--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgToolFactory2.py	Thu Jan 15 07:43:13 2015 -0500
@@ -0,0 +1,959 @@
+# rgToolFactoryMultIn.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
+#
+# January 2015
+# in the process of building a complex tool
+# added ability to choose one of the current toolshed package_r or package_perl or package_python dependencies and source that package
+# need to add that package to tool_dependencies
+#
+# sept 2014 added additional params from
+# https://bitbucket.org/mvdbeek/dockertoolfactory/src/d4863bcf7b521532c7e8c61b6333840ba5393f73/DockerToolFactory.py?at=default
+# passing them is complex
+# and they are restricted to NOT contain commas or double quotes to ensure that they can be safely passed together on 
+# the toolfactory command line as a comma delimited double quoted string for parsing and passing to the script
+# see examples on this tool form
+
+# august 2014
+
+# Allows arbitrary number of input files
+# NOTE positional parameters are now passed to script
+# and output (may be "None") is *before* arbitrary number of inputs
+#
+# march 2014
+# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
+# grrrrr - night before a demo
+# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
+#
+# added ghostscript and graphicsmagick as dependencies 
+# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
+# errors ensued
+#
+# 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 sys 
+import shutil 
+import subprocess 
+import os 
+import time 
+import tempfile 
+import optparse
+import tarfile
+import re
+import shutil
+import math
+
+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
+
+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;",
+     "$": "\$"
+     }
+
+def html_escape(text):
+     """Produce entities within text."""
+     return "".join(html_escape_table.get(c,c) for c in text)
+
+
+def html_unescape(text):
+     """Revert entities within text."""
+     t = text.replace('&amp;','&').replace('&gt;','>').replace('&lt;','<').replace('\$','$')
+     return t
+     
+def cmd_exists(cmd):
+     return subprocess.call("type " + cmd, shell=True, 
+           stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
+
+def parse_citations(citations_text):
+    """
+    """
+    citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
+    citation_tuples = []
+    for citation in citations:
+        if citation.startswith("doi"):
+            citation_tuples.append( ("doi", citation[len("doi"):].strip() ) )
+        else:
+            citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
+    return citation_tuples
+
+def shell_source(script):
+    """need a way to source a Galaxy tool interpreter env.sh so we can use that dependency
+    package 
+    see http://pythonwise.blogspot.fr/2010/04/sourcing-shell-script.html
+    Sometime you want to emulate the action of "source" in bash,
+    settings some environment variables. Here is a way to do it.
+    Note that we have to finesse the automagic exports using nulls as newlines for env"""
+    pipe = subprocess.Popen("env -i ; . %s ; env -0" % script, stdout=subprocess.PIPE, shell=True)
+    output = pipe.communicate()[0]
+    outl = output.split('\0')
+    outl = [x for x in outl if len(x.split("=")) == 2]
+    newenv = dict((line.split("=", 1) for line in outl))
+    os.environ.update(newenv)
+    
+class ScriptRunner:
+    """class is a wrapper for an arbitrary script
+    note funky templating. this should all be done proper.
+    Problem is, this kludge developed quite naturally and seems to work ok with
+    little overhead...
+    
+    """
+
+
+    def __init__(self,opts=None,treatbashSpecial=True):
+        """
+        cleanup inputs, setup some outputs
+        
+        """
+        
+        self.toolhtmldepinterpskel = """<?xml version="1.0"?>
+        <tool_dependency>
+            <package name="ghostscript" version="9.10">
+                <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
+            </package>
+            <package name="graphicsmagick" version="1.3.18">
+                <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
+            </package>
+             <package name="%(interpreter_name)s" version="%(interpreter_version)s">
+                <repository name="%(interpreter_pack)s" owner="%(interpreter_owner)s" prior_installation_required="True" />
+            </package>
+           
+                <readme>
+                   %(readme)s
+               </readme>
+        </tool_dependency>
+        """
+        
+        self.toolhtmldepskel = """<?xml version="1.0"?>
+        <tool_dependency>
+            <package name="ghostscript" version="9.10">
+                <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
+            </package>
+            <package name="graphicsmagick" version="1.3.18">
+                <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
+            </package>
+                <readme>
+                   %(readme)s
+               </readme>
+        </tool_dependency>
+        """
+
+        self.emptytoolhtmldepskel = """<?xml version="1.0"?>
+        <tool_dependency>
+                <readme>
+                   %(readme)s
+               </readme>
+        </tool_dependency>
+        """
+
+        self.protorequirements = """<requirements>
+              <requirement type="package" version="9.10">ghostscript</requirement>
+              <requirement type="package" version="1.3.18">graphicsmagick</requirement>
+          </requirements>"""
+          
+        self.protorequirements_interpreter = """<requirements>
+              <requirement type="package" version="9.10">ghostscript</requirement>
+              <requirement type="package" version="1.3.18">graphicsmagick</requirement>
+              <requirement type="package" version="%(interpreter_version)s">%(interpreter_name)s</requirement>
+          </requirements>"""
+          
+
+        self.newCommand="""
+            %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 
+                --tool_name "%(toolname)s"
+                %(command_inputs)s
+                %(command_outputs)s
+            """
+    
+        self.tooltestsTabOnly = """
+            <test>
+            %(test1Inputs)s
+            <param name="job_name" value="test1"/>
+            <param name="runMe" value="$runMe"/>
+            <output name="output1="%(test1Output)s" ftype="tabular"/>
+            %(additionalParams)s
+            </test>
+            """
+            
+        self.tooltestsHTMLOnly = """
+            <test>
+            %(test1Inputs)s
+            <param name="job_name" value="test1"/>
+            <param name="runMe" value="$runMe"/>
+            %(additionalParams)s
+            <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
+            </test>
+            """
+            
+        self.tooltestsBoth = """
+            <test>
+            %(test1Inputs)s
+            <param name="job_name" value="test1"/>
+            <param name="runMe" value="$runMe"/>
+            %(additionalParams)s
+            <output name="output1" file="%(test1Output)s" ftype="tabular" />
+            <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
+            </test>
+            """
+
+        self.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
+%(additionalInputs)s
+</inputs>
+<outputs>
+%(outputs)s
+</outputs>
+<configfiles>
+<configfile name="runMe">
+%(script)s
+</configfile>
+</configfiles>
+<tests>
+%(tooltests)s
+</tests>
+<help>
+
+%(help)s
+
+</help>
+<citations>
+    %(citations)s
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
+</citations>
+</tool>"""
+            
+        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
+        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
+        rx = open(self.opts.script_path,'r').readlines()
+        rx = [x.rstrip() for x in rx] # remove pesky dos line endings if needed
+        self.script = '\n'.join(rx)
+        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 = "  %s" % '\n'.join([' %s' % html_escape(x) for x in rx]) # for restructured text in help
+        self.escapedScript = "%s" % '\n'.join([' %s' % html_escape(x) for x in rx])
+        self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
+        if opts.output_dir: # may not want these complexities 
+            self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
+            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.cl = []
+        self.html = []
+        self.test1Inputs = [] # now a list
+        a = self.cl.append
+        a(opts.interpreter)
+        a(self.sfile)
+        # if multiple inputs - positional or need to distinguish them with cl params
+        if opts.input_tab:
+            tests = []
+            for i,intab in enumerate(opts.input_tab): # if multiple, make tests
+                if intab.find(',') <> -1:
+                    (gpath,uname) = intab.split(',')
+                else:
+                    gpath = uname = intab
+                tests.append(os.path.basename(gpath))
+            self.test1Inputs =  '<param name="input_tab" value="%s" />' % (','.join(tests))
+        else:
+            self.test1Inputs = ''
+        # we always pass path,name pairs in using python optparse append
+        # but the command line has to be different
+        self.infile_paths = ''
+        self.infile_names = ''
+        if self.opts.input_tab:
+            self.infile_paths = ','.join([x.split(',')[0].strip() for x in self.opts.input_tab])
+            self.infile_names = ','.join([x.split(',')[1].strip() for x in self.opts.input_tab])
+        if self.opts.interpreter == 'python':
+            # yes, this is how additional parameters are always passed in python - to the TF itself and to
+            # scripts to avoid having unknown parameter names (yes, they can be parsed but...) on the command line
+            if self.opts.input_tab:
+                a('--INPATHS "%s"' % (self.infile_paths)) 
+                a('--INNAMES "%s"' % (self.infile_names)) 
+            if self.opts.output_tab:
+                a('--OUTPATH "%s"' % self.opts.output_tab) 
+            for p in opts.additional_parameters:
+                p = p.replace('"','')
+                psplit = p.split(',')
+                param = html_unescape(psplit[0])
+                value = html_unescape(psplit[1])
+                a('%s="%s"' % (param,value))
+        if (self.opts.interpreter == 'Rscript'):
+            # pass params on command line
+            if self.opts.input_tab:
+                a('INPATHS="%s"' % self.infile_paths)
+                a('INNAMES="%s"' % self.infile_names)
+            if self.opts.output_tab:
+                a('OUTPATH="%s"' % self.opts.output_tab) 
+            for p in opts.additional_parameters:
+                p = p.replace('"','')
+                psplit = p.split(',')
+                param = html_unescape(psplit[0])
+                value = html_unescape(psplit[1])
+                a('%s="%s"' % (param,value))
+        if (self.opts.interpreter == 'perl'):
+            # pass params on command line
+            if self.opts.input_tab:
+                a('%s' % self.infile_paths)
+                a('%s' % self.infile_names)
+            if self.opts.output_tab:
+                a('%s' % self.opts.output_tab)
+            for p in opts.additional_parameters:
+                p = p.replace('"','')
+                psplit = p.split(',')
+                param = html_unescape(psplit[0])
+                value = html_unescape(psplit[1])
+                if (value.find(' ') <> -1):
+                    a('%s="%s"' % (param,value))
+                else:
+                    a('%s=%s' % (param,value))
+        if self.opts.interpreter == 'sh' or self.opts.interpreter == 'bash':
+              # more is better - now move all params into environment AND drop on to command line.
+              self.cl.insert(0,'env')
+              if self.opts.input_tab:
+                  self.cl.insert(1,'INPATHS=%s' % (self.infile_paths))
+                  self.cl.insert(2,'INNAMES=%s' % (self.infile_names))
+              if self.opts.output_tab:
+                  self.cl.insert(3,'OUTPATH=%s' % (self.opts.output_tab))
+                  a('OUTPATH=%s' % (self.opts.output_tab))
+              # sets those environment variables for the script
+              # additional params appear in CL - yes, it's confusing
+              for i,p in enumerate(opts.additional_parameters):
+                  psplit = p.split(',')
+                  param = html_unescape(psplit[0])
+                  value = html_unescape(psplit[1])
+                  if (value.find(' ') <> -1):
+                    a('%s="%s"' % (param,value))
+                    self.cl.insert(4+i,'%s="%s"' % (param,value))
+                  else:
+                    a('%s=%s' % (param,value))
+                    self.cl.insert(4+i,'%s=%s' % (param,value))
+        self.interp_owner = None
+        self.interp_pack = None
+        self.interp_revision = None
+        self.interp_version = None
+        if opts.envshpath <> 'system': # need to parse out details for our tool_dependency
+            try:
+                packdetails = opts.envshpath.split(os.path.sep)[-4:-1]  # eg ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
+                self.interpreter_owner = packdetails[0]
+                self.interpreter_pack = packdetails[1]
+                self.interpreter_name = packdetails[1].split('_')[1].upper()
+                self.interpreter_revision = packdetails[2]
+                self.interpreter_version =  '.'.join(self.interpreter_pack.split('_')[2:])
+                # hope our naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play
+            except:
+                pass
+        self.outFormats = opts.output_format
+        self.inputFormats = opts.input_formats
+        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 "$input1" --output_tab "$output1" 
+            </command>
+            <inputs>
+            <param name="input1"  type="data" format="tabular" label="Select one or more input files 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="output1q" 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>
+        
+        """ 
+
+        # these templates need a dict with the right keys to match the parameters - outputs, help, code...
+
+        xdict = {}
+        xdict['additionalParams'] = ''
+        xdict['additionalInputs'] = ''
+        if self.opts.additional_parameters:
+            if self.opts.edit_additional_parameters: # add to new tool form with default value set to original value
+                xdict['additionalInputs'] = '\n'.join(['<param name="%s" value="%s" label="%s" help="%s" type="%s"/>' % \
+                (x.split(',')[0],html_escape(x.split(',')[1]),html_escape(x.split(',')[2]),html_escape(x.split(',')[3]), x.split(',')[4]) for x in self.opts.additional_parameters])
+        xdict['additionalParams'] = '\n'.join(['<param name="%s" value="%s" />' % (x.split(',')[0],html_escape(x.split(',')[1])) for x in self.opts.additional_parameters])
+        xdict['interpreter_owner'] = self.interpreter_owner
+        xdict['interpreter_version'] = self.interpreter_version
+        xdict['interpreter_pack'] = self.interpreter_pack
+        xdict['interpreter_name'] = self.interpreter_name
+        xdict['requirements'] = ''
+        if self.opts.include_dependencies == "yes":
+            if self.opts.envshpath <> 'system':
+                xdict['requirements'] = self.protorequirements_interpreter % xdict       
+            else:    
+                xdict['requirements'] = self.protorequirements
+        xdict['tool_version'] = self.opts.tool_version
+        xdict['test1HTML'] = self.test1HTML
+        xdict['test1Output'] = self.test1Output
+        xdict['test1Inputs'] = self.test1Inputs
+        if self.opts.make_HTML and self.opts.output_tab:
+            xdict['tooltests'] = self.tooltestsBoth % xdict
+        elif self.opts.make_HTML:
+            xdict['tooltests'] = self.tooltestsHTMLOnly % xdict
+        else:
+            xdict['tooltests'] = self.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:
+            cins = ['\n',]
+            cins.append('--input_formats %s' % self.opts.input_formats)
+            cins.append('#for intab in $input1:')
+            cins.append('--input_tab "${intab},${intab.name}"')
+            cins.append('#end for\n')
+            xdict['command_inputs'] = '\n'.join(cins)
+            xdict['inputs'] = '''<param name="input_tab" multiple="true"  type="data" format="%s" label="Select one or more %s input files from your history"
+                    help="Multiple inputs may be selected assuming the script can deal with them..."/> \n''' % (self.inputFormats,self.inputFormats)
+        else:
+            xdict['command_inputs'] = '' # assume no input - eg a random data generator       
+            xdict['inputs'] = ''
+        if (len(self.opts.additional_parameters) > 0):
+            cins = ['\n',]
+            for params in self.opts.additional_parameters:
+                    psplit = params.split(',') # name,value...
+                    psplit[3] = html_escape(psplit[3])
+                    if self.opts.edit_additional_parameters:
+                        psplit[1] = '$%s' % psplit[0] # replace with form value
+                    else:
+                        psplit[1] = html_escape(psplit[1]) # leave prespecified value
+                    cins.append('--additional_parameters """%s"""' % ','.join(psplit)) 
+            xdict['command_inputs'] = '%s\n%s' % (xdict['command_inputs'],'\n'.join(cins))
+        xdict['inputs'] += '<param name="job_name" type="text" size="60" 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="${job_name}.html"/>\n'
+        else:
+            xdict['command_outputs'] += ' --output_dir "./"' 
+        if self.opts.output_tab:
+            xdict['command_outputs'] += ' --output_tab "$output1"'
+            xdict['outputs'] += ' <data format="%s" name="output1" label="${job_name}"/>\n' % self.outFormats
+        xdict['command'] = self.newCommand % xdict
+        if self.opts.citations:
+            citationstext = open(self.opts.citations,'r').read()
+            citation_tuples = parse_citations(citationstext)
+            citations_xml = ""
+            for citation_type, citation_content in citation_tuples:
+                citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content))
+                citations_xml += citation_xml
+            xdict['citations'] = citations_xml
+        else:
+            xdict['citations'] = ""
+        xmls = self.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)
+        tdir = self.toolname
+        os.mkdir(tdir)
+        self.makeXML()
+        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'
+        readme_dict = {'readme':hlp,'interpreter':self.opts.interpreter,'interpreter_version':self.interpreter_version,'interpreter_name':self.interpreter_name,
+        'interpreter_owner':self.interpreter_owner}
+        if self.opts.include_dependencies == "yes":
+            if self.opts.envshpath == 'system':
+                tooldepcontent = self.toolhtmldepskel % readme_dict
+            else:
+                tooldepcontent = self.toolhtmldepinterpskel % readme_dict
+        else:
+            tooldepcontent = self.emptytoolhtmldepskel  % readme_dictls -l
+        depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
+        depf.write(tooldepcontent)
+        depf.write('\n')
+        depf.close()
+        if self.opts.input_tab: # no reproducible test otherwise? TODO: maybe..
+            testdir = os.path.join(tdir,'test-data')
+            os.mkdir(testdir) # make tests directory
+            for i,intab in enumerate(self.opts.input_tab):
+                si = self.opts.input_tab[i]
+                if si.find(',') <> -1:
+                    s = si.split(',')[0]
+                    si = s
+                dest = os.path.join(testdir,os.path.basename(si))
+                if si <> dest:
+                    shutil.copyfile(si,dest)
+            if 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 # 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 = 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.tar.gz" % self.toolname
+        tar = tarfile.open(tarpath, "w:gz")
+        tar.add(tdir,arcname='%s' % 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)
+        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 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!
+        """
+        if self.opts.envshpath <> 'system':
+            shell_source(self.opts.envshpath)
+        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,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()
+                err = open(self.elog,'r').readlines()
+                if retval <> 0 and err: # problem
+                    print >> sys.stderr,err
+            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 = optparse.OptionParser()
+    a = op.add_option
+    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=[], action="append") # these are "galaxypath,metadataname" pairs
+    a("--input_formats",default="tabular")
+    a('--output_tab',default=None)
+    a('--output_format',default='tabular')
+    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="yes")   
+    a('--citations',default=None)
+    a('--additional_parameters', dest='additional_parameters', action='append', default=[])
+    a('--edit_additional_parameters', action="store_true", default=False)
+    a('--envshpath',default="system")   
+    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
+    opts.input_tab = [x.replace('"','').replace("'",'') for x in opts.input_tab]
+    for i,x in enumerate(opts.additional_parameters): # remove quotes we need to deal with spaces in CL params
+        opts.additional_parameters[i] = opts.additional_parameters[i].replace('"','')
+    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()
+
+