view @ 0:c34063ab3735 draft

Initial commit of code in iuc github repository
author fubar
date Thu, 01 Jan 2015 21:58:00 -0500
children 6a3c292412fa
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# see
# 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
# sept 2014 added additional params from
# passing them is complex
# and they are restricted to NOT contain commas or double quotes to ensure that they can be safely passed together on 
# the toolfactory command line as a comma delimited double quoted string for parsing and passing to the script
# see examples on this tool form

# august 2014

# Allows arbitrary number of input files
# NOTE positional parameters are now passed to script
# and output (may be "None") is *before* arbitrary number of inputs
# march 2014
# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
# grrrrr - night before a demo
# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
# added ghostscript and graphicsmagick as dependencies 
# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
# errors ensued
# august 2013
# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
# july 2013
# added ability to combine images and individual log files into html output
# just make sure there's a log file foo.log and it will be output
# together with all images named like "foo_*.pdf
# otherwise old format for html
# January 2013
# problem pointed out by Carlos Borroto
# added escaping for <>$ - thought I did that ages ago...
# August 11 2012 
# changed to use shell=False and cl as a sequence

# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
# It also serves as the wrapper for the new tool.
# you paste and run your script
# Only works for simple scripts that read one input from the history.
# Optionally can write one new history dataset,
# and optionally collect any number of outputs into links on an autogenerated HTML page.

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

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

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

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

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

progname = os.path.split(sys.argv[0])[1] 
myversion = 'V001.1 March 2014' 
verbose = False 
debug = False
toolFactoryURL = ''

# if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
# tool xml
toolhtmldepskel = """<?xml version="1.0"?>
    <package name="ghostscript" version="9.10">
        <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
    <package name="graphicsmagick" version="1.3.18">
        <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />

toolhtmldepskel = """<?xml version="1.0"?>

protorequirements = """<requirements>
      <requirement type="package" version="9.10">ghostscript</requirement>
      <requirement type="package" version="1.3.18">graphicsmagick</requirement>

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

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

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

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

def parse_citations(citations_text):
    citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
    citation_tuples = []
    for citation in citations:
        if citation.startswith("doi"):
            citation_tuples.append( ("doi", citation[len("doi"):].strip() ) )
            citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
    return citation_tuples

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

    def __init__(self,opts=None,treatbashSpecial=True):
        cleanup inputs, setup some outputs
        self.useGM = cmd_exists('gm')
        self.useIM = cmd_exists('convert')
        self.useGS = cmd_exists('gs')
        self.temp_warned = False # we want only one warning if $TMP not set
        self.treatbashSpecial = treatbashSpecial
        if opts.output_dir: # simplify for the tool tarball
        self.thumbformat = 'png'
        self.opts = opts
        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
        self.toolid = self.toolname
        self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
        self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
        self.xmlfile = '%s.xml' % self.toolname
        s = open(self.opts.script_path,'r').readlines()
        s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
        self.script = '\n'.join(s)
        fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
        tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
        self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
        self.escapedScript = '\n'.join([html_escape(x) for x in s])
        self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
        if opts.output_dir: # may not want these complexities 
            self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
            art = '%s.%s' % (self.toolname,opts.interpreter)
            artpath = os.path.join(self.opts.output_dir,art) # need full path
            artifact = open(artpath,'w') # use self.sfile as script source for Popen
            artifact.close() = []
        self.html = []
        self.test1Inputs = [] # now a list
        a =
        if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
            a('-') # stdin
        # if multiple inputs - positional or need to distinguish them with cl params
        if opts.input_tab:
            tests = []
            for i,intab in enumerate(opts.input_tab): # if multiple, make tests
                if intab.find(',') <> -1:
                    (gpath,uname) = intab.split(',')
                    gpath = uname = intab
            self.test1Inputs =  '<param name="input_tab" value="%s" />' % (','.join(tests))
            self.test1Inputs = ''
        # we always pass path,name pairs in using python optparse append
        # but the command line has to be different
        self.infile_paths = ','.join([x.split(',')[0] for x in self.opts.input_tab])
        self.infile_names = ','.join([x.split(',')[1] for x in self.opts.input_tab])
        if self.opts.interpreter == 'python':
            # yes, this is how additional parameters are always passed in python - to the TF itself and to
            # scripts to avoid having unknown parameter names (yes, they can be parsed but...) on the command line
            a('--INPATHS "%s"' % (self.infile_paths)) 
            a('--INNAMES "%s"' % (self.infile_names)) 
            if self.opts.output_tab:
                a('--OUTPATH "%s"' % self.opts.output_tab) 
            for p in opts.additional_parameters:
                p = p.replace('"','')
                param = psplit[0]
                value = psplit[1]
                a('--additional_parameters "%s,%s"' % (param,value))
        if (self.opts.interpreter == 'Rscript'):
            # pass params on command line
            a('INPATHS "%s"' % self.infile_paths)
            a('INNAMES "%s"' % self.infile_names)
            if self.opts.output_tab:
                a('OUTPATH "%s"' % self.opts.output_tab) 
            for param in opts.additional_parameters:
                param, value=param.split(',')
                a('%s="%s"' % (param,value))
        if (self.opts.interpreter == 'perl'):
            # pass params on command line
            a('%s' % self.infile_paths)
            a('%s' % self.infile_names)
            if self.opts.output_tab:
                a('%s' % self.opts.output_tab)
            for param in opts.additional_parameters:
                param, value=param.split(',')
                if (value.find(' ') <> -1):
                    a('%s="%s"' % (param,value))
                    a('%s=%s' % (param,value))
        if self.opts.interpreter == 'sh' or self.opts.interpreter == 'bash':
              # more is better - now move all params into environment AND drop on to command line.
    ,'INPATHS=%s' % (self.infile_paths))
    ,'INNAMES=%s' % (self.infile_names))
              if self.opts.output_tab:
        ,'OUTPATH=%s' % (self.opts.output_tab))
                  a('OUTPATH=%s' % (self.opts.output_tab))
              # sets those environment variables for the script
              # additional params appear in CL - yes, it's confusing
              for i,param in enumerate(opts.additional_parameters):
                  psplit = param.split(',')
                  n = psplit[0]
                  v = psplit[1]
                  if (v.find(' ') <> -1):
                    a('%s="%s"' % (n,v))
          ,'%s="%s"' % (n,v))
                    a('%s=%s' % (n,v))
          ,'%s=%s' % (n,v))

        self.outFormats = opts.output_format
        self.inputFormats = opts.input_formats
        self.test1Output = '%s_test1_output.xls' % self.toolname
        self.test1HTML = '%s_test1_output.html' % self.toolname

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

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

**What it Does**

Reverse the columns in a tabular file

            <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')

        newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
<command interpreter="python">
<configfile name="runMe">


    <citation type="doi">10.1093/bioinformatics/bts573</citation>
</tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto

        %(toolname) --script_path "$runMe" --interpreter "%(interpreter)s" 
            --tool_name "%(toolname)s"
        # may NOT be an input or htmlout - appended later
        tooltestsTabOnly = """
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="output1="%(test1Output)s" ftype="tabular"/>
        tooltestsHTMLOnly = """
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
        tooltestsBoth = """
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="output1" file="%(test1Output)s" ftype="tabular" />
        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
        xdict = {}
        xdict['additionalParams'] = ''
        xdict['additionalInputs'] = ''
        if self.opts.additional_parameters:
            if self.opts.edit_additional_parameters: # add to new tool form with default value set to original value
                xdict['additionalInputs'] = '\n'.join(['<param name="%s" value="%s" label="%s" help="%s" type="%s"/>' % (x.split(',')[0],x.split(',')[1],x.split(',')[2],
                    x.split(',')[3], x.split(',')[4]) for x in self.opts.additional_parameters])
            xdict['additionalParams'] = '\n'.join(['<param name="%s" value="%s" />' % (x.split(',')[0],x.split(',')[1]) for x in self.opts.additional_parameters])
        xdict['requirements'] = ''
        if self.opts.make_HTML:
            if self.opts.include_dependencies == "yes":
                xdict['requirements'] = protorequirements
        xdict['tool_version'] = self.opts.tool_version
        xdict['test1HTML'] = self.test1HTML
        xdict['test1Output'] = self.test1Output
        xdict['test1Inputs'] = self.test1Inputs
        if self.opts.make_HTML and self.opts.output_tab:
            xdict['tooltests'] = tooltestsBoth % xdict
        elif self.opts.make_HTML:
            xdict['tooltests'] = tooltestsHTMLOnly % xdict
            xdict['tooltests'] = tooltestsTabOnly % xdict
        xdict['script'] = self.escapedScript 
        # configfile is least painful way to embed script to avoid external dependencies
        # but requires escaping of <, > and $ to avoid Mako parsing
        if self.opts.help_text:
            helptext = open(self.opts.help_text,'r').readlines()
            helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
            xdict['help'] = ''.join([x for x in helptext])
            xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
        coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
        coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
        coda.append('See %s for details of that project' % (toolFactoryURL))
        coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
        coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
        xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
        if self.opts.tool_desc:
            xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
            xdict['tooldesc'] = ''
        xdict['command_outputs'] = '' 
        xdict['outputs'] = '' 
        if self.opts.input_tab <> 'None':
            cins = ['\n',]
            cins.append('#for intab in $input1:')
            cins.append('--input_tab "$intab,$"')
            cins.append('#end for\n')
            xdict['command_inputs'] = '\n'.join(cins)
            xdict['inputs'] = '''<param name="input_tab" multiple="true"  type="data" format="%s" label="Select one or more %s input files from your history"
                    help="Multiple inputs may be selected assuming the script can deal with them..."/> \n''' % (self.inputFormats,self.inputFormats)
            xdict['command_inputs'] = '' # assume no input - eg a random data generator       
            xdict['inputs'] = ''
        if (len(self.opts.additional_parameters) > 0):
            cins = ['\n',]
            for params in self.opts.additional_parameters:
                if self.opts.edit_additional_parameters:
                    psplit = params.split(',') # name,value...
                    psplit[1] = '$%s' % psplit[0] # replace with form value
                    cins.append('--additional_parameters "%s"' % ','.join(psplit)) 
                    cins.append('--additional_parameters "%s"' % params)
            xdict['command_inputs'] = '%s\n%s' % (xdict['command_inputs'],'\n'.join(cins))
        xdict['inputs'] += '<param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
        xdict['toolname'] = self.toolname
        xdict['toolid'] = self.toolid
        xdict['interpreter'] = self.opts.interpreter
        xdict['scriptname'] = self.sfile
        if self.opts.make_HTML:
            xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
            xdict['outputs'] +=  ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
            xdict['command_outputs'] += ' --output_dir "./"' 
        if self.opts.output_tab:
            xdict['command_outputs'] += ' --output_tab "$tab_file"'
            xdict['outputs'] += ' <data format="%s" name="output1" label="${job_name}"/>\n' % self.outFormats
        xdict['command'] = newCommand % xdict
        if self.opts.citations:
            citationstext = open(self.opts.citations,'r').read()
            citation_tuples = parse_citations(citationstext)
            citations_xml = ""
            for citation_type, citation_content in citation_tuples:
                citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content))
                citations_xml += citation_xml
            xdict['citations'] = citations_xml
            xdict['citations'] = ""
        xmls = newXML % xdict
        xf = open(self.xmlfile,'w')
        # ready for the tarball

    def makeTooltar(self):
        a tool is a gz tarball with eg
        /toolname/tool.xml /toolname/ /toolname/test-data/ ...
        retval =
        if retval:
            print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
        tdir = self.toolname
        if self.opts.make_HTML:
            if self.opts.help_text:
                hlp = open(self.opts.help_text,'r').read()
                hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
            if self.opts.include_dependencies == "yes":
                tooldepcontent = toolhtmldepskel  % hlp
                tooldepcontent = emptytoolhtmldepskel  % hlp
            depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
        if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
            testdir = os.path.join(tdir,'test-data')
            os.mkdir(testdir) # make tests directory
            for i,intab in enumerate(self.opts.input_tab):
                si = self.opts.input_tab[i]
                if si.find(',') <> -1:
                    s = si.split(',')[0]
                    si = s
                dest = os.path.join(testdir,os.path.basename(si))
                if si <> dest:
            if self.opts.output_tab <> None:
            if self.opts.make_HTML:
            if self.opts.output_dir:
        outpif = '' % self.toolname # new name
        outpiname = os.path.join(tdir,outpif) # path for the tool tarball
        pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
        notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
        notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
        notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
        pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
        notes += pi
        outpi = open(outpiname,'w')
        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):
        tarpath = "%s.tar.gz" % self.toolname
        tar =, "w:gz")
        tar.add(tdir,arcname='%s' % self.toolname)
        ## TODO: replace with optional direct upload to local toolshed?
        return retval

    def compressPDF(self,inpdf=None,thumbformat='png'):
        """need absolute path to pdf
           note that GS gets confoozled if no $TMP or $TEMP
           so we set it
        assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
        hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
        sto = open(hlog,'a')
        our_env = os.environ.copy()
        our_tmp = our_env.get('TMP',None)
        if not our_tmp:
            our_tmp = our_env.get('TEMP',None)
        if not (our_tmp and os.path.exists(our_tmp)):
            newtmp = os.path.join(self.opts.output_dir,'tmp')
                sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
            our_env['TEMP'] = newtmp
            if not self.temp_warned:
               sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
               self.temp_warned = True          
        outpdf = '%s_compressed' % inpdf
        cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
        x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
        retval1 = x.wait()
        if retval1 == 0:
        hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
        sto = open(hlog,'w')
        outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
        if self.useGM:        
            cl2 = ['gm', 'convert', inpdf, outpng]
        else: # assume imagemagick
            cl2 = ['convert', inpdf, outpng]
        x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
        retval2 = x.wait()
        if retval2 == 0:
        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" ""> 
        <html xmlns="" 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" /> 
        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
        <div class="toolFormBody"> 
        galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="">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']
        html = []
        html.append(galhtmlprefix % progname)
        html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
        fhtml = []
        if len(flist) > 0:
            logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
            logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
            logfiles.append(os.path.abspath(self.tlog)) # make it the last one
            pdflist = []
            npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
            for rownum,fname in enumerate(flist):
                dname,e = os.path.splitext(fname)
                sfsize = self.getfSize(fname,self.opts.output_dir)
                if e.lower() == '.pdf' : # compress and make a thumbnail
                    thumb = '%s.%s' % (dname,self.thumbformat)
                    pdff = os.path.join(self.opts.output_dir,fname)
                    retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
                    if retval == 0:
                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))
                    fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
            for logfname in logfiles: # expect at least tlog - if more
                if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
                    sectionname = 'All tool run'
                    if (len(logfiles) > 1):
                        sectionname = 'Other'
                    ourpdfs = pdflist
                    realname = os.path.basename(logfname)
                    sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
                    ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
                    pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
                nacross = 1
                npdf = len(ourpdfs)

                if npdf > 0:
                    nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
                    if int(nacross)**2 != npdf:
                        nacross += 1
                    nacross = int(nacross)
                    width = min(400,int(1200/nacross))
                    html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
                    html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
                    ntogo = nacross # counter for table row padding with empty cells
                    html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
                    for i,paths in enumerate(ourpdfs): 
                        fname,thumb = paths
                        s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" 
                           alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
                        if ((i+1) % nacross == 0):
                            s += '</tr>\n'
                            ntogo = 0
                            if i < (npdf - 1): # more to come
                               s += '<tr>'
                               ntogo = nacross
                            ntogo -= 1
                    if html[-1].strip().endswith('</tr>'):
                        if ntogo > 0: # pad
                logt = open(logfname,'r').readlines()
                logtext = [x for x in logt if x.strip() > '']
                html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
                if len(logtext) > 1:
                    html += logtext
                    html.append('%s is empty<br/>' % logfname)
        if len(fhtml) > 0:
           fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
           html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
           html += fhtml # add all non-pdf files to the end of the display
            html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
        htmlf = file(self.opts.output_html,'w')
        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()
            if self.opts.output_dir:
                ste = open(self.elog,'w')
                sto = open(self.tlog,'w')
                sto.write('## Toolfactory generated command line = %s\n' % ' '.join(
                p = subprocess.Popen(,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
                p = subprocess.Popen(,shell=False,stdin=subprocess.PIPE)
            retval = p.wait()
            if self.opts.output_dir:
                err = open(self.elog,'r').readlines()
                if retval <> 0 and err: # problem
                    print >> sys.stderr,err
            if self.opts.make_HTML:
        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(
            sto = open(self.tlog,'w')
            p = subprocess.Popen(,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
            p = subprocess.Popen(,shell=False)            
        retval = p.wait()
        if self.opts.output_dir:
        if self.opts.make_HTML:
        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"> --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
    op = optparse.OptionParser()
    a = op.add_option
    a('--input_tab',default=[], action="append") # these are "galaxypath,metadataname" pairs
    a('--additional_parameters', dest='additional_parameters', action='append', default=[])
    a('--edit_additional_parameters', action="store_true", default=False)
    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:
    opts.input_tab = [x.replace('"','').replace("'",'') for x in opts.input_tab]
    for i,x in enumerate(opts.additional_parameters): # remove quotes we need to deal with spaces in CL params
        opts.additional_parameters[i] = opts.additional_parameters[i].replace('"','')
    r = ScriptRunner(opts)
    if opts.make_Tool:
        retcode = r.makeTooltar()
        retcode =
    if retcode:
        sys.exit(retcode) # indicate failure to job runner

if __name__ == "__main__":