Mercurial > repos > fubar > toolfactory

--- a/fubar-galaxytoolfactory-2e68c2a22b43/README.txt	Mon Aug 13 06:27:26 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,233 +0,0 @@
-# WARNING before you start
-# Install this tool on a private Galaxy ONLY
-# Please NEVER on a public or production instance
-
-*Short Story*
-This is an unusual Galaxy tool that generates very simple new Galaxy tools that run the user
-a supplied script (R, python, perl, bash...) over a single input file.
-Whenever you run this tool, the ToolFactory, you should have prepared a script to paste into a text box,
-and a small test input example ready to select from your history to test your new script
-
-If the script runs sucessfully, a new Galaxy tool that runs your script can be generated.
-The new tool is in the form of a special new Galaxy datatype - toolshed.gz - as the name suggests,
-it's an archive ready to upload to a Galaxy ToolShed as a new tool repository.
-
-Once it's in a ToolShed, it can be installed into any local Galaxy server from
-the server administrative interface.
-
-Once your new tool is installed, local users can run it - each time, the script that was supplied
-when it was built will be executed with the input chosen from the user's history. In other words,
-the tools you generate with the ToolFactory run just like any other Galaxy tool,
-but run your script every time.
-
-*Reasons to read further*
-
-If you use Galaxy to support your research;
-
-You and fellow users are sometimes forced to take data out of Galaxy, process it with ugly
-little perl/awk/sed/R... scripts and put it back;
-
-You do this when you can't do some transformation in Galaxy (the 90/10 rule);
-
-You don't have enough developer resources for wrapping dozens of even relatively simple tools;
-
-Your research and your institution would be far better off if those feral scripts were all tucked safely in
-your local toolshed and Galaxy histories.
-
-*The good news* If it can be trivially scripted, it can be running safely in your
-local Galaxy via your own local toolshed in a few minutes - with functional tests.
-
-
-*Value proposition* The ToolFactory allows Galaxy to efficiently take over most of your lab's dark script matter,
-making it reproducible in Galaxy and shareable through the ToolShed.
-
-That's what this tool does. You paste a simple script and the tool returns
-a new, real Galaxy tool, ready to be installed from the local toolshed to local servers.
-Scripts can be wrapped and online literally within minutes.
-
-*To fully and safely exploit the awesome power* of this tool, Galaxy and the ToolShed,
-you should be a developer installing this tool on a private/personal/scratch local instance where you are an admin_user.
-Then, if you break it, you get to keep all the pieces
-see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
-
-** Installation **
-This is a Galaxy tool. You can install it most conveniently using the administrative "Search and browse tool sheds" link.
-Find the Galaxy Test toolshed (not main) and search for the toolfactory repository.
-Open it and review the code and select the option to install it.
-
-If you can't get the tool that way, the xml and py files here need to be copied into a new tools subdirectory such as tools/toolfactory
-Your tool_conf.xml needs a new entry pointing to the xml file - something like::
-
-  <section name="Tool building tools" id="toolbuilders">
-    <tool file="toolfactory/rgToolFactory.xml"/>
-  </section>
-
-If not already there (I just added it to datatypes_conf.xml.sample), please add:
-<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
-to your local data_types_conf.xml.
-
-Ensure that html sanitization is set to False and uncommented in universe_wsgi.ini
-
-You'll have to restart the server for the new tool to be available.
-
-Of course, R, python, perl etc are needed on your path if you want to test scripts using those interpreters.
-Adding new ones to this tool code should be easy enough. Please make suggestions as bitbucket issues and code.
-The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick .
-
-* Restricted execution *
-The new tool factory tool will then be usable ONLY by admin users - people with IDs in admin_users in universe_wsgi.ini
-**Yes, that's right. ONLY admin_users can run this tool** Think about it for a moment. If allowed to run any
-arbitrary script on your Galaxy server, the only thing that would impede a miscreant bent on destroying all your
-Galaxy data would probably be lack of appropriate technical skills.
-
-*What it does* This is a tool factory for simple scripts in python, R and perl currently.
-Functional tests are automatically generated. How cool is that.
-
-LIMITED to 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
-index page for the user to navigate - useful if the script writes images and output files - pdf outputs
-are shown as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and imagemagik need to
-be avaailable.
-
-Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up since
-a generated script gets you a serious leg up to a more complex one.
-
-*What you do* You paste and run your script
-you fix the syntax errors and eventually it runs
-You can use the redo button and edit the script before
-trying to rerun it as you debug - it works pretty well.
-
-Once the script works on some test data, you can
-generate a toolshed compatible gzip file
-containing your script ready to run as an ordinary Galaxy tool in a
-repository on your local toolshed. That means safe and largely automated installation in any
-production Galaxy configured to use your toolshed.
-
-*Generated tool Security* Once you install a generated tool, it's just
-another tool - assuming 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 - it is really scary.
-
-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 and suggestions welcome as bitbucket issues please?
-
-long route to June 2012 product
-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
-
-
-
-
-copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
-
-all rights reserved
-Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
-
-Material for our more enthusiastic and voracious readers continues below - we salute you.
-
-**Motivation** Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs
-- even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible.
-
-**Benefits** For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics
-tasks. Once a user has a working R (or python or perl) script that does something Galaxy cannot currently do (eg transpose a
-tabular file) and takes parameters the way Galaxy supplies them (see example below), they:
-
-1. Install the tool factory on a personal private instance
-
-2. Upload a small test data set
-
-3. Paste the script into the 'script' text box and iteratively run the insecure tool on test data until it works right -
-there is absolutely no reason to do this anywhere other than on a personal private instance.
-
-4. Once it works right, set the 'Generate toolshed gzip' option and run it again.
-
-5. A toolshed style gzip appears ready to upload and install like any other Toolshed entry.
-
-6. Upload the new tool to the toolshed
-
-7. Ask the local admin to check the new tool to confirm it's not evil and install it in the local production galaxy
-
-**Simple examples on the tool form**
-
-A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file,
-does something (transpose in this case) and writes the results to a new tabular file::
-
- # transpose a tabular input file and write as a tabular output file
- ourargs = commandArgs(TRUE)
- inf = ourargs[1]
- outf = ourargs[2]
- inp = read.table(inf,head=F,row.names=NULL,sep='\t')
- outp = t(inp)
- write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
-
-Calculate a multiple test adjusted p value from a column of p values - for this script to be useful,
-it needs the right column for the input to be specified in the code for the
-given input file type(s) specified when the tool is generated ::
-
- # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
- column = 1 # adjust if necessary for some other kind of input
- fdrmeth = 'BH'
- ourargs = commandArgs(TRUE)
- inf = ourargs[1]
- outf = ourargs[2]
- inp = read.table(inf,head=T,row.names=NULL,sep='\t')
- p = inp[,column]
- q = p.adjust(p,method=fdrmeth)
- newval = paste(fdrmeth,'p-value',sep='_')
- q = data.frame(q)
- names(q) = newval
- outp = cbind(inp,newval=q)
- write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
-
-
-
-Another Rscript example without any input file - generates a random heatmap pdf - you must make sure the option to create an HTML output file is
-turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page::
-
- # note this script takes NO input or output because it generates random data
- foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
- bar = as.matrix(foo)
- pdf( "heattest.pdf" )
- heatmap(bar,main='Random Heatmap')
- dev.off()
-
-A Python example that reverses each row of a tabular file. You'll need to remove the leading spaces for this to work if cut
-and pasted into the script box. Note that you can already do this in Galaxy by setting up the cut columns tool with the
-correct number of columns in reverse order,but this script will work for any number of columns so is completely generic::
-
-# 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()
-
-
-**Attribution** Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
-
-All rights reserved.
-
-Licensed under the LGPL
-
-
-**Obligatory screenshot**
-
-http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
-
Binary file fubar-galaxytoolfactory-2e68c2a22b43/images/dynamicScriptTool.png has changed
--- a/fubar-galaxytoolfactory-2e68c2a22b43/rgToolFactory.py	Mon Aug 13 06:27:26 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,541 +0,0 @@
-# rgToolFactory.py
-# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
-#
-# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
-#
-# all rights reserved
-# Licensed under the LGPL
-# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
-
-# 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 binds 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.
-#
-
-#
-# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
-#
-# all rights reserved
-# Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
-
-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 = 'V000.2 June 2012'
-verbose = False
-debug = False
-toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
-
-def timenow():
-    """return current time as a string
-    """
-    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
-
-
-class ScriptRunner:
-    """class is a wrapper for an arbitrary script
-    """
-
-    def __init__(self,opts=None,treatbashSpecial=True):
-        """
-        cleanup inputs, setup some outputs
-
-        """
-        self.treatbashSpecial = treatbashSpecial
-        if opts.output_dir: # simplify for the tool tarball
-            os.chdir(opts.output_dir)
-        self.thumbformat = 'jpg'
-        self.opts = opts
-        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
-        self.toolid = self.toolname
-        self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
-        self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
-        self.xmlfile = '%s.xml' % self.toolname
-        s = open(self.opts.script_path,'r').readlines()
-        s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
-        self.script = '\n'.join(s)
-        fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=opts.interpreter)
-        tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
-        tscript.write(self.script)
-        tscript.close()
-        self.indentedScript = ''.join([' %s' % x for x in s]) # for restructured text in help
-        if opts.output_dir: # may not want these complexities
-            self.tlog = os.path.join(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 = []
-        a = self.cl.append
-        a(opts.interpreter)
-        if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
-            a(self.sfile)
-        else:
-            a('-') # stdin
-        a(opts.input_tab)
-        a(opts.output_tab)
-        self.outFormats = 'tabular' # TODO make this an option at tool generation time
-        self.inputFormats = 'tabular' # TODO make this an option at tool generation time
-        self.test1Input = '%s_test1_input.xls' % self.toolname
-        self.test1Output = '%s_test1_output.xls' % self.toolname
-        self.test1HTML = '%s_test1_output.html' % self.toolname
-
-    def makeXML(self):
-        """
-        Create a Galaxy xml tool wrapper for the new script as a string to write out
-        fixme - use templating or something less fugly than this example of what we produce
-
-        <tool id="reverse" name="reverse" version="0.01">
-            <description>a tabular file</description>
-            <command interpreter="python">
-            reverse.py --script_path "$runMe" --interpreter "python"
-            --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
-            </command>
-            <inputs>
-            <param name="input1"  type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
-
-            </inputs>
-            <outputs>
-            <data format="tabular" name="tab_file" label="${job_name}"/>
-
-            </outputs>
-            <help>
-
-**What it Does**
-
-Reverse the columns in a tabular file
-
-            </help>
-            <configfiles>
-            <configfile name="runMe">
-
-# reverse order of columns in a tabular file
-import sys
-inp = sys.argv[1]
-outp = sys.argv[2]
-i = open(inp,'r')
-o = open(outp,'w')
-for row in i:
-     rs = row.rstrip().split('\t')
-     rs.reverse()
-     o.write('\t'.join(rs))
-     o.write('\n')
-i.close()
-o.close()
-
-
-            </configfile>
-            </configfiles>
-            </tool>
-
-        """
-        newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
-            %(tooldesc)s
-            %(command)s
-            <inputs>
-            %(inputs)s
-            </inputs>
-            <outputs>
-            %(outputs)s
-            </outputs>
-            <configfiles>
-            <configfile name="runMe">
-            %(script)s
-            </configfile>
-            </configfiles>
-            %(tooltests)s
-            <help>
-            %(help)s
-            </help>
-            </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
-
-        newCommand="""<command interpreter="python">
-            %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
-            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
-            </command>""" # may NOT be an input or htmlout
-        tooltestsTabOnly = """<tests><test>
-        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
-        <param name="job_name" value="test1"/>
-        <param name="runMe" value="$runMe"/>
-        <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
-        </test></tests>"""
-        tooltestsHTMLOnly = """<tests><test>
-        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
-        <param name="job_name" value="test1"/>
-        <param name="runMe" value="$runMe"/>
-        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
-        </test></tests>"""
-        tooltestsBoth = """<tests><test>
-        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
-        <param name="job_name" value="test1"/>
-        <param name="runMe" value="$runMe"/>
-        <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
-        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
-        </test></tests>"""
-        xdict = {}
-        xdict['tool_version'] = self.opts.tool_version
-        xdict['test1Input'] = self.test1Input
-        xdict['test1HTML'] = self.test1HTML
-        xdict['test1Output'] = self.test1Output
-        if self.opts.make_HTML and self.opts.output_tab <> 'None':
-            xdict['tooltests'] = tooltestsBoth % xdict
-        elif self.opts.make_HTML:
-            xdict['tooltests'] = tooltestsHTMLOnly % xdict
-        else:
-            xdict['tooltests'] = tooltestsTabOnly % xdict
-        xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
-        if self.opts.help_text:
-            xdict['help'] = open(self.opts.help_text,'r').read()
-        else:
-            xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
-        coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
-        coda.append(self.indentedScript)
-        coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
-        coda.append('See %s for details of that project' % (toolFactoryURL))
-        xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
-        if self.opts.tool_desc:
-            xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
-        else:
-            xdict['tooldesc'] = ''
-        xdict['command_outputs'] = ''
-        xdict['outputs'] = ''
-        if self.opts.input_tab <> 'None':
-            xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
-            xdict['inputs'] = '<param name="input1"  type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
-        else:
-            xdict['command_inputs'] = '' # assume no input - eg a random data generator
-            xdict['inputs'] = ''
-        xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
-        xdict['toolname'] = self.toolname
-        xdict['toolid'] = self.toolid
-        xdict['interpreter'] = self.opts.interpreter
-        xdict['scriptname'] = self.sfile
-        if self.opts.make_HTML:
-            xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
-            xdict['outputs'] +=  ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
-        if self.opts.output_tab <> 'None':
-            xdict['command_outputs'] += ' --output_tab "$tab_file"'
-            xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
-        xdict['command'] = newCommand % xdict
-        xmls = newXML % xdict
-        xf = open(self.xmlfile,'w')
-        xf.write(xmls)
-        xf.write('\n')
-        xf.close()
-        # ready for the tarball
-
-
-    def makeTooltar(self):
-        """
-        a tool is a gz tarball with eg
-        /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
-        """
-        retval = self.run()
-        if retval:
-            print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
-            sys.exit(1)
-        self.makeXML()
-        tdir = self.toolname
-        os.mkdir(tdir)
-        if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
-            testdir = os.path.join(tdir,'test-data')
-            os.mkdir(testdir) # make tests directory
-            shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
-            if self.opts.output_tab <> 'None':
-                shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
-            if self.opts.make_HTML:
-                shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
-            if self.opts.output_dir:
-                shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
-        op = '%s.py' % self.toolname # new name
-        outpiname = os.path.join(tdir,op) # path for the tool tarball
-        pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
-        notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
-        notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
-        notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
-        pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
-        notes += pi
-        outpi = open(outpiname,'w')
-        outpi.write(''.join(notes))
-        outpi.write('\n')
-        outpi.close()
-        shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
-        shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
-        tarpath = "%s.gz" % self.toolname
-        tar = tarfile.open(tarpath, "w:gz")
-        tar.add(tdir,arcname=self.toolname)
-        tar.close()
-        shutil.copyfile(tarpath,self.opts.new_tool)
-        shutil.rmtree(tdir)
-        ## TODO: replace with optional direct upload to local toolshed?
-        return retval
-
-    def compressPDF(self,inpdf=None,thumbformat='png'):
-        """need absolute path to pdf
-        """
-        assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
-        hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
-        sto = open(hlog,'w')
-        outpdf = '%s_compressed' % inpdf
-        cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
-        x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
-        retval1 = x.wait()
-        if retval1 == 0:
-            os.unlink(inpdf)
-            shutil.move(outpdf,inpdf)
-        outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
-        cl2 = ['convert', inpdf, outpng]
-        x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
-        retval2 = x.wait()
-        sto.close()
-        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:
-            pdflist = []
-            npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
-            nacross = 1
-            if npdf > 0:
-               nacross = int(round(math.log(npdf,2)))
-            nacross = max(1,nacross)
-            width = min(400,int(1200/nacross))
-            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))
-                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))
-            ntogo = nacross # counter for table row padding with empty cells
-            if len(pdflist) > 0:
-                html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
-                for i,paths in enumerate(pdflist):
-                    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')
-        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 += 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)
-        rlog = open(self.tlog,'r').readlines()
-        rlog = [x for x in rlog if x.strip() > '']
-        if len(rlog) > 1:
-            html.append('<div class="toolFormTitle">%s log</div><pre>\n' % self.opts.interpreter)
-            html += rlog
-            html.append('</pre>\n')
-        html.append(galhtmlattr % (self.toolname))
-        html.append(galhtmlpostfix)
-        htmlf = file(self.opts.output_html,'w')
-        htmlf.write('\n'.join(html))
-        htmlf.write('\n')
-        htmlf.close()
-        self.html = html
-
-
-    def run(self):
-        """
-        scripts must be small enough not to fill the pipe!
-        """
-        if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
-          retval = self.runBash()
-        else:
-            if self.opts.output_dir:
-                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=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
-            else:
-                p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
-            p.stdin.write(self.script)
-            p.stdin.close()
-            retval = p.wait()
-            if self.opts.output_dir:
-                sto.close()
-            if self.opts.make_HTML:
-                self.makeHtml()
-        os.unlink(self.sfile)
-        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=None)
-    a('--output_html',default=None)
-    a('--input_tab',default="None")
-    a('--output_tab',default="None")
-    a('--user_email',default='Unknown')
-    a('--bad_user',default=None)
-    a('--make_Tool',default=None)
-    a('--make_HTML',default=None)
-    a('--help_text',default=None)
-    a('--tool_desc',default=None)
-    a('--new_tool',default=None)
-    a('--tool_version',default=None)
-    opts, args = op.parse_args()
-    assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
-    assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
-    assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
-    assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
-    if opts.output_dir:
-        try:
-            os.makedirs(opts.output_dir)
-        except:
-            pass
-    r = ScriptRunner(opts)
-    if opts.make_Tool:
-        retcode = r.makeTooltar()
-    else:
-        retcode = r.run()
-    if retcode:
-        sys.exit(retcode) # indicate failure to job runner
-
-
-if __name__ == "__main__":
-    main()
-
-
--- a/fubar-galaxytoolfactory-2e68c2a22b43/rgToolFactory.xml	Mon Aug 13 06:27:26 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,233 +0,0 @@
-<tool id="rgTF" name="Tool Factory" version="0.09">
-  <description>Makes scripts into tools</description>
-  <command interpreter="python">
-#if ( $__user_email__ not in $__admin_users__ ):
-     rgToolFactory.py --bad_user $__user_email__
-  #else:
-    rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
-     --tool_name "$tool_name"  --user_email "$__user_email__"
-    #if $make_TAB.value=="yes":
-       --output_tab "$tab_file"
-    #end if
-    #if $makeMode.make_Tool=="yes":
-      --make_Tool "$makeMode.make_Tool"
-      --tool_desc "$makeMode.tool_desc"
-      --tool_version "$makeMode.tool_version"
-      --new_tool "$new_tool"
-      --help_text "$helpme"
-    #end if
-    #if $make_HTML.value=="yes":
-      --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
-    #end if
-    #if $input1 != 'None':
-       --input_tab "$input1"
-    #end if
-#end if
-  </command>
-  <inputs>
-    <param name="input1"  type="data"  label="Select an input file from your history" optional="true" size="120"
-       help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
-    <param name="tool_name" type="text" value="My dynamic script"   label="New tool ID and title for outputs" size="60"
-         help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
-        <sanitizer invalid_char="">
-            <valid initial="string.letters,string.digits"/>
-        </sanitizer>
-    </param>
-    <conditional name="makeMode">
-        <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!" size="60">
-        <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
-        <option value="" selected="true">No. Just run the script please</option>
-        </param>
-        <when value = "yes">
-            <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
-            help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
-            <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
-             help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
-            <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
-             size="8x120" value="**What it Does**"
-             help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
-                <sanitizer>
-                    <valid initial="string.printable">
-                    </valid>
-                    <mapping initial="none"/>
-                </sanitizer>
-            </param>
-        </when>
-        <when value = "">
-        </when>
-    </conditional>
-    <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
-         help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
-        <option value="yes">Yes, arrange all outputs in an HTML output</option>
-        <option value="" selected="true">No, no HTML output file thanks</option>
-    </param>
-
-
-    <param name="make_TAB" type="select" label="Create a new (default tabular) history output"
-         help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
-        <option value="yes" selected="true">My script writes to a new history output</option>
-        <option value="">I only want an HTML output file</option>
-    </param>
-    <param name="out_format" type="select" label="Galaxy datatype for your tool's output file" help="You may need to edit the xml to extend this list">
-    <option value="tabular" selected="true">Tabular</option>
-    <option value="interval">Interval</option>
-    <option value="gz">gz</option>
-    <option value="text">text</option>
-    </param>
-    <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
-        <option value="Rscript" selected="true">Rscript</option>
-        <option value="python">python</option>
-        <option value="perl">perl</option>
-        <option value="sh">sh</option>
-    </param>
-    <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120"
-      help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None').">
-      <sanitizer>
-         <valid initial="string.printable">
-         </valid>
-         <mapping initial="none"/>
-      </sanitizer>
-     </param>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="tab_file" label="${tool_name}.${out_format}">
-        <filter>make_TAB=="yes"</filter>
-        <change_format>
-            <when input="out_format" value="interval"  format="interval" />
-            <when input="out_format" value="gz" format="gz" />
-            <when input="out_format" value="text"  format="text"  />
-         </change_format>
-    </data>
-    <data format="html" name="html_file" label="${tool_name}.html">
-        <filter>make_HTML == "yes"</filter>
-    </data>
-    <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
-        <filter>makeMode['make_Tool'] == "yes"</filter>
-    </data>
-  </outputs>
-<configfiles>
-<configfile name="runme">$dynScript</configfile>
-<configfile name="helpme">
-#if $makeMode.make_Tool == "yes":
-${makeMode.help_text}
-#end if
-</configfile>
-</configfiles>
-<help>
-
-.. class:: warningmark
-
-**Local Admins ONLY** Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
-
-**What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
-
-**Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history.
-
-**Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
-a new HTML report linking all the files and images created by the script can be automatically generated.
-
-**Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file
-ready to upload to your local toolshed for sharing and installation. Provide a small sample input when you run generate the tool because
-it will become the input for the generated functional test.
-
-.. class:: warningmark
-
-**Note to system administrators** This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
-Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
-
-.. class:: warningmark
-
-**Use on public servers**  is STRONGLY discouraged for obvious reasons
-
-The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation.
-We recommend that you follow the good code hygiene practices associated with safe toolshed.
-
-**Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not select one, and the path to the optional
-output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below.
-Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output.
-This can be handy for complex scripts creating lots of output.
-
-**Simple examples**
-
-A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and writes the results to a new tabular file::
-
- # transpose a tabular input file and write as a tabular output file
- ourargs = commandArgs(TRUE)
- inf = ourargs[1]
- outf = ourargs[2]
- inp = read.table(inf,head=F,row.names=NULL,sep='\t')
- outp = t(inp)
- write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
-
-Calculate a multiple test adjusted p value from a column of p values - for this script to be useful, it needs the right column for the input to be specified in the code for the
-given input file type(s) specified when the tool is generated ::
-
- # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
- column = 1 # adjust if necessary for some other kind of input
- ourargs = commandArgs(TRUE)
- inf = ourargs[1]
- outf = ourargs[2]
- inp = read.table(inf,head=T,row.names=NULL,sep='\t')
- p = inp[,column]
- q = p.adjust(p,method='BH')
- outp = cbind(inp,'BH Adjusted p-value'=q)
- write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
-
-
-A demonstration Rscript example takes no input file but generates some random data based pdf images
-You must make sure the option to create an HTML output file is
-turned on for this to work. Images (pdf) are linked via thumbnails and
-all files have a link on the resulting HTML page::
-
- # note this script takes NO input or output because it generates random data
- foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
- bar = as.matrix(foo)
- pdf( "heattest.pdf" )
- heatmap(bar,main='Random Heatmap')
- dev.off()
- for (i in 1:49) {
-     foo = runif(100)
-     bar = rnorm(100)
-     pdf(paste('yet',i,"anotherplot.pdf",sep='_'))
-     plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)
-     dev.off()
- }
-
-A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces
-for this to work if cut and pasted into the script box)::
-
- # 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()
-
-A trivial shell script example to show that it works::
-
- #!/bin/bash
- INF=$1
- OUTF=$2
- cut -c2,4,6,8,10,12 $INF >$OUTF
-
-
-**Attribution** Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
-
-All rights reserved.
-
-Licensed under the LGPL_
-
-.. _LGPL: http://www.gnu.org/copyleft/lesser.html
-
-</help>
-
-</tool>
-
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fubar-galaxytoolfactory-ca7db160878a/README.txt	Fri Aug 31 23:04:13 2012 -0400
@@ -0,0 +1,233 @@
+# WARNING before you start
+# Install this tool on a private Galaxy ONLY
+# Please NEVER on a public or production instance
+
+*Short Story*
+This is an unusual Galaxy tool that generates very simple new Galaxy tools that run the user
+a supplied script (R, python, perl, bash...) over a single input file.
+Whenever you run this tool, the ToolFactory, you should have prepared a script to paste into a text box,
+and a small test input example ready to select from your history to test your new script
+
+If the script runs sucessfully, a new Galaxy tool that runs your script can be generated.
+The new tool is in the form of a special new Galaxy datatype - toolshed.gz - as the name suggests,
+it's an archive ready to upload to a Galaxy ToolShed as a new tool repository.
+
+Once it's in a ToolShed, it can be installed into any local Galaxy server from
+the server administrative interface.
+
+Once your new tool is installed, local users can run it - each time, the script that was supplied
+when it was built will be executed with the input chosen from the user's history. In other words,
+the tools you generate with the ToolFactory run just like any other Galaxy tool,
+but run your script every time.
+
+*Reasons to read further*
+
+If you use Galaxy to support your research;
+
+You and fellow users are sometimes forced to take data out of Galaxy, process it with ugly
+little perl/awk/sed/R... scripts and put it back;
+
+You do this when you can't do some transformation in Galaxy (the 90/10 rule);
+
+You don't have enough developer resources for wrapping dozens of even relatively simple tools;
+
+Your research and your institution would be far better off if those feral scripts were all tucked safely in
+your local toolshed and Galaxy histories.
+
+*The good news* If it can be trivially scripted, it can be running safely in your
+local Galaxy via your own local toolshed in a few minutes - with functional tests.
+
+
+*Value proposition* The ToolFactory allows Galaxy to efficiently take over most of your lab's dark script matter,
+making it reproducible in Galaxy and shareable through the ToolShed.
+
+That's what this tool does. You paste a simple script and the tool returns
+a new, real Galaxy tool, ready to be installed from the local toolshed to local servers.
+Scripts can be wrapped and online literally within minutes.
+
+*To fully and safely exploit the awesome power* of this tool, Galaxy and the ToolShed,
+you should be a developer installing this tool on a private/personal/scratch local instance where you are an admin_user.
+Then, if you break it, you get to keep all the pieces
+see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+** Installation **
+This is a Galaxy tool. You can install it most conveniently using the administrative "Search and browse tool sheds" link.
+Find the Galaxy Test toolshed (not main) and search for the toolfactory repository.
+Open it and review the code and select the option to install it.
+
+If you can't get the tool that way, the xml and py files here need to be copied into a new tools subdirectory such as tools/toolfactory
+Your tool_conf.xml needs a new entry pointing to the xml file - something like::
+
+  <section name="Tool building tools" id="toolbuilders">
+    <tool file="toolfactory/rgToolFactory.xml"/>
+  </section>
+
+If not already there (I just added it to datatypes_conf.xml.sample), please add:
+<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
+to your local data_types_conf.xml.
+
+Ensure that html sanitization is set to False and uncommented in universe_wsgi.ini
+
+You'll have to restart the server for the new tool to be available.
+
+Of course, R, python, perl etc are needed on your path if you want to test scripts using those interpreters.
+Adding new ones to this tool code should be easy enough. Please make suggestions as bitbucket issues and code.
+The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick .
+
+* Restricted execution *
+The new tool factory tool will then be usable ONLY by admin users - people with IDs in admin_users in universe_wsgi.ini
+**Yes, that's right. ONLY admin_users can run this tool** Think about it for a moment. If allowed to run any
+arbitrary script on your Galaxy server, the only thing that would impede a miscreant bent on destroying all your
+Galaxy data would probably be lack of appropriate technical skills.
+
+*What it does* This is a tool factory for simple scripts in python, R and perl currently.
+Functional tests are automatically generated. How cool is that.
+
+LIMITED to 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
+index page for the user to navigate - useful if the script writes images and output files - pdf outputs
+are shown as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and imagemagik need to
+be avaailable.
+
+Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up since
+a generated script gets you a serious leg up to a more complex one.
+
+*What you do* You paste and run your script
+you fix the syntax errors and eventually it runs
+You can use the redo button and edit the script before
+trying to rerun it as you debug - it works pretty well.
+
+Once the script works on some test data, you can
+generate a toolshed compatible gzip file
+containing your script ready to run as an ordinary Galaxy tool in a
+repository on your local toolshed. That means safe and largely automated installation in any
+production Galaxy configured to use your toolshed.
+
+*Generated tool Security* Once you install a generated tool, it's just
+another tool - assuming 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 - it is really scary.
+
+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 and suggestions welcome as bitbucket issues please?
+
+long route to June 2012 product
+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
+
+
+
+
+copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
+
+all rights reserved
+Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+Material for our more enthusiastic and voracious readers continues below - we salute you.
+
+**Motivation** Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs
+- even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible.
+
+**Benefits** For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics
+tasks. Once a user has a working R (or python or perl) script that does something Galaxy cannot currently do (eg transpose a
+tabular file) and takes parameters the way Galaxy supplies them (see example below), they:
+
+1. Install the tool factory on a personal private instance
+
+2. Upload a small test data set
+
+3. Paste the script into the 'script' text box and iteratively run the insecure tool on test data until it works right -
+there is absolutely no reason to do this anywhere other than on a personal private instance.
+
+4. Once it works right, set the 'Generate toolshed gzip' option and run it again.
+
+5. A toolshed style gzip appears ready to upload and install like any other Toolshed entry.
+
+6. Upload the new tool to the toolshed
+
+7. Ask the local admin to check the new tool to confirm it's not evil and install it in the local production galaxy
+
+**Simple examples on the tool form**
+
+A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file,
+does something (transpose in this case) and writes the results to a new tabular file::
+
+ # transpose a tabular input file and write as a tabular output file
+ ourargs = commandArgs(TRUE)
+ inf = ourargs[1]
+ outf = ourargs[2]
+ inp = read.table(inf,head=F,row.names=NULL,sep='\t')
+ outp = t(inp)
+ write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
+
+Calculate a multiple test adjusted p value from a column of p values - for this script to be useful,
+it needs the right column for the input to be specified in the code for the
+given input file type(s) specified when the tool is generated ::
+
+ # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
+ column = 1 # adjust if necessary for some other kind of input
+ fdrmeth = 'BH'
+ ourargs = commandArgs(TRUE)
+ inf = ourargs[1]
+ outf = ourargs[2]
+ inp = read.table(inf,head=T,row.names=NULL,sep='\t')
+ p = inp[,column]
+ q = p.adjust(p,method=fdrmeth)
+ newval = paste(fdrmeth,'p-value',sep='_')
+ q = data.frame(q)
+ names(q) = newval
+ outp = cbind(inp,newval=q)
+ write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
+
+
+
+Another Rscript example without any input file - generates a random heatmap pdf - you must make sure the option to create an HTML output file is
+turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page::
+
+ # note this script takes NO input or output because it generates random data
+ foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
+ bar = as.matrix(foo)
+ pdf( "heattest.pdf" )
+ heatmap(bar,main='Random Heatmap')
+ dev.off()
+
+A Python example that reverses each row of a tabular file. You'll need to remove the leading spaces for this to work if cut
+and pasted into the script box. Note that you can already do this in Galaxy by setting up the cut columns tool with the
+correct number of columns in reverse order,but this script will work for any number of columns so is completely generic::
+
+# 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()
+
+
+**Attribution** Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
+
+All rights reserved.
+
+Licensed under the LGPL
+
+
+**Obligatory screenshot**
+
+http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
+
Binary file fubar-galaxytoolfactory-ca7db160878a/images/dynamicScriptTool.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fubar-galaxytoolfactory-ca7db160878a/rgToolFactory.py	Fri Aug 31 23:04:13 2012 -0400
@@ -0,0 +1,539 @@
+# rgToolFactory.py
+# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+#
+# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
+#
+# all rights reserved
+# Licensed under the LGPL
+# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+# 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 binds 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 = 'V000.2 June 2012'
+verbose = False
+debug = False
+toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
+
+def timenow():
+    """return current time as a string
+    """
+    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+
+class ScriptRunner:
+    """class is a wrapper for an arbitrary script
+    """
+
+    def __init__(self,opts=None,treatbashSpecial=True):
+        """
+        cleanup inputs, setup some outputs
+
+        """
+        self.treatbashSpecial = treatbashSpecial
+        if opts.output_dir: # simplify for the tool tarball
+            os.chdir(opts.output_dir)
+        self.thumbformat = 'jpg'
+        self.opts = opts
+        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
+        self.toolid = self.toolname
+        self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
+        self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
+        self.xmlfile = '%s.xml' % self.toolname
+        s = open(self.opts.script_path,'r').readlines()
+        s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
+        self.script = '\n'.join(s)
+        fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
+        tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
+        tscript.write(self.script)
+        tscript.close()
+        self.indentedScript = ''.join([' %s' % x for x in s]) # for restructured text in help
+        if opts.output_dir: # may not want these complexities
+            self.tlog = os.path.join(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 = []
+        a = self.cl.append
+        a(opts.interpreter)
+        if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
+            a(self.sfile)
+        else:
+            a('-') # stdin
+        a(opts.input_tab)
+        a(opts.output_tab)
+        self.outFormats = 'tabular' # TODO make this an option at tool generation time
+        self.inputFormats = 'tabular' # TODO make this an option at tool generation time
+        self.test1Input = '%s_test1_input.xls' % self.toolname
+        self.test1Output = '%s_test1_output.xls' % self.toolname
+        self.test1HTML = '%s_test1_output.html' % self.toolname
+
+    def makeXML(self):
+        """
+        Create a Galaxy xml tool wrapper for the new script as a string to write out
+        fixme - use templating or something less fugly than this example of what we produce
+
+        <tool id="reverse" name="reverse" version="0.01">
+            <description>a tabular file</description>
+            <command interpreter="python">
+            reverse.py --script_path "$runMe" --interpreter "python"
+            --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
+            </command>
+            <inputs>
+            <param name="input1"  type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
+
+            </inputs>
+            <outputs>
+            <data format="tabular" name="tab_file" label="${job_name}"/>
+
+            </outputs>
+            <help>
+
+**What it Does**
+
+Reverse the columns in a tabular file
+
+            </help>
+            <configfiles>
+            <configfile name="runMe">
+
+# reverse order of columns in a tabular file
+import sys
+inp = sys.argv[1]
+outp = sys.argv[2]
+i = open(inp,'r')
+o = open(outp,'w')
+for row in i:
+     rs = row.rstrip().split('\t')
+     rs.reverse()
+     o.write('\t'.join(rs))
+     o.write('\n')
+i.close()
+o.close()
+
+
+            </configfile>
+            </configfiles>
+            </tool>
+
+        """
+        newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
+            %(tooldesc)s
+            %(command)s
+            <inputs>
+            %(inputs)s
+            </inputs>
+            <outputs>
+            %(outputs)s
+            </outputs>
+            <configfiles>
+            <configfile name="runMe">
+            %(script)s
+            </configfile>
+            </configfiles>
+            %(tooltests)s
+            <help>
+            %(help)s
+            </help>
+            </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
+
+        newCommand="""<command interpreter="python">
+            %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
+            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
+            </command>""" # may NOT be an input or htmlout
+        tooltestsTabOnly = """<tests><test>
+        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
+        <param name="job_name" value="test1"/>
+        <param name="runMe" value="$runMe"/>
+        <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
+        </test></tests>"""
+        tooltestsHTMLOnly = """<tests><test>
+        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
+        <param name="job_name" value="test1"/>
+        <param name="runMe" value="$runMe"/>
+        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
+        </test></tests>"""
+        tooltestsBoth = """<tests><test>
+        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
+        <param name="job_name" value="test1"/>
+        <param name="runMe" value="$runMe"/>
+        <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
+        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
+        </test></tests>"""
+        xdict = {}
+        xdict['tool_version'] = self.opts.tool_version
+        xdict['test1Input'] = self.test1Input
+        xdict['test1HTML'] = self.test1HTML
+        xdict['test1Output'] = self.test1Output
+        if self.opts.make_HTML and self.opts.output_tab <> 'None':
+            xdict['tooltests'] = tooltestsBoth % xdict
+        elif self.opts.make_HTML:
+            xdict['tooltests'] = tooltestsHTMLOnly % xdict
+        else:
+            xdict['tooltests'] = tooltestsTabOnly % xdict
+        xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
+        if self.opts.help_text:
+            xdict['help'] = open(self.opts.help_text,'r').read()
+        else:
+            xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
+        coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
+        coda.append(self.indentedScript)
+        coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
+        coda.append('See %s for details of that project' % (toolFactoryURL))
+        xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
+        if self.opts.tool_desc:
+            xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
+        else:
+            xdict['tooldesc'] = ''
+        xdict['command_outputs'] = ''
+        xdict['outputs'] = ''
+        if self.opts.input_tab <> 'None':
+            xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
+            xdict['inputs'] = '<param name="input1"  type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
+        else:
+            xdict['command_inputs'] = '' # assume no input - eg a random data generator
+            xdict['inputs'] = ''
+        xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
+        xdict['toolname'] = self.toolname
+        xdict['toolid'] = self.toolid
+        xdict['interpreter'] = self.opts.interpreter
+        xdict['scriptname'] = self.sfile
+        if self.opts.make_HTML:
+            xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
+            xdict['outputs'] +=  ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
+        if self.opts.output_tab <> 'None':
+            xdict['command_outputs'] += ' --output_tab "$tab_file"'
+            xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
+        xdict['command'] = newCommand % xdict
+        xmls = newXML % xdict
+        xf = open(self.xmlfile,'w')
+        xf.write(xmls)
+        xf.write('\n')
+        xf.close()
+        # ready for the tarball
+
+
+    def makeTooltar(self):
+        """
+        a tool is a gz tarball with eg
+        /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
+        """
+        retval = self.run()
+        if retval:
+            print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
+            sys.exit(1)
+        self.makeXML()
+        tdir = self.toolname
+        os.mkdir(tdir)
+        if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
+            testdir = os.path.join(tdir,'test-data')
+            os.mkdir(testdir) # make tests directory
+            shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
+            if self.opts.output_tab <> 'None':
+                shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
+            if self.opts.make_HTML:
+                shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
+            if self.opts.output_dir:
+                shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
+        op = '%s.py' % self.toolname # new name
+        outpiname = os.path.join(tdir,op) # path for the tool tarball
+        pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
+        notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
+        notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
+        notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
+        pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
+        notes += pi
+        outpi = open(outpiname,'w')
+        outpi.write(''.join(notes))
+        outpi.write('\n')
+        outpi.close()
+        stname = os.path.join(tdir,self.sfile)
+        if not os.path.exists(stname):
+            shutil.copyfile(self.sfile, stname)
+        xtname = os.path.join(tdir,self.xmlfile)
+        if not os.path.exists(xtname):
+            shutil.copyfile(self.xmlfile,xtname)
+        tarpath = "%s.gz" % self.toolname
+        tar = tarfile.open(tarpath, "w:gz")
+        tar.add(tdir,arcname=self.toolname)
+        tar.close()
+        shutil.copyfile(tarpath,self.opts.new_tool)
+        shutil.rmtree(tdir)
+        ## TODO: replace with optional direct upload to local toolshed?
+        return retval
+
+    def compressPDF(self,inpdf=None,thumbformat='png'):
+        """need absolute path to pdf
+        """
+        assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
+        hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
+        sto = open(hlog,'w')
+        outpdf = '%s_compressed' % inpdf
+        cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
+        x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
+        retval1 = x.wait()
+        if retval1 == 0:
+            os.unlink(inpdf)
+            shutil.move(outpdf,inpdf)
+        outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
+        cl2 = ['convert', inpdf, outpng]
+        x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
+        retval2 = x.wait()
+        sto.close()
+        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:
+            pdflist = []
+            npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
+            nacross = 1
+            if npdf > 0:
+               nacross = int(round(math.log(npdf,2)))
+            nacross = max(1,nacross)
+            width = min(400,int(1200/nacross))
+            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))
+                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))
+            ntogo = nacross # counter for table row padding with empty cells
+            if len(pdflist) > 0:
+                html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
+                for i,paths in enumerate(pdflist):
+                    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')
+        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 += 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)
+        rlog = open(self.tlog,'r').readlines()
+        rlog = [x for x in rlog if x.strip() > '']
+        if len(rlog) > 1:
+            html.append('<div class="toolFormTitle">%s log</div><pre>\n' % self.opts.interpreter)
+            html += rlog
+            html.append('</pre>\n')
+        html.append(galhtmlattr % (self.toolname))
+        html.append(galhtmlpostfix)
+        htmlf = file(self.opts.output_html,'w')
+        htmlf.write('\n'.join(html))
+        htmlf.write('\n')
+        htmlf.close()
+        self.html = html
+
+
+    def run(self):
+        """
+        scripts must be small enough not to fill the pipe!
+        """
+        if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
+          retval = self.runBash()
+        else:
+            if self.opts.output_dir:
+                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=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
+            else:
+                p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
+            p.stdin.write(self.script)
+            p.stdin.close()
+            retval = p.wait()
+            if self.opts.output_dir:
+                sto.close()
+            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=None)
+    a('--output_html',default=None)
+    a('--input_tab',default="None")
+    a('--output_tab',default="None")
+    a('--user_email',default='Unknown')
+    a('--bad_user',default=None)
+    a('--make_Tool',default=None)
+    a('--make_HTML',default=None)
+    a('--help_text',default=None)
+    a('--tool_desc',default=None)
+    a('--new_tool',default=None)
+    a('--tool_version',default=None)
+    opts, args = op.parse_args()
+    assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
+    assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
+    assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
+    assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
+    if opts.output_dir:
+        try:
+            os.makedirs(opts.output_dir)
+        except:
+            pass
+    r = ScriptRunner(opts)
+    if opts.make_Tool:
+        retcode = r.makeTooltar()
+    else:
+        retcode = r.run()
+    os.unlink(r.sfile)
+    if retcode:
+        sys.exit(retcode) # indicate failure to job runner
+
+
+if __name__ == "__main__":
+    main()
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fubar-galaxytoolfactory-ca7db160878a/rgToolFactory.xml	Fri Aug 31 23:04:13 2012 -0400
@@ -0,0 +1,263 @@
+<tool id="rgTF" name="Tool Factory" version="0.10">
+  <description>Makes scripts into tools</description>
+  <command interpreter="python">
+#if ( $__user_email__ not in $__admin_users__ ):
+     rgToolFactory.py --bad_user $__user_email__
+  #else:
+    rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
+     --tool_name "$tool_name"  --user_email "$__user_email__"
+    #if $make_TAB.value=="yes":
+       --output_tab "$tab_file"
+    #end if
+    #if $makeMode.make_Tool=="yes":
+      --make_Tool "$makeMode.make_Tool"
+      --tool_desc "$makeMode.tool_desc"
+      --tool_version "$makeMode.tool_version"
+      --new_tool "$new_tool"
+      --help_text "$helpme"
+    #end if
+    #if $make_HTML.value=="yes":
+      --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
+    #end if
+    #if $input1 != 'None':
+       --input_tab "$input1"
+    #end if
+#end if
+  </command>
+  <inputs>
+    <param name="input1"  type="data"  label="Select an input file from your history" optional="true" size="120"
+       help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
+    <param name="tool_name" type="text" value="My dynamic script"   label="New tool ID and title for outputs" size="60"
+         help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
+        <sanitizer invalid_char="">
+            <valid initial="string.letters,string.digits"/>
+        </sanitizer>
+    </param>
+    <conditional name="makeMode">
+        <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!" size="60">
+        <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
+        <option value="" selected="true">No. Just run the script please</option>
+        </param>
+        <when value = "yes">
+            <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
+            help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
+            <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
+             help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
+            <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
+             size="8x120" value="**What it Does**"
+             help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
+                <sanitizer>
+                    <valid initial="string.printable">
+                    </valid>
+                    <mapping initial="none"/>
+                </sanitizer>
+            </param>
+        </when>
+        <when value = "">
+        </when>
+    </conditional>
+    <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
+         help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
+        <option value="yes">Yes, arrange all outputs in an HTML output</option>
+        <option value="" selected="true">No, no HTML output file thanks</option>
+    </param>
+
+
+    <param name="make_TAB" type="select" label="Create a new (default tabular) history output"
+         help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
+        <option value="yes" selected="true">My script writes to a new history output</option>
+        <option value="">I only want an HTML output file</option>
+    </param>
+    <param name="out_format" type="select" label="Galaxy datatype for your tool's output file" help="You may need to edit the xml to extend this list">
+    <option value="tabular" selected="true">Tabular</option>
+    <option value="interval">Interval</option>
+    <option value="gz">gz</option>
+    <option value="text">text</option>
+    </param>
+    <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
+        <option value="Rscript" selected="true">Rscript</option>
+        <option value="python">python</option>
+        <option value="perl">perl</option>
+        <option value="sh">sh</option>
+    </param>
+    <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120"
+      help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None').">
+      <sanitizer>
+         <valid initial="string.printable">
+         </valid>
+         <mapping initial="none"/>
+      </sanitizer>
+     </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="tab_file" label="${tool_name}.${out_format}">
+        <filter>make_TAB=="yes"</filter>
+        <change_format>
+            <when input="out_format" value="interval"  format="interval" />
+            <when input="out_format" value="gz" format="gz" />
+            <when input="out_format" value="text"  format="text"  />
+         </change_format>
+    </data>
+    <data format="html" name="html_file" label="${tool_name}.html">
+        <filter>make_HTML == "yes"</filter>
+    </data>
+    <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
+        <filter>makeMode['make_Tool'] == "yes"</filter>
+    </data>
+  </outputs>
+<configfiles>
+<configfile name="runme">$dynScript</configfile>
+<configfile name="helpme">
+#if $makeMode.make_Tool == "yes":
+${makeMode.help_text}
+#end if
+</configfile>
+</configfiles>
+<help>
+
+.. class:: warningmark
+
+**Details and attribution** GTF_
+
+**Local Admins ONLY** Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
+
+**If you find a bug** please raise an issue at the bitbucket repository GTFI_
+
+**What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
+
+**Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history.
+
+**Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
+a new HTML report linking all the files and images created by the script can be automatically generated.
+
+**Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file
+ready to upload to your local toolshed for sharing and installation. Provide a small sample input when you run generate the tool because
+it will become the input for the generated functional test.
+
+.. class:: warningmark
+
+**Note to system administrators** This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
+Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
+
+.. class:: warningmark
+
+**Use on public servers**  is STRONGLY discouraged for obvious reasons
+
+The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation.
+We recommend that you follow the good code hygiene practices associated with safe toolshed.
+
+**Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not select one, and the path to the optional
+output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below.
+Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output.
+This can be handy for complex scripts creating lots of output.
+
+**Examples**
+
+Each of these following trivial examples can be cut and pasted into the script box for testing.
+Please make sure you choose the appropriate interpreter and upload and select a suitable small matching test data input
+
+A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and writes the results to a new tabular file::
+
+ # transpose a tabular input file and write as a tabular output file
+ ourargs = commandArgs(TRUE)
+ inf = ourargs[1]
+ outf = ourargs[2]
+ inp = read.table(inf,head=F,row.names=NULL,sep='\t')
+ outp = t(inp)
+ write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
+
+Calculate a multiple test adjusted p value from a column of p values - for this script to be useful, it needs the right column for the input to be specified in the code for the
+given input file type(s) specified when the tool is generated ::
+
+ # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
+ column = 1 # adjust if necessary for some other kind of input
+ ourargs = commandArgs(TRUE)
+ inf = ourargs[1]
+ outf = ourargs[2]
+ inp = read.table(inf,head=T,row.names=NULL,sep='\t')
+ p = inp[,column]
+ q = p.adjust(p,method='BH')
+ outp = cbind(inp,'BH Adjusted p-value'=q)
+ write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
+
+
+A demonstration Rscript example takes no input file but generates some random data based pdf images
+You must make sure the option to create an HTML output file is
+turned on for this to work. Images (pdf) are linked via thumbnails and
+all files have a link on the resulting HTML page::
+
+ # note this script takes NO input or output because it generates random data
+ foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
+ bar = as.matrix(foo)
+ pdf( "heattest.pdf" )
+ heatmap(bar,main='Random Heatmap')
+ dev.off()
+ for (i in 1:49) {
+     foo = runif(100)
+     bar = rnorm(100)
+     pdf(paste('yet',i,"anotherplot.pdf",sep='_'))
+     plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)
+     dev.off()
+ }
+
+A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces
+for this to work if cut and pasted into the script box)::
+
+ # 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()
+
+A trivial shell script example to show that it works::
+
+ #!/bin/bash
+ INF=$1
+ OUTF=$2
+ cut -c2,4,6,8,10,12 $INF >$OUTF
+
+A trivial perl script example to show that even perl works::
+
+ #
+ # change all occurances of a string in a file to another string
+ #
+ $oldfile = $ARGV[0];
+ $newfile = $ARGV[1];
+ $old = "gene";
+ $new = "foo";
+ open(OF, $oldfile);
+ open(NF, "&gt;$newfile");
+ # read in each line of the file
+ while ($line = &lt;OF&gt;) {
+    $line =~ s/$old/$new/;
+    print NF $line;
+ }
+ close(OF);
+ close(NF);
+
+
+**Attribution** Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
+
+All rights reserved.
+
+Licensed under the LGPL_
+
+--
+
+.. _LGPL: http://www.gnu.org/copyleft/lesser.html
+.. _GTF:  https://bitbucket.org/fubar/galaxytoolfactory
+.. _GTFI:  https://bitbucket.org/fubar/galaxytoolfactory/issues
+
+</help>
+
+</tool>
+
+