--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DockerToolFactory.py	Sat Oct 03 08:34:39 2015 -0400
@@ -0,0 +1,773 @@
+# DockerToolFactory.py
+# see https://bitbucket.org/mvdbeek/DockerToolFactory
+
+import sys
+import shutil
+import subprocess
+import os
+import time
+import tempfile
+import argparse
+import tarfile
+import re
+import shutil
+import math
+import fileinput
+from os.path import abspath
+
+progname = os.path.split(sys.argv[0])[1]
+myversion = 'V001.1 March 2014'
+verbose = False
+debug = False
+toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
+
+# if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
+# tool xml
+toolhtmldepskel = """<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ghostscript" version="9.10">
+        <repository name="package_ghostscript_9_10" owner="devteam"/>
+    </package>
+    <package name="graphicsmagick" version="1.3.20">
+        <repository name="package_graphicsmagick_1_3_20" owner="iuc"/>
+    </package>
+    <package name="docker-py" version="0.4.0">
+        <install version="1.0">
+            <actions>
+                <action type="setup_virtualenv">docker-py==0.4.0
+                </action>
+            </actions>
+        </install>
+    </package>
+        <readme>
+                %s
+       </readme>
+</tool_dependency>
+"""
+
+protorequirements = """<requirements>
+      <requirement type="package" version="9.10">ghostscript</requirement>
+      <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+      <container type="docker">toolfactory/custombuild:%s</container>
+</requirements>"""
+
+
+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
+
+
+def edit_dockerfile(dockerfile):
+    '''we have to change the userid of galaxy inside the container to the id with which the tool is run,
+       otherwise we have a mismatch in the file permissions inside the container'''
+    uid = os.getuid()
+    for line in fileinput.FileInput(dockerfile, inplace=1):
+        sys.stdout.write(re.sub("RUN adduser galaxy.*", "RUN adduser galaxy -u {0}\n".format(uid), line))
+
+
+# TODO: try to download image it it exists.
+def build_docker(dockerfile, docker_client, image_tag='base'):
+    '''Given the path to a dockerfile, and a docker_client, try to build the image, if it does not
+    exist yet.'''
+    image_id = 'toolfactory/custombuild:' + image_tag
+    existing_images = ", ".join(["".join(d['RepoTags']) for d in docker_client.images()])
+    if image_id in existing_images:
+        print 'docker container exists, skipping build'
+        return image_id
+    print "Building Docker image, using Dockerfile:{0}".format(dockerfile)
+    build_process = docker_client.build(fileobj=open(dockerfile, 'r'), tag=image_id)
+    print "succesfully dispatched docker build process, building now"
+    build_log = [line for line in build_process]  # will block until image is built.
+    return image_id
+
+
+def construct_bind(host_path, container_path=False, binds=None, ro=True):
+    # TODO remove container_path if it's alwyas going to be the same as host_path
+    '''build or extend binds dictionary with container path. binds is used
+    to mount all files using the docker-py client.'''
+    if not binds:
+        binds = {}
+    if isinstance(host_path, list):
+        for k, v in enumerate(host_path):
+            if not container_path:
+                container_path = host_path[k]
+            binds[host_path[k]] = {'bind': container_path, 'ro': ro}
+            container_path = False  # could be more elegant
+        return binds
+    else:
+        if not container_path:
+            container_path = host_path
+        binds[host_path] = {'bind': container_path, 'ro': ro}
+        return binds
+
+
+def exists_boot2docker():
+    '''
+    Try to see if boot2docker command is available.
+    If it is, run boot2docker shellinit
+    '''
+    return cmd_exists('boot2docker')
+
+
+def boot2docker_shellinit():
+    '''
+    '''
+    cmd = "eval \"\$(boot2docker shellinit)\""
+    subprocess.call(cmd, shell=True)
+
+
+def switch_to_docker(opts):
+    import docker  # need local import, as container does not have docker-py
+    if exists_boot2docker():
+        boot2docker_shellinit()
+        from docker.utils import kwargs_from_env
+        kwargs = kwargs_from_env()
+        kwargs['tls'].assert_hostname = False
+        docker_client = docker.Client(**kwargs)
+    else:
+        docker_client = docker.Client()
+    toolfactory_path = abspath(sys.argv[0])
+    dockerfile = os.path.dirname(toolfactory_path) + '/Dockerfile'
+    edit_dockerfile(dockerfile)
+    image_id = build_docker(dockerfile, docker_client)
+    binds = construct_bind(host_path=opts.script_path, ro=False)
+    binds = construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False)
+    if len(opts.input_tab) > 0:
+        binds = construct_bind(binds=binds, host_path=opts.input_tab, ro=True)
+    if not opts.output_tab == 'None':
+        binds = construct_bind(binds=binds, host_path=opts.output_tab, ro=False)
+    if opts.make_HTML:
+        binds = construct_bind(binds=binds, host_path=opts.output_html, ro=False)
+    if opts.make_Tool:
+        binds = construct_bind(binds=binds, host_path=opts.new_tool, ro=False)
+        binds = construct_bind(binds=binds, host_path=opts.help_text, ro=True)
+    binds = construct_bind(binds=binds, host_path=toolfactory_path)
+    volumes = binds.keys()
+    sys.argv = [abspath(opts.output_dir) if sys.argv[i - 1] == '--output_dir' else arg for i, arg in
+                enumerate(sys.argv)]  ##inject absolute path of working_dir
+    cmd = ['python', '-u'] + sys.argv + ['--dockerized', '1']
+    container = docker_client.create_container(
+        image=image_id,
+        user=os.getuid(),
+        volumes=volumes,
+        command=cmd
+    )
+    docker_client.start(container=container[u'Id'], binds=binds)
+    docker_client.wait(container=container[u'Id'])
+    logs = docker_client.logs(container=container[u'Id'])
+    print "".join([log for log in logs])
+
+
+class ScriptRunner:
+    """class is a wrapper for an arbitrary script
+    """
+
+    def __init__(self, opts=None, treatbashSpecial=True, image_tag='base'):
+        """
+        cleanup inputs, setup some outputs
+        
+        """
+        self.opts = opts
+        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
+        self.treatbashSpecial = treatbashSpecial
+        self.image_tag = image_tag
+        os.chdir(abspath(opts.output_dir))
+        self.thumbformat = 'png'
+        self.toolname_sanitized = re.sub('[^a-zA-Z0-9_]+', '_', opts.tool_name)  # a sanitizer now does this but..
+        self.toolname = opts.tool_name
+        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_sanitized
+        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_sanitized, 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' % html_escape(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_sanitized)
+        if opts.output_dir:  # may not want these complexities
+            self.tlog = os.path.join(self.opts.output_dir, "%s_runner.log" % self.toolname_sanitized)
+            art = '%s.%s' % (self.toolname_sanitized, 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.cl = []
+        self.html = []
+        a = self.cl.append
+        a(opts.interpreter)
+        if self.treatbashSpecial and opts.interpreter in ['bash', 'sh']:
+            a(self.sfile)
+        else:
+            a('-')  # stdin
+        for input in opts.input_tab:
+            a(input)
+        if opts.output_tab == 'None':  # If tool generates only HTML, set output name to toolname
+            a(str(self.toolname_sanitized) + '.out')
+        a(opts.output_tab)
+        for param in opts.additional_parameters:
+            param, value = param.split(',')
+            a('--' + param)
+            a(value)
+        # print self.cl
+        self.outFormats = opts.output_format
+        self.inputFormats = [formats for formats in opts.input_formats]
+        self.test1Input = '%s_test1_input.xls' % self.toolname_sanitized
+        self.test1Output = '%s_test1_output.xls' % self.toolname_sanitized
+        self.test1HTML = '%s_test1_output.html' % self.toolname_sanitized
+
+    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"/>
+
+            </inputs>
+            <outputs>
+            <data format=opts.output_format name="tab_file"/>
+
+            </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
+%(requirements)s
+<command interpreter="python">
+%(command)s
+</command>
+<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, toolname_sanitized, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
+
+        newCommand = """
+        %(toolname_sanitized)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 
+            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """
+        # may NOT be an input or htmlout - appended later
+        tooltestsTabOnly = """
+        <tests>
+        <test>
+        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
+        <param name="runMe" value="$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="runMe" value="$runMe"/>
+        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
+        </test>
+        </tests>
+        """
+        tooltestsBoth = """<tests>
+        <test>
+        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
+        <param name="runMe" value="$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['requirements'] = ''
+        # if self.opts.make_HTML:
+        xdict['requirements'] = protorequirements % self.image_tag
+        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:
+            helptext = open(self.opts.help_text, 'r').readlines()
+            helptext = [html_escape(x) for x in helptext]  # must html escape here too - thanks to Marius van den Beek
+            xdict['help'] = ''.join([x for x in helptext])
+        else:
+            xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (
+            self.opts.user_email)
+        coda = ['**Script**',
+                'Pressing execute will run the following code over your input file and generate some outputs in your history::']
+        coda.append('\n')
+        coda.append(self.indentedScript)
+        coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (
+        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\n')
+        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'
+            xdict['inputs'] = ''
+            for i, input in enumerate(self.inputFormats):
+                xdict[
+                    'inputs'] += '<param name="input{0}"  type="data" format="{1}" label="Select a suitable input file from your history"/> \n'.format(
+                    i + 1, input)
+                xdict['command_inputs'] += ' $input{0}'.format(i + 1)
+        else:
+            xdict['command_inputs'] = ''  # assume no input - eg a random data generator
+            xdict['inputs'] = ''
+        # I find setting the job name not very logical. can be changed in workflows anyway. xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
+        xdict['toolname'] = self.toolname
+        xdict['toolname_sanitized'] = self.toolname_sanitized
+        xdict['toolid'] = self.toolid
+        xdict['interpreter'] = self.opts.interpreter
+        xdict['scriptname'] = self.sfile
+        if self.opts.make_HTML:
+            xdict[
+                'command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
+            xdict['outputs'] += ' <data format="html" name="html_file"/>\n'
+        else:
+            xdict['command_outputs'] += ' --output_dir "./"'
+            # print self.opts.output_tab
+        if self.opts.output_tab != "None":
+            xdict['command_outputs'] += ' --output_tab "$tab_file"'
+            xdict['outputs'] += ' <data format="%s" name="tab_file"/>\n' % self.outFormats
+        xdict['command'] = newCommand % xdict
+        # print xdict['outputs']
+        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_sanitized/tool.xml /toolname_sanitized/tool.py /toolname_sanitized/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)
+        tdir = self.toolname_sanitized
+        os.mkdir(tdir)
+        self.makeXML()
+        if self.opts.make_HTML:
+            if self.opts.help_text:
+                hlp = open(self.opts.help_text, 'r').read()
+            else:
+                hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
+            if self.opts.include_dependencies:
+                tooldepcontent = toolhtmldepskel % hlp
+                depf = open(os.path.join(tdir, 'tool_dependencies.xml'), 'w')
+                depf.write(tooldepcontent)
+                depf.write('\n')
+                depf.close()
+        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
+            for i in self.opts.input_tab:
+                # print i
+                shutil.copyfile(i, os.path.join(testdir, self.test1Input))
+            if not self.opts.output_tab:
+                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'))
+        outpif = '%s.py' % self.toolname_sanitized  # new name
+        outpiname = os.path.join(tdir, outpif)  # 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' % (outpiname, 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 = [line.replace('if opts.dockerized==0:', 'if False:') for line in
+              open(self.pyfile)]  # do not run docker in the generated tool
+        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_sanitized
+        tar = tarfile.open(tarpath, "w:gz")
+        tar.add(tdir, arcname=self.toolname_sanitized)
+        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)
+        hlog = os.path.join(self.opts.output_dir, "compress_%s.txt" % os.path.basename(inpdf))
+        sto = open(hlog, 'a')
+        our_env = os.environ.copy()
+        our_tmp = our_env.get('TMP', None)
+        if not our_tmp:
+            our_tmp = our_env.get('TEMP', None)
+        if not (our_tmp and os.path.exists(our_tmp)):
+            newtmp = os.path.join(self.opts.output_dir, 'tmp')
+            try:
+                os.mkdir(newtmp)
+            except:
+                sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
+            our_env['TEMP'] = newtmp
+            if not self.temp_warned:
+                sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
+                self.temp_warned = True
+        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)
+        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:
+            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"> 
+        """
+        galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""
+        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 abspath(x) <> abspath(self.tlog)]
+            logfiles.append(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 abspath(logfname) == 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!
+        """
+        if self.treatbashSpecial and self.opts.interpreter in ['bash', 'sh']:
+            retval = self.runBash()
+        else:
+            if self.opts.output_dir:
+                ste = open(self.elog, 'w')
+                sto = open(self.tlog, 'w')
+                sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
+                sto.flush()
+                p = subprocess.Popen(self.cl, shell=False, stdout=sto, stderr=ste, stdin=subprocess.PIPE,
+                                     cwd=self.opts.output_dir)
+            else:
+                p = subprocess.Popen(self.cl, shell=False, stdin=subprocess.PIPE)
+            p.stdin.write(self.script)
+            p.stdin.close()
+            retval = p.wait()
+            if self.opts.output_dir:
+                sto.close()
+                ste.close()
+                err = open(self.elog, 'r').readlines()
+                if retval <> 0 and err:  # problem
+                    print >> sys.stderr, err  # same problem, need to capture docker stdin/stdout
+            if self.opts.make_HTML:
+                self.makeHtml()
+        return retval
+
+    def 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)
+            sto = open(self.tlog, 'w')
+            sto.write(s)
+            sto.flush()
+            p = subprocess.Popen(self.cl, shell=False, stdout=sto, stderr=sto, cwd=self.opts.output_dir)
+        else:
+            p = subprocess.Popen(self.cl, shell=False)
+        retval = p.wait()
+        if self.opts.output_dir:
+            sto.close()
+        if self.opts.make_HTML:
+            self.makeHtml()
+        return retval
+
+
+def main():
+    u = """
+    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" --tool_name "foo" --interpreter "Rscript"
+    </command>
+    """
+    op = argparse.ArgumentParser()
+    a = op.add_argument
+    a('--script_path', default=None)
+    a('--tool_name', default=None)
+    a('--interpreter', default=None)
+    a('--output_dir', default='./')
+    a('--output_html', default=None)
+    a('--input_tab', default='None', nargs='*')
+    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)
+    a('--include_dependencies', default=None)
+    a('--dockerized', default=0)
+    a('--output_format', default='tabular')
+    a('--input_format', dest='input_formats', action='append', default=[])
+    a('--additional_parameters', dest='additional_parameters', action='append', default=[])
+    opts = 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
+    if opts.dockerized == 0:
+        switch_to_docker(opts)
+        return
+    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()