.com/fubar2/toolfactory"
ourdelim = "~~~"
ALOT = 10000000  # srsly. command or test overrides use read() so just in case
STDIOXML = """<stdio>
<exit_code range="100:" level="debug" description="shite happens" />
</stdio>"""

# --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label

            "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.args.tool_name,
            self.tool_id,
            self.args.tool_version,
            self.args.tool_desc,
            FAKEEXE,
        )
        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 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.cl_prefix:  # DIY CL start
            clp = self.args.cl_prefix.split(" ")
            for c in clp:
                aCL(c)
                aXCL(c)
        else:
            if self.args.runmode == "Executable":
                if self.args.script_path:
                    aCL(self.executeme)
                    aCL(self.sfile)
                    aXCL(self.executeme)
                    aXCL("$runme")
                else:
                    aCL(self.executeme)  # this little CL will just run
                    aXCL(self.executeme)
            else:
                if self.args.script_path:
                    aCL(self.executeme)
                    aCL(self.sfile)
                    aXCL(self.executeme)
                    aXCL("$runme")
                else:
                    aCL(self.executeme)  # this little CL will just run
                    aXCL(self.executeme)
        self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
        self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)

        if self.args.parampass == "0":
            self.clsimple()
        else:
            clsuffix = []

                    aparm.positional = int(oldcl)
                    aparm.command_line_override = "$%s" % newcl
            self.toutputs.append(aparm)
            usetest = None
            ld = None
            if test > "":
                if test.startswith("diff"):
                    usetest = "diff"
                    if test.split(":")[1].isdigit:
                        ld = int(test.split(":")[1])
                else:
                    usetest = test
            tp = gxtp.TestOutput(
                name=newcl,
                value="%s_sample" % newcl,
                format=newfmt,
                compare=usetest,
                lines_diff=ld,
                delta=None,
            )
            self.testparam.append(tp)
        for p in self.infiles:
            newname = p[ICLPOS]
            newfmt = p[IFMTPOS]
            ndash = self.getNdash(newname)

        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_line_override = self.command_override  # config file
        else:
            self.newtool.command_line_override = self.xmlcl
        if self.args.help_text:
            helptext = open(self.args.help_text, "r").readlines()
            safertext = [html_escape(x) for x in helptext]
            if self.args.script_path:
                scrpt = self.script.split('\n')
                scrpt.append("```\n")
                if len(scrpt) > 300:
                    safertext = safertext + scrpt[:100] + ['>500 lines - stuff deleted','......'] + scrpt[-100:]
                else:
                    safertext = safertext + scrpt
                safertext.append("\n```")
            self.newtool.help = "".join([x for x in safertext])
        else:
            self.newtool.help = (
                "Please ask the tool author (%s) for help \
              as none was supplied at tool generation\n"
                % (self.args.user_email)
            )
        self.newtool.version_command = None  # do not want
        requirements = gxtp.Requirements()
        if self.args.packages:
            for d in self.args.packages.split(","):
                if ":" in d:
                    packg, ver = d.split(":")
                else:
                    packg = d
                    ver = ""
                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=self.script))
            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))
        self.newtool.add_comment(
            "Cite: Creating re-usable tools from scripts doi: \
            10.1093/bioinformatics/bts573"
        )
        exml0 = self.newtool.export()
        exml = exml0.replace(FAKEEXE, "")  # temporary work around until PR accepted
        if (
            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, self.test_override, part2)
            exml = fixed
        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
        """
        s = "run cl=%s" % str(self.cl)
        logging.debug(s)
        scl = " ".join(self.cl)
        err = None
        if self.args.parampass != "0":
            ste = open(self.elog, "wb")

        """
        planemo shed_create --shed_target testtoolshed
        planemo shed_update --check_diff --shed_target testtoolshed
        """
        if os.path.exists(self.tlog):
            tout = open(self.tlog, "a")
        else:
            tout = open(self.tlog, "w")
        cll = ["planemo", "shed_create", "--shed_target", "local"]
        try:
            p = subprocess.run(
                cll, shell=True, cwd=self.tooloutdir, stdout=tout, stderr=tout
            )
        except:
            pass
        if p.returncode != 0:
            print("Repository %s exists" % self.args.tool_name)
        else:

            "--shed_key",
            self.args.toolshed_api_key,
            "--tar",
            self.newtarpath,
        ]
        p = subprocess.run(cll, shell=True)
        print("Ran", " ".join(cll), "got", p.returncode)
        tout.close()
        return p.returncode

    def planemo_test(self, genoutputs=True):
        """planemo is a requirement so is available for testing
        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
        if os.path.exists(self.tlog):
            tout = open(self.tlog, "a")
        else:
            tout = open(self.tlog, "w")
        if genoutputs:
            cll = [
                "planemo",
                "test",
                "--galaxy_root",
                self.args.galaxy_root,
                "--update_test_data",
                "--galaxy_python_version",
                "3.6",
                "--no_conda_auto_install",
                "--no_conda_auto_init",
                xreal,
            ]
        else:
            cll = ["planemo", "test", "--galaxy_python_version",
                "3.6", "--galaxy_root",
                self.args.galaxy_root,
                "--no_conda_auto_install",
                "--no_conda_auto_init",
                xreal,]
        p = subprocess.run(
                cll, shell=True, cwd=self.tooloutdir, stderr=tout, stdout=tout
            )
        if genoutputs:
            with os.scandir(self.testdir) as outs:
                for entry in outs:
                    if entry.is_file():
                        dest = os.path.join(self.repdir, entry.name)
                        src = os.path.join(self.testdir, entry.name)
                        shutil.copyfile(src, dest)
                    tout.write(
                        "Copied output %s to %s after planemo test\n" % (src, dest)
                    )
        tout.close()
        return p.returncode

    def eph_galaxy_load(self):
        """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,

            print("installed %s" % self.args.tool_name)
        tout.close()
        return p.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
        """
        self.makeXML()
        if self.args.script_path:
            stname = os.path.join(self.tooloutdir, "%s" % (self.sfile))
            if not os.path.exists(stname):
                shutil.copyfile(self.sfile, stname)
        xreal = "%s.xml" % self.tool_name
        xout = os.path.join(self.tooloutdir, xreal)
        shutil.copyfile(xreal, xout)
        for p in self.infiles:
            pth = p[IPATHPOS]
            dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
            shutil.copyfile(pth, dest)
            dest = os.path.join(self.repdir, "%s.%s" % (p[ICLPOS], p[IFMTPOS]))
            shutil.copyfile(pth, dest)

    def makeToolTar(self):
        """ move outputs into test-data and prepare the tarball 
        """
        for p in self.outfiles:
            src = p[ONAMEPOS]
            if os.path.isfile(src):
                dest = os.path.join(self.testdir, "%s_sample" % src)
                shutil.copyfile(src, dest)
                dest = os.path.join(self.repdir, "%s.%s" % (src, p[OFMTPOS]))
                shutil.copyfile(src, dest)
            else:
                print(
                    "### problem - output file %s not found in tooloutdir %s"
                    % (src, self.tooloutdir)
                )
        self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
        tf = tarfile.open(self.newtarpath, "w:gz")
        tf.add(name=self.tooloutdir, arcname=self.tool_name)
        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() or entry.name.startswith("."):
                    continue
                if "." in entry.name:
                    nayme, ext = os.path.splitext(entry.name)
                else:
                    ext = ".txt"
                ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
                dest = os.path.join(self.repdir, ofn)
                src = os.path.join(self.tooloutdir, entry.name)
                shutil.copyfile(src, dest)


def main():
    """
    This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
    <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath"

    a("--parampass", default="positional")
    a("--tfout", default="./tfout")
    a("--new_tool", default="new_tool")
    a("--runmode", default=None)
    a("--galaxy_url", default="http://localhost:8080")
    a("--galaxy_api_key", default="fakekey")
    a("--toolshed_url", default="http://localhost:9009")
    a("--toolshed_api_key", default="fakekey")
    a("--galaxy_root", default="/galaxy-central")

    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)

    for i, x in enumerate(args.additional_parameters):
        args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
    r = ScriptRunner(args)
    r.writeShedyml()
    r.makeTool()
    if args.command_override or args.test_override:
        retcode = r.planemo_test(genoutputs=True)  # this fails :( - see PR
        r.moveRunOutputs()
        r.makeToolTar()
        retcode = r.planemo_test(genoutputs=False)
        r.moveRunOutputs()
        if args.make_Tool == "gentestinstall":
            r.planemo_shedload()
            r.eph_galaxy_load()
    else:
        retcode = r.run()
        if retcode:
            sys.stderr.write(
                "## Run failed with return code %d. Cannot build yet. Please fix and retry"
                % retcode
            )
            sys.exit(1)
        else:
            r.moveRunOutputs()
            r.makeToolTar()
            if args.make_Tool in ["gentestinstall", "gentest"]:
                r.planemo_test(genoutputs=False)
                r.moveRunOutputs()
                if args.make_Tool == "gentestinstall":
                    r.planemo_shedload()
                    r.eph_galaxy_load()


if __name__ == "__main__":
    main()