Mercurial > repos > fubar > biocdepgen_r_3_1_2

--- a/r_bioc_depgen_4/r_bioc_depgen_4.py	Tue Jan 20 05:08:04 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,968 +0,0 @@
-# r_bioc_depgen_4/r_bioc_depgen_4.py - a self annotated version of rgToolFactory2.py generated by running rgToolFactory2.py
-# to make a new Galaxy tool called r_bioc_depgen_4
-# User ross.lazarus@gmail.com at 16/01/2015 13:03:33
-# 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
-                   This file was autogenerated by the Galaxy Tool Factory 2
-               </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
-                   This file was autogenerated by the Galaxy Tool Factory 2
-               </readme>
-        </tool_dependency>
-        """
-
-        self.emptytoolhtmldepskel = """<?xml version="1.0"?>
-        <tool_dependency>
-                <readme>
-                   %(readme)s
-                This file was autogenerated by the Galaxy Tool Factory 2
-               </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
-
-This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
-https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2
-</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: # fragile - depends on common naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play
-
-                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(packdetails[1].split('_')[2:])
-            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,'interpreter_pack':self.interpreter_pack}
-        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()
-
-
-
--- a/r_bioc_depgen_4/r_bioc_depgen_4.xml	Tue Jan 20 05:08:04 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,294 +0,0 @@
-<tool id="r_bioc_depgen_4" name="r_bioc_depgen_4" version="0.01">
-<description>Generate dependencies for R/BioC packages</description>
-<requirements>
-              <requirement type="package" version="9.10">ghostscript</requirement>
-              <requirement type="package" version="1.3.18">graphicsmagick</requirement>
-              <requirement type="package" version="3.1.2">R</requirement>
-          </requirements>
-<command interpreter="python">
-
-            r_bioc_depgen_4.py --script_path "$runMe" --interpreter "Rscript"
-                --tool_name "r_bioc_depgen_4"
-
-
-
---additional_parameters """tardir,$tardir,Save all dependency tarballs to this directory,I use a github repository for this which is specified in the xml_prefix parameter below,text"""
---additional_parameters """ourpackages,$ourpackages,SPACE (NOT comma!) separated list of package names - without versions!,Packages and dependencies for the chosen R will be found,text"""
---additional_parameters """xmlprefix,$xmlprefix,Prefix for generated tool_dependency.xml url to the permanent package archive repository,I use a github repository as the default shows - the tag will be closed with '?raw=true&lt;/package&gt;',text"""
-                 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" --output_tab "$output1"
-
-</command>
-<inputs>
-<param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="r_bioc_depgen_4"/>
-
-<param name="tardir" value="/tmp" label="Save all dependency tarballs to this directory" help="I use a github repository for this which is specified in the xml_prefix parameter below" type="text"/>
-<param name="ourpackages" value="DESeq2" label="SPACE (NOT comma!) separated list of package names - without versions!" help="Packages and dependencies for the chosen R will be found" type="text"/>
-<param name="xmlprefix" value="&lt;package&gt;https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/" label="Prefix for generated tool_dependency.xml url to the permanent package archive repository" help="I use a github repository as the default shows - the tag will be closed with '?raw=true&lt;/package&gt;'" type="text"/>
-</inputs>
-<outputs>
- <data format="html" name="html_file" label="${job_name}.html"/>
- <data format="tabular" name="output1" label="${job_name}"/>
-
-</outputs>
-<configfiles>
-<configfile name="runMe">
- ## Sample tool factory 2 script version if you
- ## define the parameters needed (!) as form elements
- ## will save ALL needed tarballs to destdir
- ## for tool_dependency use
- ### ross lazarus
- ### bah! humbug!
- ### dec 24 2014
-
- packageExpand = function(packagelist,fl) {
-   res = NULL
-   for (i in c(1:length(packagelist))) {
-     s = packagelist[i]
-     ls = nchar(s)
-     spos = which(substr(fl,1,ls) == s,arr.ind=T)
-     lspos = length(spos)
-     if (lspos &gt; 0)
-       {
-       fullname = fl[spos]
-       if (grepl('*.gz',fullname)) {
-            row = paste(ps,fullname,pe,sep='')
-            res = append(res,row)
-            }
-       }
-     }
-   return(res)
- }
-
- getPackages = function(packs)
-   {
-   packages = unlist(tools::package_dependencies(packs, available.packages(),
-         which=c("Depends", "Imports"), recursive=TRUE))
-   packages = union(packs, packages)
-   packages
-   }
-
- ### tool factory Rscript parser suggested by Forester
- ### http://www.r-bloggers.com/including-arguments-in-r-cmd-batch-mode/
- ### additional parameters will appear in the ls() below - they are available
- ### to your script
- ### echo parameters to the output file
- ourargs = commandArgs(TRUE)
- if(length(ourargs)==0){
-       print("No arguments supplied.")
-    }else{
-    for(i in 1:length(ourargs)){
-         eval(parse(text=ourargs[[i]]))
-    }
- }
-
- unesc = function(x) {
- #### needed to deal with galaxy escaping &lt;&gt; in passing the xml string we need - don't try this at home kids.
- res = x
- res = gsub('__lt__','&lt;',res)
- res = gsub('__gt__','&gt;',res)
- return(res)
- }
-
- our_packages = strsplit(ourpackages," ")[[1]]
- ### these show as attached non-base packages in sessionInfo after running the R code
- ps=unesc(xmlprefix)
- pe="?raw=true&lt;/package&gt;"
-
- print(paste('tardir=',tardir,'xmlprefix=',xmlprefix,'ourpackages=',ourpackages,'OUTPATH=',OUTPATH))
-
-
- setRepositories(ind=1:2)
- chooseBioCmirror(ind=7,graphics=F) # canberra - use eg 1 for FredHutch
- chooseCRANmirror(ind=5,graphics=F) # Melbourne - use 96 for texas
-
- ifreq = function(pkg='DESeq2') {
- if(require(package=pkg,character.only = T)){
-   print(paste(pkg,"is loaded correctly"))
- } else {
-   print(paste("trying to install",pkg))
-   install.packages(pkg)
-   if(require(package=pkg,character.only = T)){
-   print(paste(pkg,"installed and loaded correctly"))
-   } else {
-     stop(paste("Could not install",pkg))
-   }
- }
- }
-
- ifreq(pkg="BiocInstaller")
- ifreq(pkg="pkgDepTools")
- ifreq(pkg="Biobase")
-
- print.noquote('Greetings! The R you have chosen is using the following repositories:')
- print.noquote(biocinstallRepos())
- packages = getPackages(our_packages)
- download.packages(pkgs=packages,destdir=tardir, type="source", repos=biocinstallRepos())
- flist = list.files(tardir)
- allDeps = makeDepGraph(biocinstallRepos(), type="source", keep.builtin=F, dosize=F)
- res = NULL
- for (i in c(1:length(our_packages))) {
-   package = our_packages[i]
-   io = getInstallOrder(package, allDeps, needed.only=FALSE)
-   ares = packageExpand(packagelist=io\$packages,fl=flist)
-   res = append(res,ares)
-   }
- ures = unique(res)
- tout = "savedeps.xml"
- write.table(ures,file=tout,quote=F,sep="\t",row.names=F,col.names=F)
- write.table(ures,file=OUTPATH,quote=F,sep="\t",row.names=F,col.names=F)
- print.noquote(res)
- sessionInfo()
- print.noquote(date())
-</configfile>
-</configfiles>
-<tests>
-
-            <test>
-
-            <param name="job_name" value="test1"/>
-            <param name="runMe" value="$runMe"/>
-            <param name="tardir" value="/tmp" />
-<param name="ourpackages" value="DESeq2" />
-<param name="xmlprefix" value="&lt;package&gt;https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/" />
-            <output name="output1" file="r_bioc_depgen_4_test1_output.xls" ftype="tabular" />
-            <output name="html_file" file="r_bioc_depgen_4_test1_output.html" ftype="html" lines_diff="10"/>
-            </test>
-
-</tests>
-<help>
-
-
-**What it Does**
-
-
-Generates some XML for R/BioC dependencies for the packages specified and using the default R
-
-**Script**
-Pressing execute will run the following code over your input file and generate some outputs in your history::
-
-
-   ## Sample tool factory 2 script version if you
- ## define the parameters needed (!) as form elements
- ## will save ALL needed tarballs to destdir
- ## for tool_dependency use
- ### ross lazarus
- ### bah! humbug!
- ### dec 24 2014
-
- packageExpand = function(packagelist,fl) {
-   res = NULL
-   for (i in c(1:length(packagelist))) {
-     s = packagelist[i]
-     ls = nchar(s)
-     spos = which(substr(fl,1,ls) == s,arr.ind=T)
-     lspos = length(spos)
-     if (lspos &gt; 0)
-       {
-       fullname = fl[spos]
-       if (grepl('*.gz',fullname)) {
-            row = paste(ps,fullname,pe,sep='')
-            res = append(res,row)
-            }
-       }
-     }
-   return(res)
- }
-
- getPackages = function(packs)
-   {
-   packages = unlist(tools::package_dependencies(packs, available.packages(),
-         which=c("Depends", "Imports"), recursive=TRUE))
-   packages = union(packs, packages)
-   packages
-   }
-
- ### tool factory Rscript parser suggested by Forester
- ### http://www.r-bloggers.com/including-arguments-in-r-cmd-batch-mode/
- ### additional parameters will appear in the ls() below - they are available
- ### to your script
- ### echo parameters to the output file
- ourargs = commandArgs(TRUE)
- if(length(ourargs)==0){
-       print("No arguments supplied.")
-    }else{
-    for(i in 1:length(ourargs)){
-         eval(parse(text=ourargs[[i]]))
-    }
- }
-
- unesc = function(x) {
- #### needed to deal with galaxy escaping &lt;&gt; in passing the xml string we need - don't try this at home kids.
- res = x
- res = gsub('__lt__','&lt;',res)
- res = gsub('__gt__','&gt;',res)
- return(res)
- }
-
- our_packages = strsplit(ourpackages," ")[[1]]
- ### these show as attached non-base packages in sessionInfo after running the R code
- ps=unesc(xmlprefix)
- pe="?raw=true&lt;/package&gt;"
-
- print(paste('tardir=',tardir,'xmlprefix=',xmlprefix,'ourpackages=',ourpackages,'OUTPATH=',OUTPATH))
-
-
- setRepositories(ind=1:2)
- chooseBioCmirror(ind=7,graphics=F) # canberra - use eg 1 for FredHutch
- chooseCRANmirror(ind=5,graphics=F) # Melbourne - use 96 for texas
-
- ifreq = function(pkg='DESeq2') {
- if(require(package=pkg,character.only = T)){
-   print(paste(pkg,"is loaded correctly"))
- } else {
-   print(paste("trying to install",pkg))
-   install.packages(pkg)
-   if(require(package=pkg,character.only = T)){
-   print(paste(pkg,"installed and loaded correctly"))
-   } else {
-     stop(paste("Could not install",pkg))
-   }
- }
- }
-
- ifreq(pkg="BiocInstaller")
- ifreq(pkg="pkgDepTools")
- ifreq(pkg="Biobase")
-
- print.noquote('Greetings! The R you have chosen is using the following repositories:')
- print.noquote(biocinstallRepos())
- packages = getPackages(our_packages)
- download.packages(pkgs=packages,destdir=tardir, type="source", repos=biocinstallRepos())
- flist = list.files(tardir)
- allDeps = makeDepGraph(biocinstallRepos(), type="source", keep.builtin=F, dosize=F)
- res = NULL
- for (i in c(1:length(our_packages))) {
-   package = our_packages[i]
-   io = getInstallOrder(package, allDeps, needed.only=FALSE)
-   ares = packageExpand(packagelist=io\$packages,fl=flist)
-   res = append(res,ares)
-   }
- ures = unique(res)
- tout = "savedeps.xml"
- write.table(ures,file=tout,quote=F,sep="\t",row.names=F,col.names=F)
- write.table(ures,file=OUTPATH,quote=F,sep="\t",row.names=F,col.names=F)
- print.noquote(res)
- sessionInfo()
- print.noquote(date())
-
-**Attribution**
-This Galaxy tool was created by ross.lazarus@gmail.com at 16/01/2015 13:03:33
-using the Galaxy Tool Factory.
-
-See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
-Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team.
-Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
-
-
-This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
-https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2
-</help>
-<citations>
-
-    <citation type="doi">10.1093/bioinformatics/bts573</citation>
-</citations>
-</tool>
--- a/r_bioc_depgen_4/tool_dependencies.xml	Tue Jan 20 05:08:04 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-            <package name="ghostscript" version="9.10">
-                <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-            </package>
-            <package name="graphicsmagick" version="1.3.18">
-                <repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-            </package>
-             <package name="R" version="3.1.2">
-                <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-            </package>
-
-                <readme>
-
-**What it Does**
-
-
-Generates some XML for R/BioC dependencies for the packages specified and using the default R
-
-                   This file was autogenerated by the Galaxy Tool Factory 2
-               </readme>
-        </tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_bioc_depgen_r_3_1_2/r_bioc_depgen_r_3_1_2.py	Tue Jan 20 19:29:17 2015 -0500
@@ -0,0 +1,969 @@
+# r_bioc_depgen_r_3_1_2/r_bioc_depgen_r_3_1_2.py - a self annotated version of rgToolFactory2.py generated by running rgToolFactory2.py
+# to make a new Galaxy tool called r_bioc_depgen_r_3_1_2
+# User ross.lazarus@gmail.com at 21/01/2015 11:25:22
+# 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
+# add that package to tool_dependencies
+# Note that once the generated tool is loaded, it will have that package's env.sh loaded automagically so there is no
+# --envshpath in the parameters for the generated tool and it uses the system one which will be first on the adjusted path.
+#
+# 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
+                   This file was autogenerated by the Galaxy Tool Factory 2
+               </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
+                   This file was autogenerated by the Galaxy Tool Factory 2
+               </readme>
+        </tool_dependency>
+        """
+
+        self.emptytoolhtmldepskel = """<?xml version="1.0"?>
+        <tool_dependency>
+                <readme>
+                   %(readme)s
+                This file was autogenerated by the Galaxy Tool Factory 2
+               </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
+
+This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
+https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2
+</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: # fragile - depends on common naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play
+
+                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(packdetails[1].split('_')[2:])
+            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,'interpreter_pack':self.interpreter_pack}
+        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()
+        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()
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_bioc_depgen_r_3_1_2/r_bioc_depgen_r_3_1_2.xml	Tue Jan 20 19:29:17 2015 -0500
@@ -0,0 +1,294 @@
+<tool id="r_bioc_depgen_r_3_1_2" name="r_bioc_depgen_r_3_1_2" version="0.01">
+<description>Generate dependencies for R/BioC packages</description>
+<requirements>
+              <requirement type="package" version="9.10">ghostscript</requirement>
+              <requirement type="package" version="1.3.18">graphicsmagick</requirement>
+              <requirement type="package" version="3.1.2">R</requirement>
+          </requirements>
+<command interpreter="python">
+
+            r_bioc_depgen_r_3_1_2.py --script_path "$runMe" --interpreter "Rscript"
+                --tool_name "r_bioc_depgen_r_3_1_2"
+
+
+
+--additional_parameters """tardir,$tardir,Save all dependency tarballs to this directory,I use a github repository for this which is specified in the xml_prefix parameter below,text"""
+--additional_parameters """ourpackages,$ourpackages,SPACE (NOT comma!) separated list of package names - without versions!,Packages and dependencies for the chosen R will be found,text"""
+--additional_parameters """xmlprefix,$xmlprefix,Prefix for generated tool_dependency.xml url to the permanent package archive repository,I use a github repository as the default shows - the tag will be closed with '?raw=true&lt;/package&gt;',text"""
+                 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" --output_tab "$output1"
+
+</command>
+<inputs>
+<param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="r_bioc_depgen_r_3_1_2"/>
+
+<param name="tardir" value="/tmp" label="Save all dependency tarballs to this directory" help="I use a github repository for this which is specified in the xml_prefix parameter below" type="text"/>
+<param name="ourpackages" value="DESeq2" label="SPACE (NOT comma!) separated list of package names - without versions!" help="Packages and dependencies for the chosen R will be found" type="text"/>
+<param name="xmlprefix" value="&lt;package&gt;https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/" label="Prefix for generated tool_dependency.xml url to the permanent package archive repository" help="I use a github repository as the default shows - the tag will be closed with '?raw=true&lt;/package&gt;'" type="text"/>
+</inputs>
+<outputs>
+ <data format="html" name="html_file" label="${job_name}.html"/>
+ <data format="tabular" name="output1" label="${job_name}"/>
+
+</outputs>
+<configfiles>
+<configfile name="runMe">
+ ## Sample tool factory 2 script version if you
+ ## define the parameters needed (!) as form elements
+ ## will save ALL needed tarballs to destdir
+ ## for tool_dependency use
+ ### ross lazarus
+ ### bah! humbug!
+ ### dec 24 2014
+
+ packageExpand = function(packagelist,fl) {
+   res = NULL
+   for (i in c(1:length(packagelist))) {
+     s = packagelist[i]
+     ls = nchar(s)
+     spos = which(substr(fl,1,ls) == s,arr.ind=T)
+     lspos = length(spos)
+     if (lspos &gt; 0)
+       {
+       fullname = fl[spos]
+       if (grepl('*.gz',fullname)) {
+            row = paste(ps,fullname,pe,sep='')
+            res = append(res,row)
+            }
+       }
+     }
+   return(res)
+ }
+
+ getPackages = function(packs)
+   {
+   packages = unlist(tools::package_dependencies(packs, available.packages(),
+         which=c("Depends", "Imports"), recursive=TRUE))
+   packages = union(packs, packages)
+   packages
+   }
+
+ ### tool factory Rscript parser suggested by Forester
+ ### http://www.r-bloggers.com/including-arguments-in-r-cmd-batch-mode/
+ ### additional parameters will appear in the ls() below - they are available
+ ### to your script
+ ### echo parameters to the output file
+ ourargs = commandArgs(TRUE)
+ if(length(ourargs)==0){
+       print("No arguments supplied.")
+    }else{
+    for(i in 1:length(ourargs)){
+         eval(parse(text=ourargs[[i]]))
+    }
+ }
+
+ unesc = function(x) {
+ #### needed to deal with galaxy escaping &lt;&gt; in passing the xml string we need - don't try this at home kids.
+ res = x
+ res = gsub('__lt__','&lt;',res)
+ res = gsub('__gt__','&gt;',res)
+ return(res)
+ }
+
+ our_packages = strsplit(ourpackages," ")[[1]]
+ ### these show as attached non-base packages in sessionInfo after running the R code
+ ps=unesc(xmlprefix)
+ pe="?raw=true&lt;/package&gt;"
+
+ print(paste('tardir=',tardir,'xmlprefix=',xmlprefix,'ourpackages=',ourpackages,'OUTPATH=',OUTPATH))
+
+
+ setRepositories(ind=1:2)
+ chooseBioCmirror(ind=7,graphics=F) # canberra - use eg 1 for FredHutch
+ chooseCRANmirror(ind=5,graphics=F) # Melbourne - use 96 for texas
+
+ ifreq = function(pkg='DESeq2') {
+ if(require(package=pkg,character.only = T)){
+   print(paste(pkg,"is loaded correctly"))
+ } else {
+   print(paste("trying to install",pkg))
+   install.packages(pkg)
+   if(require(package=pkg,character.only = T)){
+   print(paste(pkg,"installed and loaded correctly"))
+   } else {
+     stop(paste("Could not install",pkg))
+   }
+ }
+ }
+
+ ifreq(pkg="BiocInstaller")
+ ifreq(pkg="pkgDepTools")
+ ifreq(pkg="Biobase")
+
+ print.noquote('Greetings! The R you have chosen is using the following repositories:')
+ print.noquote(biocinstallRepos())
+ packages = getPackages(our_packages)
+ download.packages(pkgs=packages,destdir=tardir, type="source", repos=biocinstallRepos())
+ flist = list.files(tardir)
+ allDeps = makeDepGraph(biocinstallRepos(), type="source", keep.builtin=F, dosize=F)
+ res = NULL
+ for (i in c(1:length(our_packages))) {
+   package = our_packages[i]
+   io = getInstallOrder(package, allDeps, needed.only=FALSE)
+   ares = packageExpand(packagelist=io\$packages,fl=flist)
+   res = append(res,ares)
+   }
+ ures = unique(res)
+ tout = "savedeps.xml"
+ write.table(ures,file=tout,quote=F,sep="\t",row.names=F,col.names=F)
+ write.table(ures,file=OUTPATH,quote=F,sep="\t",row.names=F,col.names=F)
+ print.noquote(res)
+ sessionInfo()
+ print.noquote(date())
+</configfile>
+</configfiles>
+<tests>
+
+            <test>
+
+            <param name="job_name" value="test1"/>
+            <param name="runMe" value="$runMe"/>
+            <param name="tardir" value="/tmp" />
+<param name="ourpackages" value="DESeq2" />
+<param name="xmlprefix" value="&lt;package&gt;https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/" />
+            <output name="output1" file="r_bioc_depgen_r_3_1_2_test1_output.xls" ftype="tabular" />
+            <output name="html_file" file="r_bioc_depgen_r_3_1_2_test1_output.html" ftype="html" lines_diff="10"/>
+            </test>
+
+</tests>
+<help>
+
+
+**What it Does**
+
+
+Generates some XML for R/BioC dependencies for the packages specified and using the default R
+
+**Script**
+Pressing execute will run the following code over your input file and generate some outputs in your history::
+
+
+   ## Sample tool factory 2 script version if you
+ ## define the parameters needed (!) as form elements
+ ## will save ALL needed tarballs to destdir
+ ## for tool_dependency use
+ ### ross lazarus
+ ### bah! humbug!
+ ### dec 24 2014
+
+ packageExpand = function(packagelist,fl) {
+   res = NULL
+   for (i in c(1:length(packagelist))) {
+     s = packagelist[i]
+     ls = nchar(s)
+     spos = which(substr(fl,1,ls) == s,arr.ind=T)
+     lspos = length(spos)
+     if (lspos &gt; 0)
+       {
+       fullname = fl[spos]
+       if (grepl('*.gz',fullname)) {
+            row = paste(ps,fullname,pe,sep='')
+            res = append(res,row)
+            }
+       }
+     }
+   return(res)
+ }
+
+ getPackages = function(packs)
+   {
+   packages = unlist(tools::package_dependencies(packs, available.packages(),
+         which=c("Depends", "Imports"), recursive=TRUE))
+   packages = union(packs, packages)
+   packages
+   }
+
+ ### tool factory Rscript parser suggested by Forester
+ ### http://www.r-bloggers.com/including-arguments-in-r-cmd-batch-mode/
+ ### additional parameters will appear in the ls() below - they are available
+ ### to your script
+ ### echo parameters to the output file
+ ourargs = commandArgs(TRUE)
+ if(length(ourargs)==0){
+       print("No arguments supplied.")
+    }else{
+    for(i in 1:length(ourargs)){
+         eval(parse(text=ourargs[[i]]))
+    }
+ }
+
+ unesc = function(x) {
+ #### needed to deal with galaxy escaping &lt;&gt; in passing the xml string we need - don't try this at home kids.
+ res = x
+ res = gsub('__lt__','&lt;',res)
+ res = gsub('__gt__','&gt;',res)
+ return(res)
+ }
+
+ our_packages = strsplit(ourpackages," ")[[1]]
+ ### these show as attached non-base packages in sessionInfo after running the R code
+ ps=unesc(xmlprefix)
+ pe="?raw=true&lt;/package&gt;"
+
+ print(paste('tardir=',tardir,'xmlprefix=',xmlprefix,'ourpackages=',ourpackages,'OUTPATH=',OUTPATH))
+
+
+ setRepositories(ind=1:2)
+ chooseBioCmirror(ind=7,graphics=F) # canberra - use eg 1 for FredHutch
+ chooseCRANmirror(ind=5,graphics=F) # Melbourne - use 96 for texas
+
+ ifreq = function(pkg='DESeq2') {
+ if(require(package=pkg,character.only = T)){
+   print(paste(pkg,"is loaded correctly"))
+ } else {
+   print(paste("trying to install",pkg))
+   install.packages(pkg)
+   if(require(package=pkg,character.only = T)){
+   print(paste(pkg,"installed and loaded correctly"))
+   } else {
+     stop(paste("Could not install",pkg))
+   }
+ }
+ }
+
+ ifreq(pkg="BiocInstaller")
+ ifreq(pkg="pkgDepTools")
+ ifreq(pkg="Biobase")
+
+ print.noquote('Greetings! The R you have chosen is using the following repositories:')
+ print.noquote(biocinstallRepos())
+ packages = getPackages(our_packages)
+ download.packages(pkgs=packages,destdir=tardir, type="source", repos=biocinstallRepos())
+ flist = list.files(tardir)
+ allDeps = makeDepGraph(biocinstallRepos(), type="source", keep.builtin=F, dosize=F)
+ res = NULL
+ for (i in c(1:length(our_packages))) {
+   package = our_packages[i]
+   io = getInstallOrder(package, allDeps, needed.only=FALSE)
+   ares = packageExpand(packagelist=io\$packages,fl=flist)
+   res = append(res,ares)
+   }
+ ures = unique(res)
+ tout = "savedeps.xml"
+ write.table(ures,file=tout,quote=F,sep="\t",row.names=F,col.names=F)
+ write.table(ures,file=OUTPATH,quote=F,sep="\t",row.names=F,col.names=F)
+ print.noquote(res)
+ sessionInfo()
+ print.noquote(date())
+
+**Attribution**
+This Galaxy tool was created by ross.lazarus@gmail.com at 21/01/2015 11:25:22
+using the Galaxy Tool Factory.
+
+See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
+Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team.
+Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
+
+
+This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
+https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2
+</help>
+<citations>
+
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
+</citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_bioc_depgen_r_3_1_2/test-data/r_bioc_depgen_r_3_1_2_test1_output.html	Tue Jan 20 19:29:17 2015 -0500
@@ -0,0 +1,962 @@
+<!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 rgToolFactory2.py 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">
+
+<div class="infomessage">Galaxy Tool "r_bioc_depgen_r_3_1_2" run at 21/01/2015 11:25:22</div><br/>
+<div class="toolFormTitle">r log output</div>
+
+<pre>
+
+Loading required package: BiocInstaller
+
+Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
+
+Loading required package: pkgDepTools
+
+Loading required package: methods
+
+Loading required package: graph
+
+Loading required package: RBGL
+
+Loading required package: Biobase
+
+Loading required package: BiocGenerics
+
+Loading required package: parallel
+
+Attaching package: 'BiocGenerics'
+
+The following objects are masked from 'package:parallel':
+
+    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
+
+    clusterExport, clusterMap, parApply, parCapply, parLapply,
+
+    parLapplyLB, parRapply, parSapply, parSapplyLB
+
+The following object is masked from 'package:stats':
+
+    xtabs
+
+The following objects are masked from 'package:base':
+
+    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
+
+    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
+
+    eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
+
+    mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
+
+    rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
+
+    unique, unlist, unsplit
+
+Welcome to Bioconductor
+
+    Vignettes contain introductory material; view with
+
+    'browseVignettes()'. To cite Bioconductor, see
+
+    'citation("Biobase")', and for packages 'citation("pkgname")'.
+
+trying URL 'http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/bioc/src/contrib/DESeq2_1.6.3.tar.gz'
+
+Content type 'application/x-gzip' length 1194684 bytes (1.1 Mb)
+
+opened URL
+
+==================================================
+
+downloaded 1.1 Mb
+
+trying URL 'http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/bioc/src/contrib/S4Vectors_0.4.0.tar.gz'
+
+Content type 'application/x-gzip' length 119231 bytes (116 Kb)
+
+opened URL
+
+==================================================
+
+downloaded 116 Kb
+
+trying URL 'http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/bioc/src/contrib/IRanges_2.0.1.tar.gz'
+
+Content type 'application/x-gzip' length 584602 bytes (570 Kb)
+
+opened URL
+
+==================================================
+
+downloaded 570 Kb
+
+trying URL 'http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/bioc/src/contrib/GenomicRanges_1.18.4.tar.gz'
+
+Content type 'application/x-gzip' length 672061 bytes (656 Kb)
+
+opened URL
+
+==================================================
+
+downloaded 656 Kb
+
+trying URL 'http://cran.at.r-project.org/src/contrib/Rcpp_0.11.3.tar.gz'
+
+Content type 'application/x-gzip' length 2169583 bytes (2.1 Mb)
+
+opened URL
+
+==================================================
+
+downloaded 2.1 Mb
+
+trying URL 'http://cran.at.r-project.org/src/contrib/RcppArmadillo_0.4.600.0.tar.gz'
+
+Content type 'application/x-gzip' length 938280 bytes (916 Kb)
+
+opened URL
+
+==================================================
+
+downloaded 916 Kb
+
+trying URL 'http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/bioc/src/contrib/BiocGenerics_0.12.1.tar.gz'
+
+Content type 'application/x-gzip' length 33444 bytes (32 Kb)
+
+opened URL
+
+==================================================
+
+downloaded 32 Kb
+
+trying URL 'http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/bioc/src/contrib/Biobase_2.26.0.tar.gz'
+
+Content type 'application/x-gzip' length 1674714 bytes (1.6 Mb)
+
+opened URL
+
+==================================================
+
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+
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+
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+
+1: In .local(from, to, graph) :
+
+  edges replaced: 'MafDb.ALL.wgs.phase1.release.v3.20101123|VariantFiltering', 'NA|RSQLite', 'NA|Biobase', 'NA|AnnotationDbi', 'NA|IRanges', 'NA|Biostrings', 'NA|Rsamtools', 'NA|GenomicRanges', 'NA|VariantAnnotation'
+
+2: In .local(from, to, graph) :
+
+  edges replaced: 'MafDb.ESP6500SI.V2.SSA137.dbSNP138|VariantFiltering', 'NA|RSQLite', 'NA|Biobase', 'NA|AnnotationDbi', 'NA|IRanges', 'NA|Biostrings', 'NA|GenomicRanges', 'NA|VariantAnnotation'
+
+3: In .local(from, to, graph) :
+
+  edges replaced: 'phastCons100way.UCSC.hg19|VariantFiltering', 'NA|IRanges', 'NA|GenomicRanges', 'NA|BSgenome'
+
+4: In .local(from, to, graph) : edges replaced: 'SNPRelate|gdsfmt'
+
+5: In .local(from, to, graph) : edges replaced: 'RCurl|bitops'
+
+Warning messages:
+
+1: In if (grepl("*.gz", fullname)) { :
+
+  the condition has length > 1 and only the first element will be used
+
+2: In if (grepl("*.gz", fullname)) { :
+
+  the condition has length > 1 and only the first element will be used
+
+
+</pre>
+
+<div class="toolFormTitle">Other log output</div>
+
+<pre>
+
+## Toolfactory generated command line = Rscript /mnt/galaxy/tmp/143.1.all.q/r_bioc_depgen_r_3_1_2gRKYSn.Rscript OUTPATH="/mnt/galaxy/tmp/job_working_directory/000/225/galaxy_dataset_508.dat" tardir="/tmp" ourpackages="DESeq2" xmlprefix="<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/"
+
+[1] "tardir= /tmp xmlprefix= <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/ ourpackages= DESeq2 OUTPATH= /mnt/galaxy/tmp/job_working_directory/000/225/galaxy_dataset_508.dat"
+
+[1] "BiocInstaller is loaded correctly"
+
+[1] "pkgDepTools is loaded correctly"
+
+[1] "Biobase is loaded correctly"
+
+[1] Greetings! The R you have chosen is using the following repositories:
+
+                                                                  BioCsoft
+
+           http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/bioc
+
+                                                                   BioCann
+
+http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/data/annotation
+
+                                                                   BioCexp
+
+http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/data/experiment
+
+                                                                 BioCextra
+
+          http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/extra
+
+                                                                      CRAN
+
+                                              http://cran.at.r-project.org
+
+      [,1]            [,2]
+
+ [1,] "DESeq2"        "/tmp/DESeq2_1.6.3.tar.gz"
+
+ [2,] "S4Vectors"     "/tmp/S4Vectors_0.4.0.tar.gz"
+
+ [3,] "IRanges"       "/tmp/IRanges_2.0.1.tar.gz"
+
+ [4,] "GenomicRanges" "/tmp/GenomicRanges_1.18.4.tar.gz"
+
+ [5,] "Rcpp"          "/tmp/Rcpp_0.11.3.tar.gz"
+
+ [6,] "RcppArmadillo" "/tmp/RcppArmadillo_0.4.600.0.tar.gz"
+
+ [7,] "BiocGenerics"  "/tmp/BiocGenerics_0.12.1.tar.gz"
+
+ [8,] "Biobase"       "/tmp/Biobase_2.26.0.tar.gz"
+
+ [9,] "BiocParallel"  "/tmp/BiocParallel_1.0.0.tar.gz"
+
+[10,] "genefilter"    "/tmp/genefilter_1.48.1.tar.gz"
+
+[11,] "locfit"        "/tmp/locfit_1.5-9.1.tar.gz"
+
+[12,] "geneplotter"   "/tmp/geneplotter_1.44.0.tar.gz"
+
+[13,] "ggplot2"       "/tmp/ggplot2_1.0.0.tar.gz"
+
+[14,] "Hmisc"         "/tmp/Hmisc_3.14-6.tar.gz"
+
+[15,] "foreach"       "/tmp/foreach_1.4.2.tar.gz"
+
+[16,] "BatchJobs"     "/tmp/BatchJobs_1.5.tar.gz"
+
+[17,] "BBmisc"        "/tmp/BBmisc_1.8.tar.gz"
+
+[18,] "GenomeInfoDb"  "/tmp/GenomeInfoDb_1.2.4.tar.gz"
+
+[19,] "XVector"       "/tmp/XVector_0.6.0.tar.gz"
+
+[20,] "lattice"       "/tmp/lattice_0.20-29.tar.gz"
+
+[21,] "survival"      "/tmp/survival_2.37-7.tar.gz"
+
+[22,] "Formula"       "/tmp/Formula_1.2-0.tar.gz"
+
+[23,] "latticeExtra"  "/tmp/latticeExtra_0.6-26.tar.gz"
+
+[24,] "cluster"       "/tmp/cluster_1.15.3.tar.gz"
+
+[25,] "rpart"         "/tmp/rpart_4.1-8.tar.gz"
+
+[26,] "nnet"          "/tmp/nnet_7.3-8.tar.gz"
+
+[27,] "acepack"       "/tmp/acepack_1.3-3.3.tar.gz"
+
+[28,] "foreign"       "/tmp/foreign_0.8-62.tar.gz"
+
+[29,] "AnnotationDbi" "/tmp/AnnotationDbi_1.28.1.tar.gz"
+
+[30,] "annotate"      "/tmp/annotate_1.44.0.tar.gz"
+
+[31,] "RColorBrewer"  "/tmp/RColorBrewer_1.1-2.tar.gz"
+
+[32,] "plyr"          "/tmp/plyr_1.8.1.tar.gz"
+
+[33,] "digest"        "/tmp/digest_0.6.8.tar.gz"
+
+[34,] "gtable"        "/tmp/gtable_0.1.2.tar.gz"
+
+[35,] "reshape2"      "/tmp/reshape2_1.4.1.tar.gz"
+
+[36,] "scales"        "/tmp/scales_0.2.4.tar.gz"
+
+[37,] "proto"         "/tmp/proto_0.3-10.tar.gz"
+
+[38,] "MASS"          "/tmp/MASS_7.3-37.tar.gz"
+
+[39,] "DBI"           "/tmp/DBI_0.3.1.tar.gz"
+
+[40,] "RSQLite"       "/tmp/RSQLite_1.0.0.tar.gz"
+
+[41,] "checkmate"     "/tmp/checkmate_1.5.1.tar.gz"
+
+[42,] "brew"          "/tmp/brew_1.0-6.tar.gz"
+
+[43,] "fail"          "/tmp/fail_1.2.tar.gz"
+
+[44,] "sendmailR"     "/tmp/sendmailR_1.2-1.tar.gz"
+
+[45,] "stringr"       "/tmp/stringr_0.6.2.tar.gz"
+
+[46,] "XML"           "/tmp/XML_3.98-1.1.tar.gz"
+
+[47,] "xtable"        "/tmp/xtable_1.7-4.tar.gz"
+
+[48,] "codetools"     "/tmp/codetools_0.2-10.tar.gz"
+
+[49,] "iterators"     "/tmp/iterators_1.0.7.tar.gz"
+
+[50,] "dichromat"     "/tmp/dichromat_2.0-0.tar.gz"
+
+[51,] "munsell"       "/tmp/munsell_0.4.2.tar.gz"
+
+[52,] "labeling"      "/tmp/labeling_0.3.tar.gz"
+
+[53,] "colorspace"    "/tmp/colorspace_1.2-4.tar.gz"
+
+[54,] "base64enc"     "/tmp/base64enc_0.1-2.tar.gz"
+
+ [1] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocGenerics_0.12.1.tar.gz?raw=true</package>
+
+ [2] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/S4Vectors_0.4.0.tar.gz?raw=true</package>
+
+ [3] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/IRanges_2.0.1.tar.gz?raw=true</package>
+
+ [4] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomeInfoDb_1.2.4.tar.gz?raw=true</package>
+
+ [5] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XVector_0.6.0.tar.gz?raw=true</package>
+
+ [6] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomicRanges_1.18.4.tar.gz?raw=true</package>
+
+ [7] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RcppArmadillo_0.4.600.0.tar.gz?raw=true</package>
+
+ [8] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Rcpp_0.11.3.tar.gz?raw=true</package>
+
+ [9] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RcppArmadillo_0.4.600.0.tar.gz?raw=true</package>
+
+[10] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Biobase_2.26.0.tar.gz?raw=true</package>
+
+[11] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/iterators_1.0.7.tar.gz?raw=true</package>
+
+[12] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/foreach_1.4.2.tar.gz?raw=true</package>
+
+[13] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/checkmate_1.5.1.tar.gz?raw=true</package>
+
+[14] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BBmisc_1.8.tar.gz?raw=true</package>
+
+[15] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/brew_1.0-6.tar.gz?raw=true</package>
+
+[16] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DBI_0.3.1.tar.gz?raw=true</package>
+
+[17] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/digest_0.6.8.tar.gz?raw=true</package>
+
+[18] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/fail_1.2.tar.gz?raw=true</package>
+
+[19] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RSQLite_1.0.0.tar.gz?raw=true</package>
+
+[20] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/base64enc_0.1-2.tar.gz?raw=true</package>
+
+[21] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/sendmailR_1.2-1.tar.gz?raw=true</package>
+
+[22] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/stringr_0.6.2.tar.gz?raw=true</package>
+
+[23] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BatchJobs_1.5.tar.gz?raw=true</package>
+
+[24] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocParallel_1.0.0.tar.gz?raw=true</package>
+
+[25] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/AnnotationDbi_1.28.1.tar.gz?raw=true</package>
+
+[26] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XML_3.98-1.1.tar.gz?raw=true</package>
+
+[27] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/xtable_1.7-4.tar.gz?raw=true</package>
+
+[28] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/annotate_1.44.0.tar.gz?raw=true</package>
+
+[29] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/genefilter_1.48.1.tar.gz?raw=true</package>
+
+[30] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/locfit_1.5-9.1.tar.gz?raw=true</package>
+
+[31] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RColorBrewer_1.1-2.tar.gz?raw=true</package>
+
+[32] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/geneplotter_1.44.0.tar.gz?raw=true</package>
+
+[33] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/plyr_1.8.1.tar.gz?raw=true</package>
+
+[34] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gtable_0.1.2.tar.gz?raw=true</package>
+
+[35] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/reshape2_1.4.1.tar.gz?raw=true</package>
+
+[36] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/dichromat_2.0-0.tar.gz?raw=true</package>
+
+[37] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/colorspace_1.2-4.tar.gz?raw=true</package>
+
+[38] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/munsell_0.4.2.tar.gz?raw=true</package>
+
+[39] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/labeling_0.3.tar.gz?raw=true</package>
+
+[40] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/scales_0.2.4.tar.gz?raw=true</package>
+
+[41] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/proto_0.3-10.tar.gz?raw=true</package>
+
+[42] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/ggplot2_1.0.0.tar.gz?raw=true</package>
+
+[43] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.1-2.tar.gz?raw=true</package>
+
+[44] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.2-0.tar.gz?raw=true</package>
+
+[45] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/latticeExtra_0.6-26.tar.gz?raw=true</package>
+
+[46] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/acepack_1.3-3.3.tar.gz?raw=true</package>
+
+[47] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Hmisc_3.14-6.tar.gz?raw=true</package>
+
+[48] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DESeq2_1.6.3.tar.gz?raw=true</package>
+
+R version 3.1.2 (2014-10-31)
+
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+locale:
+
+[1] C
+
+attached base packages:
+
+[1] parallel  methods   stats     graphics  grDevices utils     datasets
+
+[8] base
+
+other attached packages:
+
+[1] Biobase_2.26.0       BiocGenerics_0.12.1  pkgDepTools_1.32.0
+
+[4] RBGL_1.42.0          graph_1.44.1         BiocInstaller_1.16.1
+
+loaded via a namespace (and not attached):
+
+[1] stats4_3.1.2 tools_3.1.2
+
+[1] Wed Jan 21 11:25:22 2015
+
+
+</pre>
+
+<div class="toolFormTitle">All output files available for downloading</div>
+
+<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
+
+<tr><td><a href="r_bioc_depgen_r_3_1_2.Rscript">r_bioc_depgen_r_3_1_2.Rscript</a></td><td>3.1 KB</td></tr>
+<tr class="odd_row"><td><a href="r_bioc_depgen_r_3_1_2_error.log">r_bioc_depgen_r_3_1_2_error.log</a></td><td>15.5 KB</td></tr>
+<tr><td><a href="r_bioc_depgen_r_3_1_2_runner.log">r_bioc_depgen_r_3_1_2_runner.log</a></td><td>11.9 KB</td></tr>
+<tr class="odd_row"><td><a href="savedeps.xml">savedeps.xml</a></td><td>6.0 KB</td></tr>
+</table></div><br/>
+</div></body></html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_bioc_depgen_r_3_1_2/test-data/r_bioc_depgen_r_3_1_2_test1_output.xls	Tue Jan 20 19:29:17 2015 -0500
@@ -0,0 +1,47 @@
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocGenerics_0.12.1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/S4Vectors_0.4.0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/IRanges_2.0.1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomeInfoDb_1.2.4.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XVector_0.6.0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomicRanges_1.18.4.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RcppArmadillo_0.4.600.0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Rcpp_0.11.3.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Biobase_2.26.0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/iterators_1.0.7.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/foreach_1.4.2.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/checkmate_1.5.1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BBmisc_1.8.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/brew_1.0-6.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DBI_0.3.1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/digest_0.6.8.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/fail_1.2.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RSQLite_1.0.0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/base64enc_0.1-2.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/sendmailR_1.2-1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/stringr_0.6.2.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BatchJobs_1.5.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocParallel_1.0.0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/AnnotationDbi_1.28.1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XML_3.98-1.1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/xtable_1.7-4.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/annotate_1.44.0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/genefilter_1.48.1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/locfit_1.5-9.1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RColorBrewer_1.1-2.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/geneplotter_1.44.0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/plyr_1.8.1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gtable_0.1.2.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/reshape2_1.4.1.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/dichromat_2.0-0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/colorspace_1.2-4.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/munsell_0.4.2.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/labeling_0.3.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/scales_0.2.4.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/proto_0.3-10.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/ggplot2_1.0.0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.1-2.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.2-0.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/latticeExtra_0.6-26.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/acepack_1.3-3.3.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Hmisc_3.14-6.tar.gz?raw=true</package>
+<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DESeq2_1.6.3.tar.gz?raw=true</package>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_bioc_depgen_r_3_1_2/test-data/test1_out.log	Tue Jan 20 19:29:17 2015 -0500
@@ -0,0 +1,136 @@
+## Toolfactory generated command line = Rscript /mnt/galaxy/tmp/143.1.all.q/r_bioc_depgen_r_3_1_2gRKYSn.Rscript OUTPATH="/mnt/galaxy/tmp/job_working_directory/000/225/galaxy_dataset_508.dat" tardir="/tmp" ourpackages="DESeq2" xmlprefix="<package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/"
+[1] "tardir= /tmp xmlprefix= <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/ ourpackages= DESeq2 OUTPATH= /mnt/galaxy/tmp/job_working_directory/000/225/galaxy_dataset_508.dat"
+[1] "BiocInstaller is loaded correctly"
+[1] "pkgDepTools is loaded correctly"
+[1] "Biobase is loaded correctly"
+[1] Greetings! The R you have chosen is using the following repositories:
+                                                                  BioCsoft
+           http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/bioc
+                                                                   BioCann
+http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/data/annotation
+                                                                   BioCexp
+http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/data/experiment
+                                                                 BioCextra
+          http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/extra
+                                                                      CRAN
+                                              http://cran.at.r-project.org
+      [,1]            [,2]
+ [1,] "DESeq2"        "/tmp/DESeq2_1.6.3.tar.gz"
+ [2,] "S4Vectors"     "/tmp/S4Vectors_0.4.0.tar.gz"
+ [3,] "IRanges"       "/tmp/IRanges_2.0.1.tar.gz"
+ [4,] "GenomicRanges" "/tmp/GenomicRanges_1.18.4.tar.gz"
+ [5,] "Rcpp"          "/tmp/Rcpp_0.11.3.tar.gz"
+ [6,] "RcppArmadillo" "/tmp/RcppArmadillo_0.4.600.0.tar.gz"
+ [7,] "BiocGenerics"  "/tmp/BiocGenerics_0.12.1.tar.gz"
+ [8,] "Biobase"       "/tmp/Biobase_2.26.0.tar.gz"
+ [9,] "BiocParallel"  "/tmp/BiocParallel_1.0.0.tar.gz"
+[10,] "genefilter"    "/tmp/genefilter_1.48.1.tar.gz"
+[11,] "locfit"        "/tmp/locfit_1.5-9.1.tar.gz"
+[12,] "geneplotter"   "/tmp/geneplotter_1.44.0.tar.gz"
+[13,] "ggplot2"       "/tmp/ggplot2_1.0.0.tar.gz"
+[14,] "Hmisc"         "/tmp/Hmisc_3.14-6.tar.gz"
+[15,] "foreach"       "/tmp/foreach_1.4.2.tar.gz"
+[16,] "BatchJobs"     "/tmp/BatchJobs_1.5.tar.gz"
+[17,] "BBmisc"        "/tmp/BBmisc_1.8.tar.gz"
+[18,] "GenomeInfoDb"  "/tmp/GenomeInfoDb_1.2.4.tar.gz"
+[19,] "XVector"       "/tmp/XVector_0.6.0.tar.gz"
+[20,] "lattice"       "/tmp/lattice_0.20-29.tar.gz"
+[21,] "survival"      "/tmp/survival_2.37-7.tar.gz"
+[22,] "Formula"       "/tmp/Formula_1.2-0.tar.gz"
+[23,] "latticeExtra"  "/tmp/latticeExtra_0.6-26.tar.gz"
+[24,] "cluster"       "/tmp/cluster_1.15.3.tar.gz"
+[25,] "rpart"         "/tmp/rpart_4.1-8.tar.gz"
+[26,] "nnet"          "/tmp/nnet_7.3-8.tar.gz"
+[27,] "acepack"       "/tmp/acepack_1.3-3.3.tar.gz"
+[28,] "foreign"       "/tmp/foreign_0.8-62.tar.gz"
+[29,] "AnnotationDbi" "/tmp/AnnotationDbi_1.28.1.tar.gz"
+[30,] "annotate"      "/tmp/annotate_1.44.0.tar.gz"
+[31,] "RColorBrewer"  "/tmp/RColorBrewer_1.1-2.tar.gz"
+[32,] "plyr"          "/tmp/plyr_1.8.1.tar.gz"
+[33,] "digest"        "/tmp/digest_0.6.8.tar.gz"
+[34,] "gtable"        "/tmp/gtable_0.1.2.tar.gz"
+[35,] "reshape2"      "/tmp/reshape2_1.4.1.tar.gz"
+[36,] "scales"        "/tmp/scales_0.2.4.tar.gz"
+[37,] "proto"         "/tmp/proto_0.3-10.tar.gz"
+[38,] "MASS"          "/tmp/MASS_7.3-37.tar.gz"
+[39,] "DBI"           "/tmp/DBI_0.3.1.tar.gz"
+[40,] "RSQLite"       "/tmp/RSQLite_1.0.0.tar.gz"
+[41,] "checkmate"     "/tmp/checkmate_1.5.1.tar.gz"
+[42,] "brew"          "/tmp/brew_1.0-6.tar.gz"
+[43,] "fail"          "/tmp/fail_1.2.tar.gz"
+[44,] "sendmailR"     "/tmp/sendmailR_1.2-1.tar.gz"
+[45,] "stringr"       "/tmp/stringr_0.6.2.tar.gz"
+[46,] "XML"           "/tmp/XML_3.98-1.1.tar.gz"
+[47,] "xtable"        "/tmp/xtable_1.7-4.tar.gz"
+[48,] "codetools"     "/tmp/codetools_0.2-10.tar.gz"
+[49,] "iterators"     "/tmp/iterators_1.0.7.tar.gz"
+[50,] "dichromat"     "/tmp/dichromat_2.0-0.tar.gz"
+[51,] "munsell"       "/tmp/munsell_0.4.2.tar.gz"
+[52,] "labeling"      "/tmp/labeling_0.3.tar.gz"
+[53,] "colorspace"    "/tmp/colorspace_1.2-4.tar.gz"
+[54,] "base64enc"     "/tmp/base64enc_0.1-2.tar.gz"
+ [1] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocGenerics_0.12.1.tar.gz?raw=true</package>
+ [2] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/S4Vectors_0.4.0.tar.gz?raw=true</package>
+ [3] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/IRanges_2.0.1.tar.gz?raw=true</package>
+ [4] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomeInfoDb_1.2.4.tar.gz?raw=true</package>
+ [5] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XVector_0.6.0.tar.gz?raw=true</package>
+ [6] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomicRanges_1.18.4.tar.gz?raw=true</package>
+ [7] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RcppArmadillo_0.4.600.0.tar.gz?raw=true</package>
+ [8] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Rcpp_0.11.3.tar.gz?raw=true</package>
+ [9] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RcppArmadillo_0.4.600.0.tar.gz?raw=true</package>
+[10] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Biobase_2.26.0.tar.gz?raw=true</package>
+[11] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/iterators_1.0.7.tar.gz?raw=true</package>
+[12] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/foreach_1.4.2.tar.gz?raw=true</package>
+[13] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/checkmate_1.5.1.tar.gz?raw=true</package>
+[14] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BBmisc_1.8.tar.gz?raw=true</package>
+[15] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/brew_1.0-6.tar.gz?raw=true</package>
+[16] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DBI_0.3.1.tar.gz?raw=true</package>
+[17] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/digest_0.6.8.tar.gz?raw=true</package>
+[18] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/fail_1.2.tar.gz?raw=true</package>
+[19] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RSQLite_1.0.0.tar.gz?raw=true</package>
+[20] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/base64enc_0.1-2.tar.gz?raw=true</package>
+[21] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/sendmailR_1.2-1.tar.gz?raw=true</package>
+[22] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/stringr_0.6.2.tar.gz?raw=true</package>
+[23] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BatchJobs_1.5.tar.gz?raw=true</package>
+[24] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocParallel_1.0.0.tar.gz?raw=true</package>
+[25] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/AnnotationDbi_1.28.1.tar.gz?raw=true</package>
+[26] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XML_3.98-1.1.tar.gz?raw=true</package>
+[27] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/xtable_1.7-4.tar.gz?raw=true</package>
+[28] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/annotate_1.44.0.tar.gz?raw=true</package>
+[29] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/genefilter_1.48.1.tar.gz?raw=true</package>
+[30] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/locfit_1.5-9.1.tar.gz?raw=true</package>
+[31] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RColorBrewer_1.1-2.tar.gz?raw=true</package>
+[32] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/geneplotter_1.44.0.tar.gz?raw=true</package>
+[33] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/plyr_1.8.1.tar.gz?raw=true</package>
+[34] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gtable_0.1.2.tar.gz?raw=true</package>
+[35] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/reshape2_1.4.1.tar.gz?raw=true</package>
+[36] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/dichromat_2.0-0.tar.gz?raw=true</package>
+[37] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/colorspace_1.2-4.tar.gz?raw=true</package>
+[38] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/munsell_0.4.2.tar.gz?raw=true</package>
+[39] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/labeling_0.3.tar.gz?raw=true</package>
+[40] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/scales_0.2.4.tar.gz?raw=true</package>
+[41] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/proto_0.3-10.tar.gz?raw=true</package>
+[42] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/ggplot2_1.0.0.tar.gz?raw=true</package>
+[43] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.1-2.tar.gz?raw=true</package>
+[44] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.2-0.tar.gz?raw=true</package>
+[45] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/latticeExtra_0.6-26.tar.gz?raw=true</package>
+[46] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/acepack_1.3-3.3.tar.gz?raw=true</package>
+[47] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Hmisc_3.14-6.tar.gz?raw=true</package>
+[48] <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DESeq2_1.6.3.tar.gz?raw=true</package>
+R version 3.1.2 (2014-10-31)
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+locale:
+[1] C
+
+attached base packages:
+[1] parallel  methods   stats     graphics  grDevices utils     datasets
+[8] base
+
+other attached packages:
+[1] Biobase_2.26.0       BiocGenerics_0.12.1  pkgDepTools_1.32.0
+[4] RBGL_1.42.0          graph_1.44.1         BiocInstaller_1.16.1
+
+loaded via a namespace (and not attached):
+[1] stats4_3.1.2 tools_3.1.2
+[1] Wed Jan 21 11:25:22 2015
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_bioc_depgen_r_3_1_2/tool_dependencies.xml	Tue Jan 20 19:29:17 2015 -0500
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool_dependency>
+            <package name="ghostscript" version="9.10">
+                <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+            </package>
+            <package name="graphicsmagick" version="1.3.18">
+                <repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+            </package>
+             <package name="R" version="3.1.2">
+                <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+            </package>
+
+                <readme>
+
+**What it Does**
+
+
+Generates some XML for R/BioC dependencies for the packages specified and using the default R
+
+                   This file was autogenerated by the Galaxy Tool Factory 2
+               </readme>
+        </tool_dependency>