# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# 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://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# july 2014
# added buffered read of sterror after run
#
# august 2013
# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
#
# july 2013
# added ability to combine images and individual log files into html output
# just make sure there's a log file foo.log and it will be output
# together with all images named like "foo_*.pdf
# otherwise old format for html
#
# January 2013
# problem pointed out by Carlos Borroto
# added escaping for <>$ - thought I did that ages ago...
#
# August 11 2012
# changed to use shell=False and cl as a sequence

# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
# It also serves as the wrapper for the new tool.
#
# you paste and run your script
# Only works for 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 page.

# DO NOT install on a public or important site - please.

# installed generated tools are fine if the script is safe.
# They just run normally and their user cannot do anything unusually insecure
# but please, practice safe toolshed.
# Read the fucking code before you install any tool
# especially this one

# After you get the script working on some test data, you can
# optionally generate a toolshed compatible gzip file
# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
# safe and largely automated installation in a production Galaxy.

# If you opt for an HTML output, you get all the script outputs arranged
# as a single Html history item - all output files are linked, thumbnails for all the pdfs.
# Ugly but really inexpensive.
#
# Patches appreciated please.
#
#
# long route to June 2012 product
# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
# derived from an integrated script model
# called rgBaseScriptWrapper.py
# Note to the unwary:
#   This tool allows arbitrary scripting on your Galaxy as the Galaxy user
#   There is nothing stopping a malicious user doing whatever they choose
#   Extremely dangerous!!
#   Totally insecure. So, trusted users only
#
# preferred model is a developer using their throw away workstation instance - ie a private site.
# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
#

import math
import optparse
import os
import re
import shutil
import subprocess
import sys
import tarfile
import tempfile
import time

progname = os.path.split(sys.argv[0])[1]
myversion = 'V000.2 June 2012'
verbose = False
debug = False
toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
buffsize = 1048576


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


html_escape_table = {
    "&": "&amp;",
    ">": "&gt;",
    "<": "&lt;",
    "$": "\$"}


def html_escape(text):
    """Produce entities within text."""
    return "".join(html_escape_table.get(c, c) for c in text)


def cmd_exists(cmd):
    return subprocess.call("type " + cmd, shell=True,
                           stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0


class ScriptRunner:
    """class is a wrapper for an arbitrary script
    """

    def __init__(self, opts=None):
        """
        cleanup inputs, setup some outputs
        """
        self.useGM = cmd_exists('gm')
        self.useIM = cmd_exists('convert')
        self.useGS = cmd_exists('gs')
        self.temp_warned = False  # we want only one warning if $TMP not set
        if opts.output_dir:  # simplify for the tool tarball
            os.chdir(opts.output_dir)
        self.thumbformat = 'png'
        self.opts = opts
        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name)  # a sanitizer now does this but..
        self.toolid = self.toolname
        self.myname = sys.argv[0]  # get our name because we write ourselves out as a tool later
        self.pyfile = self.myname  # crude but efficient - the cruft won't hurt much
        self.xmlfile = '%s.xml' % self.toolname
        s = open(self.opts.script_path, 'r').readlines()
        s = [x.rstrip() for x in s]  # remove pesky dos line endings if needed
        self.script = '\n'.join(s)
        fhandle, self.sfile = tempfile.mkstemp(prefix=self.toolname, suffix=".%s" % (opts.interpreter))
        tscript = open(self.sfile, 'w')  # use self.sfile as script source for Popen
        tscript.write(self.script)
        tscript.close()
        self.indentedScript = '\n'.join([' %s' % x for x in s])  # for restructured text in help
        self.escapedScript = '\n'.join([html_escape(x) for x in s])
        self.elog = os.path.join(self.opts.output_dir, "%s_error.log" % self.toolname)
        self.tlog = os.path.join(self.opts.output_dir, "%s_runner.log" % self.toolname)
        if opts.output_dir:  # may not want these complexities
            art = '%s.%s' % (self.toolname, opts.interpreter)
            artpath = os.path.join(self.opts.output_dir, art)  # need full path
            artifact = open(artpath, 'w')  # use self.sfile as script source for Popen
            artifact.write(self.script)
            artifact.close()
        self.html = []
        self.cl = (opts.interpreter, self.sfile)
        self.outFormats = 'tabular'  # TODO make this an option at tool generation time
        self.inputFormats = 'tabular'  # TODO make this an option at tool generation time
        self.test1Input = '%s_test1_input.xls' % self.toolname
        self.test1Output = '%s_test1_output.xls' % self.toolname
        self.test1HTML = '%s_test1_output.html' % self.toolname

    def makeXML(self):
        """
        Create a Galaxy xml tool wrapper for the new script as a string to write out
        fixme - use templating or something less fugly than this example of what we produce

        <tool id="reverse" name="reverse" version="0.01">
            <description>a tabular file</description>
            <command interpreter="python">
            reverse.py --script_path "$runMe" --interpreter "python"
            --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
            </command>
            <inputs>
            <param name="input1"  type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>

            </inputs>
            <outputs>
            <data format="tabular" name="tab_file" label="${job_name}"/>

            </outputs>
            <help>

**What it Does**

Reverse the columns in a tabular file

            </help>
            <configfiles>
            <configfile name="runMe">
# reverse order of columns in a tabular file
import sys
inp = sys.argv[1]
outp = sys.argv[2]
i = open(inp,'r')
o = open(outp,'w')
for row in i:
     rs = row.rstrip().split('\t')
     rs.reverse()
     o.write('\t'.join(rs))
     o.write('\n')
i.close()
o.close()
            </configfile>
            </configfiles>
            </tool>
        """
        newXML = """<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
            %(tooldesc)s
            %(command)s
            <inputs>
            %(inputs)s
            </inputs>
            <outputs>
            %(outputs)s
            </outputs>
            <configfiles>
            <configfile name="runMe">
            %(script)s
            </configfile>
            </configfiles>
            %(tooltests)s
            <help>
            %(help)s
            </help>
            </tool>"""  # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto

        newCommand = """<command interpreter="python">
            %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
            </command>"""  # may NOT be an input or htmlout
        tooltestsTabOnly = """<tests><test>
        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
        </test></tests>"""
        tooltestsHTMLOnly = """<tests><test>
        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
        </test></tests>"""
        tooltestsBoth = """<tests><test>
        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
        </test></tests>"""
        xdict = {}
        xdict['tool_version'] = self.opts.tool_version
        xdict['test1Input'] = self.test1Input
        xdict['test1HTML'] = self.test1HTML
        xdict['test1Output'] = self.test1Output
        if self.opts.make_HTML and self.opts.output_tab != 'None':
            xdict['tooltests'] = tooltestsBoth % xdict
        elif self.opts.make_HTML:
            xdict['tooltests'] = tooltestsHTMLOnly % xdict
        else:
            xdict['tooltests'] = tooltestsTabOnly % xdict
        xdict['script'] = self.escapedScript
        # configfile is least painful way to embed script to avoid external dependencies
        # but requires escaping of <, > and $ to avoid Mako parsing
        if self.opts.help_text:
            xdict['help'] = open(self.opts.help_text, 'r').read()
        else:
            xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
        coda = ['**Script**', 'Pressing execute will run the following code over your input file and generate some outputs in your history::']
        coda.append(self.indentedScript)
        coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email, timenow()))
        coda.append('See %s for details of that project' % (toolFactoryURL))
        coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
        coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573')
        xdict['help'] = '%s\n%s' % (xdict['help'], '\n'.join(coda))
        if self.opts.tool_desc:
            xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
        else:
            xdict['tooldesc'] = ''
        xdict['command_outputs'] = ''
        xdict['outputs'] = ''
        if self.opts.input_tab != 'None':
            xdict['command_inputs'] = '--input_tab "$input1" '  # the space may matter a lot if we append something
            xdict['inputs'] = '<param name="input1"  type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
        else:
            xdict['command_inputs'] = ''  # assume no input - eg a random data generator
            xdict['inputs'] = ''
        xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
        xdict['toolname'] = self.toolname
        xdict['toolid'] = self.toolid
        xdict['interpreter'] = self.opts.interpreter
        xdict['scriptname'] = self.sfile
        if self.opts.make_HTML:
            xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
            xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
        if self.opts.output_tab != 'None':
            xdict['command_outputs'] += ' --output_tab "$tab_file"'
            xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
        xdict['command'] = newCommand % xdict
        xmls = newXML % xdict
        xf = open(self.xmlfile, 'w')
        xf.write(xmls)
        xf.write('\n')
        xf.close()
        # ready for the tarball

    def makeTooltar(self):
        """
        a tool is a gz tarball with eg
        /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
        """
        retval = self.run()
        if retval:
            print >> sys.stderr, '## Run failed. Cannot build yet. Please fix and retry'
            sys.exit(1)
        self.makeXML()
        tdir = self.toolname
        os.mkdir(tdir)
        if self.opts.input_tab != 'None':  # no reproducible test otherwise? TODO: maybe..
            testdir = os.path.join(tdir, 'test-data')
            os.mkdir(testdir)  # make tests directory
            shutil.copyfile(self.opts.input_tab, os.path.join(testdir, self.test1Input))
            if self.opts.output_tab != 'None':
                shutil.copyfile(self.opts.output_tab, os.path.join(testdir, self.test1Output))
            if self.opts.make_HTML:
                shutil.copyfile(self.opts.output_html, os.path.join(testdir, self.test1HTML))
            if self.opts.output_dir:
                shutil.copyfile(self.tlog, os.path.join(testdir, 'test1_out.log'))
        op = '%s.py' % self.toolname  # new name
        outpiname = os.path.join(tdir, op)  # path for the tool tarball
        pyin = os.path.basename(self.pyfile)  # our name - we rewrite ourselves (TM)
        notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op, pyin, pyin), ]
        notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
        notes.append('# User %s at %s\n' % (self.opts.user_email, timenow()))
        pi = open(self.pyfile, 'r').readlines()  # our code becomes new tool wrapper (!) - first Galaxy worm
        notes += pi
        outpi = open(outpiname, 'w')
        outpi.write(''.join(notes))
        outpi.write('\n')
        outpi.close()
        stname = os.path.join(tdir, 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 = "%s.gz" % self.toolname
        tar = tarfile.open(tarpath, "w:gz")
        tar.add(tdir, arcname=self.toolname)
        tar.close()
        shutil.copyfile(tarpath, self.opts.new_tool)
        shutil.rmtree(tdir)
        # TODO: replace with optional direct upload to local toolshed?
        return retval

    def compressPDF(self, inpdf=None, thumbformat='png'):
        """need absolute path to pdf
           note that GS gets confoozled if no $TMP or $TEMP
           so we set it
        """
        assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf, self.myName)
        our_env = os.environ.copy()
        if not (our_env.get('TMP', None) or our_env.get('TEMP', None)):
            our_env['TMP'] = '/tmp'
            if not self.temp_warned:
                print >> sys.stdout, '## WARNING - no $TMP or $TEMP!!! Please fix - using /tmp temporarily'
                self.temp_warned = True
        hlog = os.path.join(self.opts.output_dir, "compress_%s.txt" % os.path.basename(inpdf))
        sto = open(hlog, 'w')
        outpdf = '%s_compressed' % inpdf
        cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH", "-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf, inpdf]
        x = subprocess.Popen(cl, stdout=sto, stderr=sto, cwd=self.opts.output_dir, env=our_env)
        retval1 = x.wait()
        sto.close()
        if retval1 == 0:
            os.unlink(inpdf)
            shutil.move(outpdf, inpdf)
            os.unlink(hlog)
        else:
            x = open(hlog, 'r').readlines()
            print >> sys.stdout, x
        hlog = os.path.join(self.opts.output_dir, "thumbnail_%s.txt" % os.path.basename(inpdf))
        sto = open(hlog, 'w')
        outpng = '%s.%s' % (os.path.splitext(inpdf)[0], thumbformat)
        if self.useGM:
            cl2 = ['gm', 'convert', inpdf, outpng]
        else:  # assume imagemagick
            cl2 = ['convert', inpdf, outpng]
        x = subprocess.Popen(cl2, stdout=sto, stderr=sto, cwd=self.opts.output_dir, env=our_env)
        retval2 = x.wait()
        sto.close()
        if retval2 != 0:
            x = open(hlog, 'r').readlines()
            print >> sys.stdout, x
        else:
            os.unlink(hlog)
        retval = retval1 or retval2
        return retval

    def getfSize(self, fpath, outpath):
        """
        format a nice file size string
        """
        size = ''
        fp = os.path.join(outpath, fpath)
        if os.path.isfile(fp):
            size = '0 B'
            n = float(os.path.getsize(fp))
            if n > 2**20:
                size = '%1.1f MB' % (n / 2**20)
            elif n > 2**10:
                size = '%1.1f KB' % (n / 2**10)
            elif n > 0:
                size = '%d B' % (int(n))
        return size

    def makeHtml(self):
        """ Create an HTML file content to list all the artifacts found in the output_dir
        """

        galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
        <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
        <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
        <title></title>
        <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
        </head>
        <body>
        <div class="toolFormBody">
        """
        galhtmlpostfix = """</div></body></html>\n"""

        flist = os.listdir(self.opts.output_dir)
        flist = [x for x in flist if x != 'Rplots.pdf']
        flist.sort()
        html = []
        html.append(galhtmlprefix % progname)
        html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname, timenow()))
        fhtml = []
        if len(flist) > 0:
            logfiles = [x for x in flist if x.lower().endswith('.log')]  # log file names determine sections
            logfiles.sort()
            logfiles = [x for x in logfiles if os.path.abspath(x) != os.path.abspath(self.tlog)]
            logfiles.append(os.path.abspath(self.tlog))  # make it the last one
            pdflist = []
            npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
            for rownum, fname in enumerate(flist):
                dname, e = os.path.splitext(fname)
                sfsize = self.getfSize(fname, self.opts.output_dir)
                if e.lower() == '.pdf':  # compress and make a thumbnail
                    thumb = '%s.%s' % (dname, self.thumbformat)
                    pdff = os.path.join(self.opts.output_dir, fname)
                    retval = self.compressPDF(inpdf=pdff, thumbformat=self.thumbformat)
                    if retval == 0:
                        pdflist.append((fname, thumb))
                    else:
                        pdflist.append((fname, fname))
                if (rownum + 1) % 2 == 0:
                    fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname, fname, sfsize))
                else:
                    fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname, fname, sfsize))
            for logfname in logfiles:  # expect at least tlog - if more
                if os.path.abspath(logfname) == os.path.abspath(self.tlog):  # handled later
                    sectionname = 'All tool run'
                    if (len(logfiles) > 1):
                        sectionname = 'Other'
                    ourpdfs = pdflist
                else:
                    realname = os.path.basename(logfname)
                    sectionname = os.path.splitext(realname)[0].split('_')[0]  # break in case _ added to log
                    ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
                    pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] != sectionname]  # remove
                nacross = 1
                npdf = len(ourpdfs)

                if npdf > 0:
                    nacross = math.sqrt(npdf)  # int(round(math.log(npdf,2)))
                    if int(nacross)**2 != npdf:
                        nacross += 1
                    nacross = int(nacross)
                    width = min(400, int(1200 / nacross))
                    html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
                    html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
                    ntogo = nacross  # counter for table row padding with empty cells
                    html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
                    for i, paths in enumerate(ourpdfs):
                        fname, thumb = paths
                        s = """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
                           alt="Image called %s"/></a></td>\n""" % (fname, thumb, fname, width, fname)
                        if (i + 1) % nacross == 0:
                            s += '</tr>\n'
                            ntogo = 0
                            if i < (npdf - 1):  # more to come
                                s += '<tr>'
                                ntogo = nacross
                        else:
                            ntogo -= 1
                        html.append(s)
                    if html[-1].strip().endswith('</tr>'):
                        html.append('</table></div>\n')
                    else:
                        if ntogo > 0:  # pad
                            html.append('<td>&nbsp;</td>' * ntogo)
                        html.append('</tr></table></div>\n')
                logt = open(logfname, 'r').readlines()
                logtext = [x for x in logt if x.strip() > '']
                html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
                if len(logtext) > 1:
                    html.append('\n<pre>\n')
                    html += logtext
                    html.append('\n</pre>\n')
                else:
                    html.append('%s is empty<br/>' % logfname)
        if len(fhtml) > 0:
            fhtml.insert(0, '<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
            fhtml.append('</table></div><br/>')
            html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
            html += fhtml  # add all non-pdf files to the end of the display
        else:
            html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
        html.append(galhtmlpostfix)
        htmlf = file(self.opts.output_html, 'w')
        htmlf.write('\n'.join(html))
        htmlf.write('\n')
        htmlf.close()
        self.html = html

    def run(self):
        """
        scripts must be small enough not to fill the pipe!
        """
        my_env = os.environ.copy()
        if self.opts.output_dir:
            ste = open(self.elog, 'w')
            sto = open(self.tlog, 'w')
            sto.write('## Toolfactory running %s as %s script\n' % (self.toolname, self.opts.interpreter))
            sto.flush()
            p = subprocess.Popen(self.cl, shell=False, stdout=sto, stderr=ste, cwd=self.opts.output_dir, env=my_env)
            retval = p.wait()
            sto.close()
            ste.close()
            # get stderr, allowing for case where it's very large
            tmp_stderr = open( self.elog, 'rb' )
            stderr = ''
            try:
                while True:
                    stderr += tmp_stderr.read( buffsize )
                    if not stderr or len( stderr ) % buffsize != 0:
                        break
            except OverflowError:
                pass
            tmp_stderr.close()
        else:
            p = subprocess.Popen(self.cl, shell=False, env=my_env)
            retval = p.wait()
        if self.opts.make_HTML:
            self.makeHtml()
        return retval

    def remove_me_runBash(self):
        """
        cannot use - for bash so use self.sfile
        """
        if self.opts.output_dir:
            s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
            ste = open(self.elog, 'w')
            sto = open(self.tlog, 'w')
            sto.write(s)
            sto.flush()
            p = subprocess.Popen(self.cl, shell=False, stdout=sto, stderr=ste, cwd=self.opts.output_dir)
        else:
            p = subprocess.Popen(self.cl, shell=False)
        retval = p.wait()
        if self.opts.output_dir:
            sto.close()
            ste.close()
            # get stderr, allowing for case where it's very large
            tmp_stderr = open(self.elog, 'rb' )
            stderr = ''
            try:
                while True:
                    stderr += tmp_stderr.read( buffsize )
                    if not stderr or len( stderr ) % buffsize != 0:
                        break
            except OverflowError:
                pass
            tmp_stderr.close()
        return retval


def main():
    """
    This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as (eg):
    <command interpreter="python">rgToolFactory.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
    </command>
    The tool writes a script to a scriptPath using a configfile.
    Some things in the script are templates.
    The idea here is that depending on how this code is called, it uses the specified interpreter
    to run a (hopefully correct) script/template. Optionally generates a clone of itself
    which will run that same script/template as a toolshed repository tarball for uploading to a toolshed.
    There's now an updated version which allows arbitrary parameters.
    And so it goes.
    """
    op = optparse.OptionParser()
    a = op.add_option
    a('--script_path', default=None)
    a('--tool_name', default=None)
    a('--interpreter', default=None)
    a('--output_dir', default=None)
    a('--output_html', default=None)
    a('--input_tab', default="None")
    a('--output_tab', default="None")
    a('--user_email', default='Unknown')
    a('--bad_user', default=None)
    a('--make_Tool', default=None)
    a('--make_HTML', default=None)
    a('--help_text', default=None)
    a('--tool_desc', default=None)
    a('--new_tool', default=None)
    a('--tool_version', default=None)
    opts, args = op.parse_args()
    assert not opts.bad_user, 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user, opts.bad_user)
    assert opts.tool_name, '## Tool Factory expects a tool name - eg --tool_name=DESeq'
    assert opts.interpreter, '## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
    assert os.path.isfile(opts.script_path), '## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
    if opts.output_dir:
        try:
            os.makedirs(opts.output_dir)
        except:
            pass
    r = ScriptRunner(opts)
    if opts.make_Tool:
        retcode = r.makeTooltar()
    else:
        retcode = r.run()
    os.unlink(r.sfile)
    if retcode:
        sys.exit(retcode)  # indicate failure to job runner


if __name__ == "__main__":
    main()
