changeset 0:2122e630b13a draft

Initial commit of replacement for edger_test
author fubar
date Fri, 26 Jul 2013 23:50:59 -0400
parents
children df4fea3be1b3
files rgedgeR/rgToolFactory.py rgedgeR/rgedgeRpaired.xml rgedgeR/test-data/edgeRtest1out.html rgedgeR/test-data/edgeRtest1out.xls rgedgeR/test-data/gentestdata.sh rgedgeR/test-data/test_bams2mx.xls rgedgeR/tool_dependencies.xml
diffstat 7 files changed, 6701 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/rgToolFactory.py	Fri Jul 26 23:50:59 2013 -0400
@@ -0,0 +1,599 @@
+# 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
+#
+# july 2013
+# added ability to combine images and individual log files into html output
+# just make sure there's a log file foo.log and it will be output
+# together with all images named like "foo_*.pdf
+# otherwise old format for html
+#
+# January 2013
+# problem pointed out by Carlos Borroto
+# added escaping for <>$ - thought I did that ages ago...
+#
+# August 11 2012 
+# changed to use shell=False and cl as a sequence
+
+# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
+# It also serves as the wrapper for the new tool.
+# 
+# you paste and run your script
+# Only works for simple scripts that read one input from the history.
+# Optionally can write one new history dataset,
+# and optionally collect any number of outputs into links on an autogenerated HTML page.
+
+# DO NOT install on a public or important site - please.
+
+# installed generated tools are fine if the script is safe.
+# They just run normally and their user cannot do anything unusually insecure
+# but please, practice safe toolshed.
+# Read the fucking code before you install any tool 
+# especially this one
+
+# After you get the script working on some test data, you can
+# optionally generate a toolshed compatible gzip file
+# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
+# safe and largely automated installation in a production Galaxy.
+
+# If you opt for an HTML output, you get all the script outputs arranged
+# as a single Html history item - all output files are linked, thumbnails for all the pdfs.
+# Ugly but really inexpensive.
+# 
+# Patches appreciated please. 
+#
+#
+# long route to June 2012 product
+# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
+# derived from an integrated script model  
+# called rgBaseScriptWrapper.py
+# Note to the unwary:
+#   This tool allows arbitrary scripting on your Galaxy as the Galaxy user
+#   There is nothing stopping a malicious user doing whatever they choose
+#   Extremely dangerous!!
+#   Totally insecure. So, trusted users only
+#
+# preferred model is a developer using their throw away workstation instance - ie a private site.
+# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
+#
+
+import sys 
+import shutil 
+import subprocess 
+import os 
+import time 
+import tempfile 
+import optparse
+import tarfile
+import re
+import shutil
+import math
+
+progname = os.path.split(sys.argv[0])[1] 
+myversion = '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()))
+
+html_escape_table = {
+     "&": "&amp;",
+     ">": "&gt;",
+     "<": "&lt;",
+     "$": "\$"
+     }
+
+def html_escape(text):
+     """Produce entities within text."""
+     return "".join(html_escape_table.get(c,c) for c in text)
+
+def cmd_exists(cmd):
+     return subprocess.call("type " + cmd, shell=True, 
+           stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
+
+
+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.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 = '\n'.join([' %s' % x for x in s]) # for restructured text in help
+        self.escapedScript = '\n'.join([html_escape(x) for x in s])
+        if opts.output_dir: # may not want these complexities 
+            self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
+            art = '%s.%s' % (self.toolname,opts.interpreter)
+            artpath = os.path.join(self.opts.output_dir,art) # need full path
+            artifact = open(artpath,'w') # use self.sfile as script source for Popen
+            artifact.write(self.script)
+            artifact.close()
+        self.cl = []
+        self.html = []
+        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.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:
+            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))
+        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')
+        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","-dPDFSETTINGS=/printer", "-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)
+        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)
+        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:
+            logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
+            logfiles.sort()
+            logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
+            logfiles.append(os.path.abspath(self.tlog)) # make it the last one
+            pdflist = []
+            npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
+            for rownum,fname in enumerate(flist):
+                dname,e = os.path.splitext(fname)
+                sfsize = self.getfSize(fname,self.opts.output_dir)
+                if e.lower() == '.pdf' : # compress and make a thumbnail
+                    thumb = '%s.%s' % (dname,self.thumbformat)
+                    pdff = os.path.join(self.opts.output_dir,fname)
+                    retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
+                    if retval == 0:
+                        pdflist.append((fname,thumb))
+                if (rownum+1) % 2 == 0:
+                    fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
+                else:
+                    fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
+            for logfname in logfiles: # expect at least tlog - if more
+                if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
+                    sectionname = 'All tool run'
+                    if (len(logfiles) > 1):
+                        sectionname = 'Other'
+                    ourpdfs = pdflist
+                else:
+                    realname = os.path.basename(logfname)
+                    sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
+                    ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
+                    pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
+                nacross = 1
+                npdf = len(ourpdfs)
+
+                if npdf > 0:
+                    nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
+                    if int(nacross)**2 != npdf:
+                        nacross += 1
+                    nacross = int(nacross)
+                    width = min(400,int(1200/nacross))
+                    html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
+                    html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
+                    ntogo = nacross # counter for table row padding with empty cells
+                    html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
+                    for i,paths in enumerate(ourpdfs): 
+                        fname,thumb = paths
+                        s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" 
+                           alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
+                        if ((i+1) % nacross == 0):
+                            s += '</tr>\n'
+                            ntogo = 0
+                            if i < (npdf - 1): # more to come
+                               s += '<tr>'
+                               ntogo = nacross
+                        else:
+                            ntogo -= 1
+                        html.append(s)
+                    if html[-1].strip().endswith('</tr>'):
+                        html.append('</table></div>\n')
+                    else:
+                        if ntogo > 0: # pad
+                           html.append('<td>&nbsp;</td>'*ntogo)
+                        html.append('</tr></table></div>\n')
+                logt = open(logfname,'r').readlines()
+                logtext = [x for x in logt if x.strip() > '']
+                html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
+                if len(logtext) > 1:
+                    html.append('\n<pre>\n')
+                    html += logtext
+                    html.append('\n</pre>\n')
+                else:
+                    html.append('%s is empty<br/>' % logfname)
+        if len(fhtml) > 0:
+           fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
+           fhtml.append('</table></div><br/>')
+           html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
+           html += fhtml # add all non-pdf files to the end of the display
+        else:
+            html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
+        html.append(galhtmlpostfix)
+        htmlf = file(self.opts.output_html,'w')
+        htmlf.write('\n'.join(html))
+        htmlf.write('\n')
+        htmlf.close()
+        self.html = html
+
+
+    def run(self):
+        """
+        scripts must be small enough not to fill the pipe!
+        """
+        if self.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/rgedgeR/rgedgeRpaired.xml	Fri Jul 26 23:50:59 2013 -0400
@@ -0,0 +1,867 @@
+<tool id="rgDifferentialCount" name="Differential_Count" version="0.20">
+  <description>models using BioConductor packages</description>
+  <requirements>
+      <requirement type="package" version="2.12">biocbasics</requirement>
+      <requirement type="package" version="3.0.1">r3</requirement>
+  </requirements>
+  
+  <command interpreter="python">
+     rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts" 
+    --output_dir "$html_file.files_path" --output_html "$html_file" --output_tab "$outtab" --make_HTML "yes"
+  </command>
+  <inputs>
+    <param name="input1"  type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
+       help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>
+    <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs" 
+           help="Supply a meaningful name here to remind you what the outputs contain">
+      <sanitizer invalid_char="">
+        <valid initial="string.letters,string.digits"><add value="_" /> </valid>
+      </sanitizer>
+    </param>
+    <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
+    <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True" 
+         multiple="true" use_header_names="true" size="120" display="checkboxes">
+        <validator type="no_options" message="Please select at least one column."/>
+    </param>
+    <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
+    <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True" 
+         multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
+    </param>
+    <param name="subjectids" type="text" optional="true" size="120" value = ""
+       label="IF SUBJECTS NOT ALL INDEPENDENT! Enter integers to indicate sample pairing for every column in input"
+       help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter '1,2,1,2'">
+      <sanitizer>
+        <valid initial="string.digits"><add value="," /> </valid>
+      </sanitizer>
+    </param>
+    <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs"
+     help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/>
+    <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1" 
+              label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"
+     help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/>
+
+    <conditional name="edgeR">
+    <param name="doedgeR" type="select" 
+       label="Run this model using edgeR"
+       help="edgeR uses a negative binomial model and seems to be powerful, even with few replicates">
+      <option value="F">Do not run edgeR</option>
+      <option value="T" selected="true">Run edgeR</option>
+     </param>
+     <when value="T">
+      <param name="edgeR_priordf" type="integer" value="20" size="3" 
+       label="prior.df for tagwise dispersion - lower value = more emphasis on each tag's variance. Replaces prior.n  and prior.df = prior.n * residual.df"
+       help="0 = Use edgeR default. Use a small value to 'smooth' small samples. See edgeR docs and note below"/>
+     </when>
+     <when value="F"> </when>
+    </conditional>
+    <conditional name="DESeq2">
+    <param name="doDESeq2" type="select" 
+       label="Run the same model with DESeq2 and compare findings"
+       help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR">
+      <option value="F" selected="true">Do not run DESeq2</option>
+      <option value="T">Run DESeq2 (only works if NO second GLM factor supplied at present)</option>
+     </param>
+     <when value="T">
+         <param name="DESeq_fitType" type="select">
+            <option value="parametric" selected="true">Parametric (default) fit for dispersions</option>
+            <option value="local">Local fit - use this if parametric fails</option>
+            <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual</option>
+         </param> 
+     </when>
+     <when value="F"> </when>
+    </conditional>
+    <param name="doVoom" type="select" 
+       label="Run the same model with Voom/limma and compare findings"
+       help="The VOOM transformation allows analysis of count data using limma">
+      <option value="F" selected="true">Do not run VOOM</option>
+      <option value="T">Run VOOM</option>
+     </param>
+    <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
+     help="Conventional default value of 0.05 recommended"/>
+    <param name="fdrtype" type="select" label="FDR (Type II error) control method" 
+         help="Use fdr or bh typically to control for the number of tests in a reliable way">
+            <option value="fdr" selected="true">fdr</option>
+            <option value="BH">Benjamini Hochberg</option>
+            <option value="BY">Benjamini Yukateli</option>
+            <option value="bonferroni">Bonferroni</option>
+            <option value="hochberg">Hochberg</option>
+            <option value="holm">Holm</option>
+            <option value="hommel">Hommel</option>
+            <option value="none">no control for multiple tests</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="outtab" label="${title}.xls"/>
+    <data format="html" name="html_file" label="${title}.html"/>
+  </outputs>
+ <stdio>
+     <exit_code range="4"   level="fatal"   description="Number of subject ids must match total number of samples in the input matrix" />
+ </stdio>
+ <tests>
+<test>
+<param name='input1' value='test_bams2mx.xls' ftype='tabular' />
+ <param name='treatment_name' value='case' />
+ <param name='title' value='edgeRtest' />
+ <param name='useNDF' value='' />
+ <param name='doedgeR' value='T' />
+ <param name='doVoom' value='T' />
+ <param name='doDESeq2' value='T' />
+ <param name='fdrtype' value='fdr' />
+ <param name='edgeR_priordf' value="8" />
+ <param name='fdrthresh' value="0.05" />
+ <param name='control_name' value='control' />
+ <param name='subjectids' value='' />
+  <param name='Treat_cols' value='3,4,5,9' />
+ <param name='Control_cols' value='2,6,7,8' />
+ <output name='outtab' file='edgeRtest1out.xls' compare='diff' />
+ <output name='html_file' file='edgeRtest1out.html'  compare='diff' lines_diff='20' />
+</test>
+</tests>
+
+<configfiles>
+<configfile name="runme">
+<![CDATA[
+# 
+# edgeR.Rscript
+# updated npv 2011 for R 2.14.0 and edgeR 2.4.0 by ross
+# Performs DGE on a count table containing n replicates of two conditions
+#
+# Parameters
+#
+# 1 - Output Dir
+
+# Original edgeR code by: S.Lunke and A.Kaspi
+reallybig = log10(.Machine\$double.xmax)
+reallysmall = log10(.Machine\$double.xmin)
+library('stringr')
+library('gplots')
+library('edgeR')
+hmap2 = function(cmat,nsamp=100,outpdfname='heatmap2.pdf', TName='Treatment',group=NA,myTitle='title goes here')
+{
+# Perform clustering for significant pvalues after controlling FWER
+    samples = colnames(cmat)
+    gu = unique(group)
+    if (length(gu) == 2) {
+        col.map = function(g) {if (g==gu[1]) "#FF0000" else "#0000FF"}
+        pcols = unlist(lapply(group,col.map))        
+        } else {
+        colours = rainbow(length(gu),start=0,end=4/6)
+        pcols = colours[match(group,gu)]        }
+    gn = rownames(cmat)
+    dm = cmat[(! is.na(gn)),] 
+    # remove unlabelled hm rows
+    nprobes = nrow(dm)
+    # sub = paste('Showing',nprobes,'contigs ranked for evidence of differential abundance')
+    if (nprobes > nsamp) {
+      dm =dm[1:nsamp,]
+      #sub = paste('Showing',nsamp,'contigs ranked for evidence for differential abundance out of',nprobes,'total')
+    }
+    newcolnames = substr(colnames(dm),1,20)
+    colnames(dm) = newcolnames
+    pdf(outpdfname)
+    heatmap.2(dm,main=myTitle,ColSideColors=pcols,col=topo.colors(100),dendrogram="col",key=T,density.info='none',
+         Rowv=F,scale='row',trace='none',margins=c(8,8),cexRow=0.4,cexCol=0.5)
+    dev.off()
+}
+
+hmap = function(cmat,nmeans=4,outpdfname="heatMap.pdf",nsamp=250,TName='Treatment',group=NA,myTitle="Title goes here")
+{
+    # for 2 groups only was
+    #col.map = function(g) {if (g==TName) "#FF0000" else "#0000FF"}
+    #pcols = unlist(lapply(group,col.map))
+    gu = unique(group)
+    colours = rainbow(length(gu),start=0.3,end=0.6)
+    pcols = colours[match(group,gu)]
+    nrows = nrow(cmat)
+    mtitle = paste(myTitle,'Heatmap: n contigs =',nrows)
+    if (nrows > nsamp)  {
+               cmat = cmat[c(1:nsamp),]
+               mtitle = paste('Heatmap: Top ',nsamp,' DE contigs (of ',nrows,')',sep='')
+          }
+    newcolnames = substr(colnames(cmat),1,20)
+    colnames(cmat) = newcolnames
+    pdf(outpdfname)
+    heatmap(cmat,scale='row',main=mtitle,cexRow=0.3,cexCol=0.4,Rowv=NA,ColSideColors=pcols)
+    dev.off()
+}
+
+qqPlot = function(descr='qqplot',pvector, outpdf='qqplot.pdf',...)
+# stolen from https://gist.github.com/703512
+{
+    o = -log10(sort(pvector,decreasing=F))
+    e = -log10( 1:length(o)/length(o) )
+    o[o==-Inf] = reallysmall
+    o[o==Inf] = reallybig
+    maint = descr
+    pdf(outpdf)
+    plot(e,o,pch=19,cex=1, main=maint, ...,
+        xlab=expression(Expected~~-log[10](italic(p))),
+        ylab=expression(Observed~~-log[10](italic(p))),
+        xlim=c(0,max(e)), ylim=c(0,max(o)))
+    lines(e,e,col="red")
+    grid(col = "lightgray", lty = "dotted")
+    dev.off()
+}
+
+smearPlot = function(DGEList,deTags, outSmear, outMain)
+        {
+        pdf(outSmear)
+        plotSmear(DGEList,de.tags=deTags,main=outMain)
+        grid(col="lightgray", lty="dotted")
+        dev.off()
+        }
+        
+boxPlot = function(rawrs,cleanrs,maint,myTitle,pdfname)
+{   # 
+        nc = ncol(rawrs)
+        for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA}
+        fullnames = colnames(rawrs)
+        newcolnames = substr(colnames(rawrs),1,20)
+        colnames(rawrs) = newcolnames
+        newcolnames = substr(colnames(cleanrs),1,20)
+        colnames(cleanrs) = newcolnames
+        defpar = par(no.readonly=T)
+        print.noquote('raw contig counts by sample:')
+        print.noquote(summary(rawrs))
+        print.noquote('normalised contig counts by sample:')
+        print.noquote(summary(cleanrs))
+        pdf(pdfname)
+        par(mfrow=c(1,2))
+        boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('Raw:',maint))
+        grid(col="lightgray",lty="dotted")
+        boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('After ',maint))
+        grid(col="lightgray",lty="dotted")
+        dev.off()
+        pdfname = "sample_counts_histogram.pdf" 
+        nc = ncol(rawrs)
+        print.noquote(paste('Using ncol rawrs=',nc))
+        ncroot = round(sqrt(nc))
+        if (ncroot*ncroot < nc) { ncroot = ncroot + 1 }
+        m = c()
+        for (i in c(1:nc)) {
+              rhist = hist(rawrs[,i],breaks=100,plot=F)
+              m = append(m,max(rhist\$counts))
+             }
+        ymax = max(m)
+        pdf(pdfname)
+        par(mfrow=c(ncroot,ncroot))
+        for (i in c(1:nc)) {
+                 hist(rawrs[,i], main=paste("Contig logcount",i), xlab='log raw count', col="maroon", 
+                 breaks=100,sub=fullnames[i],cex=0.8,ylim=c(0,ymax))
+             }
+        dev.off()
+        par(defpar)
+      
+}
+
+cumPlot = function(rawrs,cleanrs,maint,myTitle)
+{   # updated to use ecdf
+        pdfname = "Filtering_rowsum_bar_charts.pdf"
+        defpar = par(no.readonly=T)
+        lrs = log(rawrs,10) 
+        lim = max(lrs)
+        pdf(pdfname)
+        par(mfrow=c(2,1))
+        hist(lrs,breaks=100,main=paste('Before:',maint),xlab="# Reads (log)",
+             ylab="Count",col="maroon",sub=myTitle, xlim=c(0,lim),las=1)
+        grid(col="lightgray", lty="dotted")
+        lrs = log(cleanrs,10) 
+        hist(lrs,breaks=100,main=paste('After:',maint),xlab="# Reads (log)",
+             ylab="Count",col="maroon",sub=myTitle,xlim=c(0,lim),las=1)
+        grid(col="lightgray", lty="dotted")
+        dev.off()
+        par(defpar)
+}
+
+cumPlot1 = function(rawrs,cleanrs,maint,myTitle)
+{   # updated to use ecdf
+        pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_')
+        pdf(pdfname)
+        par(mfrow=c(2,1))
+        lastx = max(rawrs)
+        rawe = knots(ecdf(rawrs))
+        cleane = knots(ecdf(cleanrs))
+        cy = 1:length(cleane)/length(cleane)
+        ry = 1:length(rawe)/length(rawe)
+        plot(rawe,ry,type='l',main=paste('Before',maint),xlab="Log Contig Total Reads",
+             ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
+        grid(col="blue")
+        plot(cleane,cy,type='l',main=paste('After',maint),xlab="Log Contig Total Reads",
+             ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
+        grid(col="blue")
+        dev.off()
+}
+
+
+
+doGSEA = function(y=NULL,design=NULL,histgmt="",
+                  bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
+                  ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
+{
+  sink('Camera.log')
+  genesets = c()
+  if (bigmt > "")
+  {
+    bigenesets = readLines(bigmt)
+    genesets = bigenesets
+  }
+  if (histgmt > "")
+  {
+    hgenesets = readLines(histgmt)
+    if (bigmt > "") {
+      genesets = rbind(genesets,hgenesets)
+    } else {
+      genesets = hgenesets
+    } # use only history if no bi
+  }
+  print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
+  genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
+  outf = outfname
+  head=paste(myTitle,'edgeR GSEA')
+  write(head,file=outfname,append=F)
+  ntest=length(genesets)
+  urownames = toupper(rownames(y))
+  upcam = c()
+  downcam = c()
+  for (i in 1:ntest) {
+    gs = unlist(genesets[i])
+    g = gs[1] # geneset_id
+    u = gs[2]
+    if (u > "") { u = paste("<a href=\'",u,"\'>",u,"</a>",sep="") }
+    glist = gs[3:length(gs)] # member gene symbols
+    glist = toupper(glist)
+    inglist = urownames %in% glist
+    nin = sum(inglist)
+    if ((nin > minnin) && (nin < maxnin)) {
+      ### print(paste('@@found',sum(inglist),'genes in glist'))
+      camres = camera(y=y,index=inglist,design=design)
+      if (! is.null(camres)) {
+      rownames(camres) = g # gene set name
+      camres = cbind(GeneSet=g,URL=u,camres)
+      if (camres\$Direction == "Up") 
+        {
+        upcam = rbind(upcam,camres) } else {
+          downcam = rbind(downcam,camres)
+        }
+      }
+   }
+  }
+  uscam = upcam[order(upcam\$PValue),]
+  unadjp = uscam\$PValue
+  uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
+  nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
+  dscam = downcam[order(downcam\$PValue),]
+  unadjp = dscam\$PValue
+  dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
+  ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
+  write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
+  write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
+  print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
+  write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
+  print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
+  write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
+  sink()
+}
+
+
+
+edgeIt = function (Count_Matrix,group,outputfilename,fdrtype='fdr',priordf=5, 
+        fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F,
+        filterquantile=0.2, subjects=c(),mydesign=NULL,
+        doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19',
+        histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
+        doCook=F,DESeq_fitType="parameteric") 
+{
+  # Error handling
+  if (length(unique(group))!=2){
+    print("Number of conditions identified in experiment does not equal 2")
+    q()
+    }
+  require(edgeR)
+  options(width = 512) 
+  mt = paste(unlist(strsplit(myTitle,'_')),collapse=" ")
+  allN = nrow(Count_Matrix)
+  nscut = round(ncol(Count_Matrix)/2)
+  colTotmillionreads = colSums(Count_Matrix)/1e6
+  counts.dataframe = as.data.frame(c()) 
+  rawrs = rowSums(Count_Matrix)
+  nonzerod = Count_Matrix[(rawrs > 0),] # remove all zero count genes
+  nzN = nrow(nonzerod)
+  nzrs = rowSums(nonzerod)
+  zN = allN - nzN
+  print('# Quantiles for non-zero row counts:',quote=F)
+  print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F)
+  if (useNDF == "T")
+  {
+    gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut
+    lo = colSums(Count_Matrix[!gt1rpin3,])
+    workCM = Count_Matrix[gt1rpin3,]
+    cleanrs = rowSums(workCM)
+    cleanN = length(cleanrs)
+    meth = paste( "After removing",length(lo),"contigs with fewer than ",nscut," sample read counts >= 1 per million, there are",sep="")
+    print(paste("Read",allN,"contigs. Removed",zN,"contigs with no reads.",meth,cleanN,"contigs"),quote=F)
+    maint = paste('Filter >=1/million reads in >=',nscut,'samples')
+  }   else {        
+    useme = (nzrs > quantile(nzrs,filterquantile))
+    workCM = nonzerod[useme,]
+    lo = colSums(nonzerod[!useme,])
+    cleanrs = rowSums(workCM)
+    cleanN = length(cleanrs)
+    meth = paste("After filtering at count quantile =",filterquantile,", there are",sep="")
+    print(paste('Read',allN,"contigs. Removed",zN,"with no reads.",meth,cleanN,"contigs"),quote=F)
+    maint = paste('Filter below',filterquantile,'quantile')
+  }
+  cumPlot(rawrs=rawrs,cleanrs=cleanrs,maint=maint,myTitle=myTitle)
+  allgenes = rownames(workCM)
+  reg = "^chr([0-9]+):([0-9]+)-([0-9]+)"
+  genecards="<a href=\'http://www.genecards.org/index.php?path=/Search/keyword/"
+  ucsc = paste("<a href=\'http://genome.ucsc.edu/cgi-bin/hgTracks?db=",org,sep='')
+  testreg = str_match(allgenes,reg)
+  if (sum(!is.na(testreg[,1]))/length(testreg[,1]) > 0.8) # is ucsc style string
+  {
+    print("@@ using ucsc substitution for urls")
+    contigurls = paste0(ucsc,"&amp;position=chr",testreg[,2],":",testreg[,3],"-",testreg[,4],"\'>",allgenes,"</a>")
+  } else {
+    print("@@ using genecards substitution for urls")
+    contigurls = paste0(genecards,allgenes,"\'>",allgenes,"</a>")
+  }
+  print.noquote("# urls")
+  print.noquote(head(contigurls))
+  print(paste("# Total low count contigs per sample = ",paste(lo,collapse=',')),quote=F) 
+  cmrowsums = rowSums(workCM)
+  TName=unique(group)[1]
+  CName=unique(group)[2]
+  if (is.null(mydesign)) {
+    if (length(subjects) == 0) 
+    {
+      mydesign = model.matrix(~group)
+    } 
+    else { 
+      subjf = factor(subjects)
+      mydesign = model.matrix(~subjf+group) # we block on subject so make group last to simplify finding it
+    }
+  } 
+  print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=',')))
+  print.noquote('Using design matrix:')
+  print.noquote(mydesign)
+  if (doedgeR) {
+  sink('edgeR.log')
+  #### Setup DGEList object
+  DGEList = DGEList(counts=workCM, group = group)
+  DGEList = calcNormFactors(DGEList)
+
+  DGEList = estimateGLMCommonDisp(DGEList,mydesign)
+  comdisp = DGEList\$common.dispersion
+  DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
+  if (edgeR_priordf > 0) {
+    print.noquote(paste("prior.df =",edgeR_priordf))
+    DGEList = estimateGLMTagwiseDisp(DGEList,mydesign,prior.df = edgeR_priordf)
+  } else {
+    DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
+  }
+  DGLM = glmFit(DGEList,design=mydesign)
+  DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
+  efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
+  normData = (1e+06*DGEList\$counts/efflib)
+  uoutput = cbind( 
+    Name=as.character(rownames(DGEList\$counts)),
+    DE\$table,
+    adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
+    Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums,normData,
+    DGEList\$counts
+  )
+  soutput = uoutput[order(DE\$table\$PValue),] # sorted into p value order - for quick toptable
+  goodness = gof(DGLM, pcutoff=fdrthresh)
+  if (sum(goodness\$outlier) > 0) {
+    print.noquote('GLM outliers:')
+    print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F)
+    } else { 
+      print('No GLM fit outlier genes found\n')
+    }
+  z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2)
+  pdf("edgeR_GoodnessofFit.pdf")
+  qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion")
+  abline(0,1,lwd=3)
+  points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon")
+  dev.off()
+  estpriorn = getPriorN(DGEList)
+  print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
+  efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
+  normData = (1e+06*DGEList\$counts/efflib)
+  uniqueg = unique(group)
+  #### Plot MDS
+  sample_colors =  match(group,levels(group))
+  sampleTypes = levels(factor(group))
+  print.noquote(sampleTypes)
+  pdf("edgeR_MDSplot.pdf")
+  plotMDS.DGEList(DGEList,main=paste("edgeR MDS for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors)
+  legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19)
+  grid(col="blue")
+  dev.off()
+  colnames(normData) = paste( colnames(normData),'N',sep="_")
+  print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=',')))
+  nzd = data.frame(log(nonzerod + 1e-2,10))
+  boxPlot(rawrs=nzd,cleanrs=log(normData,10),maint='TMM Normalisation',myTitle=myTitle,pdfname="edgeR_raw_norm_counts_box.pdf")
+  write.table(soutput,outputfilename, quote=FALSE, sep="\t",row.names=F)
+  tt = cbind( 
+    Name=as.character(rownames(DGEList\$counts)),
+    DE\$table,
+    adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
+    Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums
+  )
+  print.noquote("# edgeR Top tags\n")
+  tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
+  tt = tt[order(DE\$table\$PValue),] 
+  print.noquote(tt[1:50,])
+  deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
+  nsig = length(deTags)
+  print(paste('#',nsig,'tags significant at adj p=',fdrthresh),quote=F)
+  deColours = ifelse(deTags,'red','black')
+  pdf("edgeR_BCV_vs_abundance.pdf")
+  plotBCV(DGEList, cex=0.3, main="Biological CV vs abundance")
+  dev.off()
+  dg = DGEList[order(DE\$table\$PValue),]
+  #normData = (1e+06 * dg\$counts/expandAsMatrix(dg\$samples\$lib.size, dim(dg)))
+  efflib = dg\$samples\$lib.size*dg\$samples\$norm.factors
+  normData = (1e+06*dg\$counts/efflib)
+  outpdfname="edgeR_heatmap.pdf"
+  hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=myTitle)
+  outSmear = "edgeR_smearplot.pdf"
+  outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
+  smearPlot(DGEList=DGEList,deTags=deTags, outSmear=outSmear, outMain = outMain)
+  qqPlot(descr=paste(myTitle,'edgeR QQ plot'),pvector=DE\$table\$PValue,outpdf='edgeR_qqplot.pdf')
+  norm.factor = DGEList\$samples\$norm.factors
+  topresults.edgeR = soutput[which(soutput\$adj.p.value < fdrthresh), ]
+  edgeRcountsindex = which(allgenes %in% rownames(topresults.edgeR))
+  edgeRcounts = rep(0, length(allgenes))
+  edgeRcounts[edgeRcountsindex] = 1  # Create venn diagram of hits
+  sink()
+  } ### doedgeR
+  if (doDESeq2 == T)
+  {
+    sink("DESeq2.log")
+    # DESeq2
+    require('DESeq2')
+    library('RColorBrewer')
+    pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM))        
+    deSEQds = DESeqDataSetFromMatrix(countData = workCM,  colData = pdata, design = formula(~ Rx))
+    #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype)
+    #rDESeq = results(DESeq2)
+    #newCountDataSet(workCM, group)
+    deSeqDatsizefac = estimateSizeFactors(deSEQds)
+    deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType)
+    resDESeq = nbinomWaldTest(deSeqDatdisp, pAdjustMethod=fdrtype)
+    rDESeq = as.data.frame(results(resDESeq))
+    rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls)
+    srDESeq = rDESeq[order(rDESeq\$pvalue),]
+    qqPlot(descr=paste(myTitle,'DESeq2 qqplot'),pvector=rDESeq\$pvalue,outpdf='DESeq2_qqplot.pdf')
+    cat("# DESeq top 50\n")
+    print.noquote(srDESeq[1:50,])
+    write.table(srDESeq,paste(mt,'DESeq2_TopTable.xls',sep='_'), quote=FALSE, sep="\t",row.names=F)
+    topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ]
+    DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq))
+    DESeqcounts = rep(0, length(allgenes))
+    DESeqcounts[DESeqcountsindex] = 1
+    pdf("DESeq2_dispersion_estimates.pdf")
+    plotDispEsts(resDESeq)
+    dev.off()
+    ysmall = abs(min(rDESeq\$log2FoldChange))
+    ybig = abs(max(rDESeq\$log2FoldChange))
+    ylimit = min(4,ysmall,ybig)
+    pdf("DESeq2_MA_plot.pdf")
+    plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
+    dev.off()
+    rlogres = rlogTransformation(resDESeq)
+    sampledists = dist( t( assay(rlogres) ) )
+    sdmat = as.matrix(sampledists)
+    pdf("DESeq2_sample_distance_plot.pdf")
+    heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"),
+         col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
+    dev.off()
+    sink()
+    result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) )
+    if ("try-error" %in% class(result)) {
+         print.noquote('DESeq2 plotPCA failed.')
+         } else {
+         pdf("DESeq2_PCA_plot.pdf")
+         #### wtf - print? Seems needed to get this to work
+         print(ppca)
+         dev.off()
+        }
+  }
+
+  if (doVoom == T) {
+      sink('VOOM.log')
+      pdf("VOOM_mean_variance_plot.pdf")
+      dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)
+      dev.off()
+      # Use limma to fit data
+      fit = lmFit(dat.voomed, mydesign)
+      fit = eBayes(fit)
+      rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none")
+      qqPlot(descr=paste(myTitle,'VOOM-limma QQ plot'),pvector=rvoom\$P.Value,outpdf='VOOM_qqplot.pdf')
+      rownames(rvoom) = rownames(workCM)
+      rvoom = cbind(rvoom,NReads=cmrowsums,URL=contigurls)
+      srvoom = rvoom[order(rvoom\$P.Value),]
+      write.table(srvoom,paste(mt,'VOOM_topTable.xls',sep='_'), quote=FALSE, sep="\t",row.names=F)
+      # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma
+      topresults.voom = srvoom[which(rvoom\$adj.P.Val < fdrthresh), ]
+      voomcountsindex = which(allgenes %in% topresults.voom\$ID)
+      voomcounts = rep(0, length(allgenes))
+      voomcounts[voomcountsindex] = 1
+      cat("# VOOM top 50\n")
+      print(srvoom[1:50,])
+      sink()
+  }
+
+  if (doCamera) {
+  doGSEA(y=DGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
+    outfname=paste(mt,"GSEA.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype)
+  }
+
+  if ((doDESeq2==T) || (doVoom==T) || (doedgeR==T)) {
+    if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) {
+        vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh)
+        counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, 
+                                       VOOM_limma = voomcounts, row.names = allgenes)
+       } else if ((doDESeq2==T) && (doedgeR==T))  {
+         vennmain = paste(mt,'DESeq2 and edgeR overlap at FDR=',fdrthresh)
+         counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, row.names = allgenes)
+       } else if ((doVoom==T) && (doedgeR==T)) {
+        vennmain = paste(mt,'Voom and edgeR overlap at FDR=',fdrthresh)
+        counts.dataframe = data.frame(edgeR = edgeRcounts, VOOM_limma = voomcounts, row.names = allgenes)
+       }
+    
+    if (nrow(counts.dataframe > 1)) {
+      counts.venn = vennCounts(counts.dataframe)
+      vennf = "Venn_significant_genes_overlap.pdf" 
+      pdf(vennf)
+      vennDiagram(counts.venn,main=vennmain,col="maroon")
+      dev.off()
+    }
+  } #### doDESeq2 or doVoom
+  #Return our main table
+  uoutput 
+  
+}
+#### Done
+
+###sink(stdout(),append=T,type="message")
+builtin_gmt=""
+history_gmt=""
+doDESeq2 = $DESeq2.doDESeq2 # make these T or F
+doVoom = $doVoom
+doCamera = F 
+doedgeR = $edgeR.doedgeR
+edgeR_priordf = 0
+
+#if $DESeq2.doDESeq2 == "T"
+  DESeq_fitType = "$DESeq2.DESeq_fitType"
+#end if
+#if $edgeR.doedgeR == "T"
+edgeR_priordf = $edgeR.edgeR_priordf
+#end if
+
+
+Out_Dir = "$html_file.files_path"
+Input =  "$input1"
+TreatmentName = "$treatment_name"
+TreatmentCols = "$Treat_cols"
+ControlName = "$control_name"
+ControlCols= "$Control_cols"
+outputfilename = "$outtab"
+org = "$input1.dbkey"
+if (org == "") { org = "hg19"}
+fdrtype = "$fdrtype"
+fdrthresh = $fdrthresh
+useNDF = "$useNDF"
+fQ = $fQ # non-differential centile cutoff
+myTitle = "$title"
+subjects = c($subjectids)
+nsubj = length(subjects)
+if (nsubj > 0) {
+if (doDESeq2) {
+ print('WARNING - cannot yet use DESeq2 for 2 way anova - see the docs')
+ doDESeq2 = F
+ }
+}
+TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1
+CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1 
+cat('Got TCols=')
+cat(TCols)
+cat('; CCols=')
+cat(CCols)
+cat('\n')
+useCols = c(TCols,CCols)
+if (file.exists(Out_Dir) == F) dir.create(Out_Dir)
+Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header
+snames = colnames(Count_Matrix)
+nsamples = length(snames)
+if (nsubj >  0 & nsubj != nsamples) {
+options("show.error.messages"=T)
+mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','),
+   'has length',nsubj,'but there are',nsamples,'samples',paste(snames,collapse=','))
+write(mess, stderr())
+quit(save="no",status=4)
+}
+
+Count_Matrix = Count_Matrix[,useCols] ### reorder columns
+if (length(subjects) != 0) {subjects = subjects[useCols]}
+rn = rownames(Count_Matrix)
+islib = rn %in% c('librarySize','NotInBedRegions')
+LibSizes = Count_Matrix[subset(rn,islib),][1] # take first
+Count_Matrix = Count_Matrix[subset(rn,! islib),]
+group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) )             #Build a group descriptor
+group = factor(group, levels=c(ControlName,TreatmentName))
+colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")                   #Relable columns
+results = edgeIt(Count_Matrix=Count_Matrix,group=group,outputfilename=outputfilename,
+                 fdrtype='BH',priordf=edgeR_priordf,fdrthresh=0.05,outputdir='.',
+                 myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=c(),
+                 doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,
+                 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType)
+sessionInfo()
+]]>
+</configfile>
+</configfiles>
+<help>
+
+----
+
+**What it does**
+
+Allows short read sequence counts from controlled experiments to be analysed for differentially expressed genes.
+Optionally adds a term for subject if not all samples are independent or if some other factor needs to be blocked in the design.
+
+**Input**
+
+Requires a count matrix as a tabular file. These are best made using the companion HTSeq_ based counter Galaxy wrapper
+and your fave gene model to generate inputs. Each row is a genomic feature (gene or exon eg) and each column the 
+non-negative integer count of reads from one sample overlapping the feature. 
+The matrix must have a header row uniquely identifying the source samples, and unique row names in 
+the first column. Typically the row names are gene symbols or probe ids for downstream use in GSEA and other methods.
+
+**Specifying comparisons**
+
+This is basically dumbed down for two factors - case vs control.
+
+More complex interfaces are possible but painful at present. 
+Probably need to specify a phenotype file to do this better.
+Work in progress. Send code.
+
+If you have (eg) paired samples and wish to include a term in the GLM to account for some other factor (subject in the case of paired samples),
+put a comma separated list of indicators for every sample (whether modelled or not!) indicating (eg) the subject number or 
+A list of integers, one for each subject or an empty string if samples are all independent.
+If not empty, there must be exactly as many integers in the supplied integer list as there are columns (samples) in the count matrix.
+Integers for samples that are not in the analysis *must* be present in the string as filler even if not used.
+
+So if you have 2 pairs out of 6 samples, you need to put in unique integers for the unpaired ones
+eg if you had 6 samples with the first two independent but the second and third pairs each being from independent subjects. you might use
+8,9,1,1,2,2 
+as subject IDs to indicate two paired samples from the same subject in columns 3/4 and 5/6
+
+**Methods available**
+
+You can run 3 popular Bioconductor packages available for count data.
+
+edgeR - see edgeR_ for details
+
+VOOM/limma - see limma_VOOM_ for details
+
+DESeq2 - see DESeq2_ for details
+
+and optionally camera in edgeR which works better if MSigDB is installed.
+
+**Outputs**
+
+Some helpful plots and analysis results. Note that most of these are produced using R code 
+suggested by the excellent documentation and vignettes for the Bioconductor
+packages invoked. The Tool Factory is used to automatically lay these out for you to enjoy.
+
+***old rant on changes to Bioconductor package variable names between versions***
+
+The edgeR authors made a small cosmetic change in the name of one important variable (from p.value to PValue) 
+breaking this and all other code that assumed the old name for this variable, 
+between edgeR2.4.4 and 2.4.6 (the version for R 2.14 as at the time of writing). 
+This means that all code using edgeR is sensitive to the version. I think this was a very unwise thing 
+to do because it wasted hours of my time to track down and will similarly cost other edgeR users dearly
+when their old scripts break. This tool currently now works with 2.4.6.
+
+**Note on prior.N**
+
+http://seqanswers.com/forums/showthread.php?t=5591 says:
+
+*prior.n*
+
+The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion. 
+You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood 
+in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your 
+tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the 
+common likelihood the weight of one observation.
+
+In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value, 
+or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that 
+you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation 
+(squeezing) of the tagwise dispersions. How many samples do you have in your experiment? 
+What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10. 
+If you have more samples, then the tagwise dispersion estimates will be more reliable, 
+so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5. 
+
+
+From Bioconductor Digest, Vol 118, Issue 5, Gordon writes:
+
+Dear Dorota,
+
+The important settings are prior.df and trend.
+
+prior.n and prior.df are related through prior.df = prior.n * residual.df,
+and your experiment has residual.df = 36 - 12 = 24.  So the old setting of
+prior.n=10 is equivalent for your data to prior.df = 240, a very large
+value.  Going the other way, the new setting of prior.df=10 is equivalent
+to prior.n=10/24.
+
+To recover old results with the current software you would use
+
+  estimateTagwiseDisp(object, prior.df=240, trend="none")
+
+To get the new default from old software you would use
+
+  estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE)
+
+Actually the old trend method is equivalent to trend="loess" in the new
+software. You should use plotBCV(object) to see whether a trend is
+required.
+
+Note you could also use
+
+  prior.n = getPriorN(object, prior.df=10)
+
+to map between prior.df and prior.n.
+
+----
+
+**Attributions**
+
+edgeR - edgeR_ 
+
+VOOM/limma - limma_VOOM_ 
+
+DESeq2 - DESeq2_ for details
+
+See above for Bioconductor package documentation for packages exposed in Galaxy by this tool and app store package.
+
+Galaxy_ (that's what you are using right now!) for gluing everything together 
+
+Otherwise, all code and documentation comprising this tool was written by Ross Lazarus and is 
+licensed to you under the LGPL_ like other rgenetics artefacts
+
+.. _LGPL: http://www.gnu.org/copyleft/lesser.html
+.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
+.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
+.. _DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
+.. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html
+.. _Galaxy: http://getgalaxy.org
+</help>
+
+</tool>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/test-data/edgeRtest1out.html	Fri Jul 26 23:50:59 2013 -0400
@@ -0,0 +1,813 @@
+<!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 rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" /> 
+        <title></title> 
+        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
+        </head> 
+        <body> 
+        <div class="toolFormBody"> 
+        
+<div class="infomessage">Galaxy Tool "edgeR" run at 12/06/2013 16:42:51</div><br/>
+<div><table class="simple" cellpadding="2" cellspacing="2">
+<tr>
+<td><a href="edgeRtest_BCV_vs_abundance.pdf"><img src="edgeRtest_BCV_vs_abundance.jpg" title="Click to download a PDF of edgeRtest_BCV_vs_abundance.pdf" hspace="5" width="400" 
+                       alt="Image called edgeRtest_BCV_vs_abundance.pdf"/></a></td>
+
+<td><a href="edgeRtest_MDSplot.pdf"><img src="edgeRtest_MDSplot.jpg" title="Click to download a PDF of edgeRtest_MDSplot.pdf" hspace="5" width="400" 
+                       alt="Image called edgeRtest_MDSplot.pdf"/></a></td>
+
+<td><a href="edgeRtest_RowsumCum.pdf"><img src="edgeRtest_RowsumCum.jpg" title="Click to download a PDF of edgeRtest_RowsumCum.pdf" hspace="5" width="400" 
+                       alt="Image called edgeRtest_RowsumCum.pdf"/></a></td>
+</tr>
+<tr>
+<td><a href="edgeRtest_Smearplot.pdf"><img src="edgeRtest_Smearplot.jpg" title="Click to download a PDF of edgeRtest_Smearplot.pdf" hspace="5" width="400" 
+                       alt="Image called edgeRtest_Smearplot.pdf"/></a></td>
+
+<td><a href="edgeRtest_heatmap.pdf"><img src="edgeRtest_heatmap.jpg" title="Click to download a PDF of edgeRtest_heatmap.pdf" hspace="5" width="400" 
+                       alt="Image called edgeRtest_heatmap.pdf"/></a></td>
+
+<td><a href="edgeRtest_pval_qq.pdf"><img src="edgeRtest_pval_qq.jpg" title="Click to download a PDF of edgeRtest_pval_qq.pdf" hspace="5" width="400" 
+                       alt="Image called edgeRtest_pval_qq.pdf"/></a></td>
+</tr>
+<tr>
+<td><a href="edgeRtest_sampleBoxplot.pdf"><img src="edgeRtest_sampleBoxplot.jpg" title="Click to download a PDF of edgeRtest_sampleBoxplot.pdf" hspace="5" width="400" 
+                       alt="Image called edgeRtest_sampleBoxplot.pdf"/></a></td>
+
+<td><a href="edgeRtest_samplehistplot.pdf"><img src="edgeRtest_samplehistplot.jpg" title="Click to download a PDF of edgeRtest_samplehistplot.pdf" hspace="5" width="400" 
+                       alt="Image called edgeRtest_samplehistplot.pdf"/></a></td>
+
+<td><a href="edgeRtest_venn.pdf"><img src="edgeRtest_venn.jpg" title="Click to download a PDF of edgeRtest_venn.pdf" hspace="5" width="400" 
+                       alt="Image called edgeRtest_venn.pdf"/></a></td>
+</tr>
+<tr>
+<td><a href="edgeRtest_voomplot.pdf"><img src="edgeRtest_voomplot.jpg" title="Click to download a PDF of edgeRtest_voomplot.pdf" hspace="5" width="400" 
+                       alt="Image called edgeRtest_voomplot.pdf"/></a></td>
+
+<td>&nbsp;</td><td>&nbsp;</td>
+</tr></table></div>
+
+<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
+
+<tr><td><a href="edgeR.Rscript">edgeR.Rscript</a></td><td>19.7 KB)</td></tr>
+<tr class="odd_row"><td><a href="edgeR_runner.log">edgeR_runner.log</a></td><td>79.2 KB)</td></tr>
+<tr><td><a href="edgeRtest_BCV_vs_abundance.pdf">edgeRtest_BCV_vs_abundance.pdf</a></td><td>16.4 KB)</td></tr>
+<tr class="odd_row"><td><a href="edgeRtest_DESeq_TopTable.xls">edgeRtest_DESeq_TopTable.xls</a></td><td>135.1 KB)</td></tr>
+<tr><td><a href="edgeRtest_MDSplot.pdf">edgeRtest_MDSplot.pdf</a></td><td>4.9 KB)</td></tr>
+<tr class="odd_row"><td><a href="edgeRtest_RowsumCum.pdf">edgeRtest_RowsumCum.pdf</a></td><td>6.3 KB)</td></tr>
+<tr><td><a href="edgeRtest_Smearplot.pdf">edgeRtest_Smearplot.pdf</a></td><td>16.7 KB)</td></tr>
+<tr class="odd_row"><td><a href="edgeRtest_VOOM_topTable.xls">edgeRtest_VOOM_topTable.xls</a></td><td>131.4 KB)</td></tr>
+<tr><td><a href="edgeRtest_heatmap.pdf">edgeRtest_heatmap.pdf</a></td><td>11.3 KB)</td></tr>
+<tr class="odd_row"><td><a href="edgeRtest_pval_qq.pdf">edgeRtest_pval_qq.pdf</a></td><td>15.9 KB)</td></tr>
+<tr><td><a href="edgeRtest_sampleBoxplot.pdf">edgeRtest_sampleBoxplot.pdf</a></td><td>7.8 KB)</td></tr>
+<tr class="odd_row"><td><a href="edgeRtest_samplehistplot.pdf">edgeRtest_samplehistplot.pdf</a></td><td>10.9 KB)</td></tr>
+<tr><td><a href="edgeRtest_venn.pdf">edgeRtest_venn.pdf</a></td><td>9.7 KB)</td></tr>
+<tr class="odd_row"><td><a href="edgeRtest_voomplot.pdf">edgeRtest_voomplot.pdf</a></td><td>16.7 KB)</td></tr>
+</table></div><br/>
+<div class="toolFormTitle">Rscript log</div><pre>
+
+## Toolfactory generated command line = Rscript - None /data/home/rlazarus/galaxy-central/database/files/000/dataset_2.dat
+
+Loading required package: gtools
+
+Loading required package: gdata
+
+gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
+
+gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
+
+Attaching package: ‘gdata’
+
+The following object(s) are masked from ‘package:stats’:
+
+    nobs
+
+The following object(s) are masked from ‘package:utils’:
+
+    object.size
+
+Loading required package: caTools
+
+Loading required package: grid
+
+Loading required package: KernSmooth
+
+KernSmooth 2.23 loaded
+
+Copyright M. P. Wand 1997-2009
+
+Loading required package: MASS
+
+Attaching package: ‘gplots’
+
+The following object(s) are masked from ‘package:stats’:
+
+    lowess
+
+Loading required package: Biobase
+
+Loading required package: BiocGenerics
+
+Loading required package: methods
+
+Attaching package: ‘BiocGenerics’
+
+The following object(s) are masked from ‘package:gdata’:
+
+    combine
+
+The following object(s) are masked from ‘package:stats’:
+
+    xtabs
+
+The following object(s) are masked from ‘package:base’:
+
+    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
+
+    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
+
+    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
+
+    rownames, sapply, setdiff, table, tapply, union, unique
+
+Welcome to Bioconductor
+
+    Vignettes contain introductory material; view with
+
+    'browseVignettes()'. To cite Bioconductor, see
+
+    'citation("Biobase")', and for packages 'citation("pkgname")'.
+
+Loading required package: locfit
+
+locfit 1.5-9.1 	 2013-03-22
+
+Loading required package: lattice
+
+Warning message:
+
+found methods to import for function ‘eapply’ but not the generic itself 
+
+Loading required package: limma
+
+Attaching package: ‘limma’
+
+The following object(s) are masked from ‘package:DESeq’:
+
+    plotMA
+
+# got TCols=2 3 4 8; CCols=1 5 6 7
+
+[1] # Quantiles for non-zero row counts:
+
+       0%       10%       20%       30%       40%       50%       60%       70%       80%       90%      100% 
+
+      1.0       1.0       2.0       3.0       4.0       8.0      13.0      24.0      86.6     753.0 2325567.0 
+
+[1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs
+
+[1] # Total low count contigs per sample =  145,111,155,120,170,67,203,86
+
+Calculating library sizes from column totals.
+
+[1] Using samples: case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam,case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam,case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam,case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam,control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam,control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam,control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam,control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam
+
+[1] Using design matrix:
+
+  (Intercept) groupcase
+
+1           1         1
+
+2           1         1
+
+3           1         1
+
+4           1         1
+
+5           1         0
+
+6           1         0
+
+7           1         0
+
+8           1         0
+
+attr(,"assign")
+
+[1] 0 1
+
+attr(,"contrasts")
+
+attr(,"contrasts")$group
+
+[1] contr.treatment
+
+[1] "No GLM fit outlier genes found\n"
+
+[1] Common Dispersion = 0.24088423096811 CV =  0.490799583300669 getPriorN =  3.33333333333333
+
+[1] "Raw sample read totals 1440960,1341813,2888924,1428365,2443751,1644652,1682104,1806045"
+
+[1] raw contig counts by sample:
+
+ case_X11706He_AGTTCC case_X11699He_GGCTAC case_X11698He_TAGCTT case_X11700He_CTTGTA control_X11706Liv_CA control_X11700Liv_AT control_X11698Liv_AC control_X11699Liv_AT
+
+ Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043      
+
+ 1st Qu.:0.0043       1st Qu.:0.0043       1st Qu.:0.0043       1st Qu.:0.0043       1st Qu.:0.3032       1st Qu.:0.0043       1st Qu.:0.3032       1st Qu.:0.0043      
+
+ Median :0.4786       Median :0.4786       Median :0.4786       Median :0.4786       Median :0.7789       Median :0.6031       Median :0.6998       Median :0.6031      
+
+ Mean   :0.9210       Mean   :0.9428       Mean   :1.0205       Mean   :0.9753       Mean   :1.0519       Mean   :1.0343       Mean   :0.9855       Mean   :0.9966      
+
+ 3rd Qu.:1.5770       3rd Qu.:1.5855       3rd Qu.:1.7161       3rd Qu.:1.6022       3rd Qu.:1.5410       3rd Qu.:1.6335       3rd Qu.:1.4473       3rd Qu.:1.5534      
+
+ Max.   :5.3609       Max.   :5.3589       Max.   :5.6967       Max.   :5.3702       Max.   :5.8209       Max.   :5.6905       Max.   :5.7999       Max.   :5.7215      
+
+ NA's   :902          NA's   :957          NA's   :821          NA's   :950          NA's   :650          NA's   :969          NA's   :664          NA's   :886         
+
+[1] normalised contig counts by sample:
+
+ case_X11706He_AGTTCC case_X11699He_GGCTAC case_X11698He_TAGCTT case_X11700He_CTTGTA control_X11706Liv_CA control_X11700Liv_AT control_X11698Liv_AC control_X11699Liv_AT
+
+ Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf        
+
+ 1st Qu.:-Inf         1st Qu.:-Inf         1st Qu.:-Inf         1st Qu.:-Inf         1st Qu.:   0         1st Qu.:-Inf         1st Qu.:   0         1st Qu.:-Inf        
+
+ Median :   0         Median :   0         Median :   0         Median :   0         Median :   0         Median :   0         Median :   0         Median :   0        
+
+ Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf        
+
+ 3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1        
+
+ Max.   :   5         Max.   :   5         Max.   :   6         Max.   :   5         Max.   :   6         Max.   :   6         Max.   :   6         Max.   :   5        
+
+[1] Using ncol rawrs= 8
+
+[1] # writing output
+
+[1] # urls
+
+<a href='http://www.genecards.org/index.php?path=/Search/keyword/0610005C13Rik'></a>0610005C13Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610007N19Rik'></a>0610007N19Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610008F07Rik'></a>0610008F07Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610009L18Rik'></a>0610009L18Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610012G03Rik'></a>0610012G03Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'></a>0610031O16Rik</a># Top tags
+
+                       Name      logFC    logCPM        LR       PValue  adj.p.value Dispersion totreads case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam
+
+Mir122a             Mir122a -10.661348 12.537949 445.91203 5.594743e-99 6.383602e-96 0.10205510    90428                                                   6.644669                                               2.864648e+00                                               2.012369e+01                                               4.756523e+00                                                   2.084166e+04                                                   1.681895e+04
+
+Mir192               Mir192  -7.109019 17.247415 366.13166 1.301558e-81 7.425390e-79 0.07765487  2325567                                                1779.663879                                               1.294412e+03                                               4.493546e+03                                               1.933526e+03                                                   4.635990e+05                                                   3.403123e+05
+
+Mir208b             Mir208b  13.423720  9.822338 355.41782 2.801296e-79 1.065426e-76 0.12444059    14756                                                1245.907022                                               5.701390e+02                                               4.930344e+03                                               8.819024e+02                                                   7.453220e-01                                                   0.000000e+00
+
+Mir208a             Mir208a  11.977586  8.388290 348.81540 7.675451e-78 2.189422e-75 0.09936798     4638                                                 433.789590                                               7.125278e+02                                               1.006599e+03                                               6.497485e+02                                                   0.000000e+00                                                   0.000000e+00
+
+Mir499               Mir499  14.488216  8.612770 291.12794 2.823507e-65 6.443244e-63 0.13481620     6527                                                 608.439028                                               5.066577e+02                                               2.521609e+03                                               2.703574e+02                                                   0.000000e+00                                                   0.000000e+00
+
+Mir149               Mir149   6.869731  8.785665 253.01986 5.702930e-57 1.084507e-54 0.09834684     6164                                                 774.657675                                               4.595714e+02                                               1.710514e+03                                               7.663947e+02                                                   1.750400e+01                                                   6.246465e+00
+
+Mir490               Mir490   8.453930  6.909596 251.05610 1.528281e-56 2.491098e-54 0.09745005     1741                                                 209.881557                                               2.177498e+02                                               5.205387e+02                                               1.957941e+02                                                   1.038505e+00                                                   5.537224e-01
+
+Mir802               Mir802 -12.499678  6.629391 237.56161 1.337812e-53 1.908055e-51 0.10939981     1514                                                   0.000000                                               0.000000e+00                                               0.000000e+00                                               0.000000e+00                                                   3.056548e+02                                                   1.641034e+02
+
+Mir204               Mir204   7.371179  7.558996 237.12302 1.667365e-53 2.113848e-51 0.10292005     2601                                                 425.578854                                               3.264164e+02                                               6.462477e+02                                               3.754819e+02                                                   3.040281e+00                                                   6.923364e-01
+
+Mir1948             Mir1948  -7.583326  7.293456 204.79641 1.875897e-46 2.140399e-44 0.11833999     2404                                                   1.216112                                               6.923364e-01                                               1.661167e+00                                               1.636942e+00                                                   6.476848e+02                                                   3.852783e+02
+
+Mir3073             Mir3073 -11.748556  5.881462 200.03350 2.053625e-45 2.130170e-43 0.11068562      904                                                   0.000000                                               0.000000e+00                                               0.000000e+00                                               0.000000e+00                                                   2.073471e+02                                                   7.546467e+01
+
+Mir194-2           Mir194-2  -5.439827  7.860048 165.57239 6.859199e-38 6.521955e-36 0.10671020     3570                                                  10.520726                                               6.138532e+00                                               1.490644e+01                                               9.513045e+00                                                   9.214105e+02                                                   6.003547e+02
+
+Mir10b               Mir10b   5.032898 13.880770 160.06580 1.094640e-36 9.607570e-35 0.10795434   197340                                               25838.822630                                               3.216361e+04                                               3.631730e+04                                               3.446522e+04                                                   1.825385e+03                                                   3.738617e+02
+
+Mir101b             Mir101b  -3.925287 11.936090 120.62427 4.618143e-28 3.763787e-26 0.09663075    59019                                                 219.816815                                               3.012250e+02                                               8.119232e+02                                               4.270695e+02                                                   1.014507e+04                                                   7.747970e+03
+
+Mir182               Mir182  -5.244384  8.942708 118.92815 1.085926e-27 8.260276e-26 0.14993443     7189                                                  16.962242                                               1.439678e+01                                               2.209871e+01                                               3.130352e+01                                                   9.840056e+02                                                   6.154406e+02
+
+Mir200b             Mir200b  -6.725348  5.765187 115.73189 5.440989e-27 3.880105e-25 0.16712490      888                                                   2.432225                                               0.000000e+00                                               1.661167e+00                                               0.000000e+00                                                   3.696797e+02                                                   9.750871e+01
+
+Mir181c             Mir181c   3.611867 10.569815 107.82011 2.943153e-25 1.975375e-23 0.09385270    23605                                                2420.852087                                               1.892879e+03                                               4.093093e+03                                               1.902590e+03                                                   2.320365e+02                                                   2.727878e+02
+
+Mir181d             Mir181d   3.489976  7.232064 102.18661 5.053019e-24 3.203053e-22 0.08738498     2139                                                 310.053946                                               2.021522e+02                                               5.398233e+02                                               2.956660e+02                                                   3.648337e+01                                                   1.453906e+01
+
+Mir21                 Mir21  -3.077771 13.881500  91.37324 1.189745e-21 7.144733e-20 0.08494272   229120                                                3207.212585                                               2.190826e+03                                               4.348911e+03                                               2.010566e+03                                                   2.715400e+04                                                   3.322794e+04
+
+Mir199b             Mir199b   5.411476  4.695869  86.70372 1.260596e-20 7.191701e-19 0.15656183      370                                                  43.403268                                               4.481024e+01                                               9.924938e+01                                               4.925255e+01                                                   1.384673e+00                                                   5.537224e-01
+
+Mir193               Mir193  -5.360157  4.775477  84.66127 3.541205e-20 1.924055e-18 0.15546497      421                                                   1.490644                                               1.189131e+00                                               2.800640e+00                                               6.940516e-01                                                   1.015454e+02                                                   3.496299e+01
+
+Mir23a               Mir23a   3.003071  9.467420  82.28684 1.177029e-19 6.104501e-18 0.08920345    10118                                                1149.889322                                               1.127958e+03                                               2.471518e+03                                               1.096325e+03                                                   1.505832e+02                                                   1.268024e+02
+
+Mir195               Mir195   3.060546  8.152797  81.39727 1.846126e-19 9.158392e-18 0.09133016     3962                                                 429.134881                                               2.831909e+02                                               9.227086e+02                                               4.708957e+02                                                   1.106253e+02                                                   7.773378e+01
+
+Ahsg                   Ahsg -10.101343  6.638589  79.82133 4.098447e-19 1.923759e-17 0.42092199     1524                                                   0.000000                                               5.537224e-01                                               0.000000e+00                                               0.000000e+00                                                   3.484153e+02                                                   1.260288e+01
+
+Mir148a             Mir148a  -2.789375 16.047169  79.76589 4.215073e-19 1.923759e-17 0.08196054  1002397                                               15925.598251                                               8.528200e+03                                               2.207082e+04                                               1.059020e+04                                                   1.927239e+05                                                   1.054456e+05
+
+Dnm3os               Dnm3os   3.189443  6.618834  79.19614 5.623979e-19 2.468062e-17 0.09496531     1401                                                 134.000827                                               8.716715e+01                                               3.652078e+02                                               1.825316e+02                                                   3.710848e+01                                                   2.498586e+01
+
+Mir27a               Mir27a   2.921772 10.581277  77.26988 1.491231e-18 6.301832e-17 0.09125059    21886                                                2383.612353                                               2.512174e+03                                               5.321988e+03                                               2.361690e+03                                                   3.285136e+02                                                   3.477377e+02
+
+Mir429               Mir429  -5.341934  4.951103  76.38758 2.331128e-18 9.499346e-17 0.18324117      499                                                   1.783696                                               7.001600e-01                                               2.082155e+00                                               1.824168e+00                                                   9.173458e+01                                                   4.540524e+01
+
+Mir214               Mir214   3.125906  6.202347  74.28213 6.771387e-18 2.664191e-16 0.09532762     1048                                                 110.058161                                               5.642542e+01                                               1.982326e+02                                               9.371492e+01                                                   3.353949e+01                                                   1.545870e+01
+
+Mir200a             Mir200a  -7.592263  4.059943  73.71426 9.028450e-18 3.433821e-16 0.22417820      264                                                   0.000000                                               0.000000e+00                                               5.945653e-01                                               0.000000e+00                                                   9.022671e+01                                                   3.222698e+01
+
+Mir194-1           Mir194-1  -3.970219  5.393899  73.22380 1.157517e-17 4.260408e-16 0.13095886      635                                                   3.567392                                               9.102080e+00                                               5.552413e+00                                               3.648337e+00                                                   7.615701e+01                                                   8.859559e+01
+
+Mir378               Mir378   2.954320  8.053368  73.09647 1.234655e-17 4.402315e-16 0.09566655     4075                                                 425.697272                                               3.921392e+02                                               1.155915e+03                                               1.883155e+02                                                   7.641369e+01                                                   3.683119e+01
+
+Mir322               Mir322   3.058569  8.948242  72.83721 1.407969e-17 4.868160e-16 0.10365695     7074                                                1012.892580                                               6.718588e+02                                               1.784708e+03                                               8.550716e+02                                                   1.587027e+02                                                   7.892635e+01
+
+Mir215               Mir215   2.908934  6.381924  70.31105 5.065317e-17 1.699861e-15 0.09002036     1182                                                 123.075020                                               1.610368e+02                                               2.727623e+02                                               1.222193e+02                                                   1.938542e+01                                                   1.716540e+01
+
+Cyp3a25             Cyp3a25  -9.778602  3.913257  70.02642 5.851533e-17 1.907600e-15 0.26445237      226                                                   0.000000                                               0.000000e+00                                               0.000000e+00                                               0.000000e+00                                                   5.664447e+01                                                   1.783696e+01
+
+Mir183               Mir183  -4.214462  5.247929  66.31101 3.851010e-16 1.220556e-14 0.15955164      563                                                   8.401920                                               1.388103e+00                                               2.432225e+00                                               2.423177e+00                                                   8.638070e+01                                                   2.905572e+01
+
+Mir181a-2         Mir181a-2   2.837713  7.573798  65.52900 5.726500e-16 1.765929e-14 0.09834030     2817                                                 288.826664                                               1.377749e+02                                               6.395494e+02                                               1.821098e+02                                                   5.813511e+01                                                   4.102501e+01
+
+Mir155               Mir155   3.734310  4.975364  65.07600 7.206449e-16 2.163831e-14 0.13295455      463                                                  33.966543                                               5.888044e+01                                               1.141565e+02                                               5.251200e+01                                                   9.716723e+00                                                   1.824168e+00
+
+Snord91a           Snord91a  -2.818342  6.592251  64.29345 1.072014e-15 3.136329e-14 0.09422446     1437                                                  13.846728                                               1.605795e+01                                               3.314807e+01                                               1.863305e+01                                                   2.158272e+02                                                   1.792410e+02
+
+Mir125b-2         Mir125b-2   2.852233  8.081093  64.20822 1.119409e-15 3.193115e-14 0.10276578     3837                                                 315.520541                                               4.404853e+02                                               7.634219e+02                                               4.852109e+02                                                   1.082721e+02                                                   9.060036e+01
+
+Serpina4-ps1   Serpina4-ps1 -10.090564  4.224051  64.02094 1.231040e-15 3.425894e-14 0.34406452      295                                                   0.000000                                               0.000000e+00                                               0.000000e+00                                               0.000000e+00                                                   1.080717e+02                                                   1.129674e+01
+
+Mir133b             Mir133b   9.293392  3.404704  63.59576 1.527577e-15 4.149919e-14 0.26404392      159                                                  17.719118                                               1.064012e+01                                               5.738979e+01                                               1.426957e+01                                                   0.000000e+00                                                   0.000000e+00
+
+Gm10069             Gm10069  -7.475459  6.400326  63.15445 1.911172e-15 5.071271e-14 0.41541432     1309                                                   1.189131                                               1.400320e+00                                               6.940516e-01                                               6.080561e-01                                                   1.914310e+02                                                   6.644669e+00
+
+Mir871               Mir871  -5.633588  4.283233  62.67513 2.437746e-15 6.321517e-14 0.21907826      290                                                   1.227706                                               7.453220e-01                                               5.945653e-01                                               0.000000e+00                                                   5.691223e+01                                                   4.925255e+01
+
+Mir184               Mir184   5.002968  4.123691  61.97642 3.475940e-15 8.813439e-14 0.19289992      247                                                  33.443087                                               1.419290e+01                                               4.983502e+01                                               2.168948e+01                                                   2.981288e+00                                                   0.000000e+00
+
+Mir132               Mir132   2.702863  5.866134  58.80773 1.738573e-14 4.312416e-13 0.09148478      857                                                  82.695634                                               4.327103e+01                                               1.821747e+02                                               6.097608e+01                                                   2.832224e+01                                                   1.308044e+01
+
+Snord104           Snord104  -2.492063 11.108871  58.55547 1.976394e-14 4.798012e-13 0.09093023    33458                                                 614.929745                                               4.378004e+02                                               8.629974e+02                                               5.144081e+02                                                   3.826761e+03                                                   4.181256e+03
+
+Mir3074-2         Mir3074-2   2.635505  7.871042  57.72938 3.007773e-14 7.149726e-13 0.09900198     3470                                                 450.903031                                               3.206519e+02                                               8.354691e+02                                               1.716994e+02                                                   8.970303e+01                                                   5.197290e+01
+
+Mir24-2             Mir24-2   2.635505  7.871042  57.68174 3.081509e-14 7.175515e-13 0.09908656     3470                                                 479.987359                                               2.746892e+02                                               9.620198e+02                                               3.442496e+02                                                   9.850509e+01                                                   4.396336e+01
+
+5430416N02Rik 5430416N02Rik  -3.267228  5.202367  56.75137 4.945455e-14 1.128553e-12 0.12456687      564                                                   6.080561                                               1.730841e+00                                               1.273562e+01                                               4.910826e+00                                                   1.453378e+02                                                   5.886197e+01
+
+              control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam
+
+Mir122a                                                         7.242557e+03                                                   8.468313e+03                                                         12                                                          7                                                         27                                                          8                                                          29767
+
+Mir192                                                          3.835916e+05                                                   1.822922e+05                                                       3214                                                       3163                                                       6029                                                       3252                                                         662133
+
+Mir208b                                                         0.000000e+00                                                   0.000000e+00                                                       2049                                                       1647                                                       8904                                                       2155                                                              1
+
+Mir208a                                                         0.000000e+00                                                   5.537224e-01                                                       1060                                                        956                                                       1693                                                        928                                                              0
+
+Mir499                                                          0.000000e+00                                                   0.000000e+00                                                        869                                                        730                                                       4147                                                        781                                                              0
+
+Mir149                                                          4.864449e+00                                                   5.538691e+00                                                       1399                                                       1123                                                       2295                                                       1289                                                             25
+
+Mir490                                                          0.000000e+00                                                   7.453220e-01                                                        353                                                        311                                                        750                                                        322                                                              3
+
+Mir802                                                          1.557723e+02                                                   2.092870e+02                                                          0                                                          0                                                          0                                                          0                                                            552
+
+Mir204                                                          5.537224e-01                                                   3.683119e+00                                                        571                                                        549                                                        923                                                        541                                                              5
+
+Mir1948                                                         1.813414e+02                                                   4.282299e+02                                                          2                                                          2                                                          3                                                          4                                                            869
+
+Mir3073                                                         7.253764e+01                                                   8.757639e+01                                                          0                                                          0                                                          0                                                          0                                                            341
+
+Mir194-2                                                        2.669366e+02                                                   3.046280e+02                                                         19                                                         15                                                         20                                                         16                                                           1316
+
+Mir10b                                                          6.583760e+02                                                   7.272114e+02                                                      34668                                                      54096                                                      51870                                                      49658                                                           3002
+
+Mir101b                                                         1.128042e+04                                                   6.628420e+03                                                        635                                                        544                                                       1984                                                        573                                                          17063
+
+Mir182                                                          2.366022e+03                                                   6.536603e+02                                                         49                                                         26                                                         54                                                         42                                                           1655
+
+Mir200b                                                         4.621056e+01                                                   1.075780e+02                                                          4                                                          0                                                          3                                                          0                                                            496
+
+Mir181c                                                         2.283131e+02                                                   2.989683e+02                                                       3488                                                       3113                                                      11824                                                       3436                                                            567
+
+Mir181d                                                         2.547123e+01                                                   1.555095e+01                                                        416                                                        340                                                        771                                                        426                                                             60
+
+Mir21                                                           2.570722e+04                                                   3.537908e+04                                                       4621                                                       3603                                                      12563                                                       3631                                                          66353
+
+Mir199b                                                         0.000000e+00                                                   2.981288e+00                                                         73                                                         64                                                        143                                                         81                                                              4
+
+Mir193                                                          3.377707e+01                                                   3.396654e+01                                                          2                                                          2                                                          4                                                          1                                                            167
+
+Mir23a                                                          8.921333e+01                                                   2.437203e+02                                                       1934                                                       1611                                                       3561                                                       1803                                                            435
+
+Mir195                                                          4.560421e+01                                                   4.154019e+01                                                        775                                                        692                                                       1238                                                        792                                                            158
+
+Ahsg                                                            6.100714e+02                                                   2.432225e+01                                                          0                                                          1                                                          0                                                          0                                                            586
+
+Mir148a                                                         1.795497e+05                                                   1.342747e+05                                                      26191                                                      24636                                                      39859                                                      25878                                                         258578
+
+Dnm3os                                                          1.216112e+01                                                   1.384673e+01                                                        242                                                        213                                                        490                                                        307                                                             53
+
+Mir27a                                                          1.636942e+02                                                   5.664447e+02                                                       4009                                                       3588                                                       7668                                                       3884                                                            949
+
+Mir429                                                          1.677865e+01                                                   7.527752e+01                                                          3                                                          1                                                          3                                                          3                                                            265
+
+Mir214                                                          1.190272e+01                                                   2.012750e+01                                                        181                                                        163                                                        358                                                        229                                                             45
+
+Mir200a                                                         1.142355e+01                                                   2.602495e+01                                                          0                                                          0                                                          1                                                          0                                                            130
+
+Mir194-1                                                        3.314807e+01                                                   1.050904e+02                                                          6                                                         13                                                          8                                                          6                                                            220
+
+Mir378                                                          9.167460e+01                                                   6.302392e+01                                                        608                                                        565                                                       1901                                                        544                                                            138
+
+Mir322                                                          5.038874e+01                                                   9.166874e+01                                                       1359                                                       1130                                                       2549                                                       1232                                                            261
+
+Mir215                                                          1.145859e+01                                                   2.683159e+01                                                        207                                                        230                                                        393                                                        201                                                             56
+
+Cyp3a25                                                         6.511488e+01                                                   1.873939e+01                                                          0                                                          0                                                          0                                                          0                                                             76
+
+Mir183                                                          1.349033e+02                                                   7.729349e+01                                                         12                                                          2                                                          4                                                          7                                                            156
+
+Mir181a-2                                                       8.051840e+01                                                   5.691223e+01                                                        475                                                        398                                                       1155                                                        445                                                             78
+
+Mir155                                                          2.769346e+00                                                   4.983502e+00                                                         83                                                         79                                                        192                                                         75                                                             14
+
+Snord91a                                                        2.484705e+02                                                   1.732960e+02                                                         40                                                         29                                                         81                                                         25                                                            363
+
+Mir125b-2                                                       2.077009e+01                                                   7.364508e+01                                                        771                                                        591                                                       1284                                                        693                                                            156
+
+Serpina4-ps1                                                    8.191872e+01                                                   9.716723e+00                                                          0                                                          0                                                          0                                                          0                                                            145
+
+Mir133b                                                         0.000000e+00                                                   0.000000e+00                                                         32                                                         26                                                         77                                                         24                                                              0
+
+Gm10069                                                         2.868741e+02                                                   2.757691e+01                                                          2                                                          2                                                          1                                                          1                                                            553
+
+Mir871                                                          1.003888e+01                                                   5.149619e+01                                                          3                                                          1                                                          1                                                          0                                                             82
+
+Mir184                                                          1.400320e+00                                                   1.388103e+00                                                         55                                                         41                                                         90                                                         53                                                              4
+
+Mir132                                                          2.100480e+01                                                   1.943345e+01                                                        136                                                        125                                                        329                                                        149                                                             38
+
+Snord104                                                        4.430701e+03                                                   4.212863e+03                                                        886                                                        720                                                       2493                                                        929                                                           9351
+
+Mir3074-2                                                       4.844593e+01                                                   8.323914e+01                                                        644                                                        462                                                       1374                                                        496                                                            162
+
+Mir24-2                                                         3.599196e+01                                                   5.729296e+01                                                        644                                                        462                                                       1374                                                        496                                                            162
+
+5430416N02Rik                                                   5.531264e+01                                                   9.786128e+01                                                         10                                                          5                                                         23                                                         12                                                            195
+
+              control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam ntotreads                                                                                                   URL
+
+Mir122a                                                                24233                                                          11911                                                          24463     90428             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'></a>Mir122a</a>
+
+Mir192                                                                490327                                                         630849                                                         526600   2325567               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'></a>Mir192</a>
+
+Mir208b                                                                    0                                                              0                                                              0     14756             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'></a>Mir208b</a>
+
+Mir208a                                                                    0                                                              0                                                              1      4638             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'></a>Mir208a</a>
+
+Mir499                                                                     0                                                              0                                                              0      6527               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'></a>Mir499</a>
+
+Mir149                                                                     9                                                              8                                                             16      6164               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'></a>Mir149</a>
+
+Mir490                                                                     1                                                              0                                                              1      1741               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'></a>Mir490</a>
+
+Mir802                                                                   401                                                            209                                                            352      1514               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'></a>Mir802</a>
+
+Mir204                                                                     2                                                              1                                                              9      2601               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'></a>Mir204</a>
+
+Mir1948                                                                  648                                                            259                                                            617      2404             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'></a>Mir1948</a>
+
+Mir3073                                                                  218                                                            131                                                            214       904             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'></a>Mir3073</a>
+
+Mir194-2                                                                 865                                                            439                                                            880      3570           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'></a>Mir194-2</a>
+
+Mir10b                                                                  1080                                                           1189                                                           1777    197340               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'></a>Mir10b</a>
+
+Mir101b                                                                11066                                                          16253                                                          10901     59019             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'></a>Mir101b</a>
+
+Mir182                                                                   879                                                           3409                                                           1075      7189               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'></a>Mir182</a>
+
+Mir200b                                                                  164                                                             66                                                            155       888             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'></a>Mir200b</a>
+
+Mir181c                                                                  366                                                            384                                                            427     23605             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'></a>Mir181c</a>
+
+Mir181d                                                                   42                                                             46                                                             38      2139             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'></a>Mir181d</a>
+
+Mir21                                                                  44582                                                          43237                                                          50530    229120                 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'></a>Mir21</a>
+
+Mir199b                                                                    1                                                              0                                                              4       370             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'></a>Mir199b</a>
+
+Mir193                                                                   101                                                             61                                                             83       421               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'></a>Mir193</a>
+
+Mir23a                                                                   229                                                            218                                                            327     10118               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'></a>Mir23a</a>
+
+Mir195                                                                   112                                                             75                                                            120      3962               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'></a>Mir195</a>
+
+Ahsg                                                                      18                                                            879                                                             40      1524                   <a href='http://www.genecards.org/index.php?path=/Search/keyword/Ahsg'></a>Ahsg</a>
+
+Mir148a                                                               177349                                                         256441                                                         193465   1002397             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'></a>Mir148a</a>
+
+Dnm3os                                                                    36                                                             20                                                             40      1401               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'></a>Dnm3os</a>
+
+Mir27a                                                                   628                                                            400                                                            760     21886               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'></a>Mir27a</a>
+
+Mir429                                                                    82                                                             41                                                            101       499               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir429'></a>Mir429</a>
+
+Mir214                                                                    26                                                             17                                                             29      1048               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'></a>Mir214</a>
+
+Mir200a                                                                   53                                                             33                                                             47       264             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'></a>Mir200a</a>
+
+Mir194-1                                                                 160                                                             81                                                            141       635           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-1'></a>Mir194-1</a>
+
+Mir378                                                                    90                                                            123                                                            106      4075               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'></a>Mir378</a>
+
+Mir322                                                                   228                                                             91                                                            224      7074               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'></a>Mir322</a>
+
+Mir215                                                                    31                                                             28                                                             36      1182               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'></a>Mir215</a>
+
+Cyp3a25                                                                   30                                                             93                                                             27       226             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'></a>Cyp3a25</a>
+
+Mir183                                                                    71                                                            181                                                            130       563               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir183'></a>Mir183</a>
+
+Mir181a-2                                                                 69                                                            115                                                             82      2817         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'></a>Mir181a-2</a>
+
+Mir155                                                                     3                                                              8                                                              9       463               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'></a>Mir155</a>
+
+Snord91a                                                                 256                                                            358                                                            285      1437           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'></a>Snord91a</a>
+
+Mir125b-2                                                                149                                                             60                                                            133      3837         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'></a>Mir125b-2</a>
+
+Serpina4-ps1                                                              19                                                            117                                                             14       295   <a href='http://www.genecards.org/index.php?path=/Search/keyword/Serpina4-ps1'></a>Serpina4-ps1</a>
+
+Mir133b                                                                    0                                                              0                                                              0       159             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'></a>Mir133b</a>
+
+Gm10069                                                                   12                                                            701                                                             37      1309             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10069'></a>Gm10069</a>
+
+Mir871                                                                    81                                                             29                                                             93       290               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir871'></a>Mir871</a>
+
+Mir184                                                                     0                                                              2                                                              2       247               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'></a>Mir184</a>
+
+Mir132                                                                    22                                                             30                                                             28       857               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'></a>Mir132</a>
+
+Snord104                                                                5610                                                           7452                                                           6017     33458           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'></a>Snord104</a>
+
+Mir3074-2                                                                127                                                             65                                                            140      3470         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'></a>Mir3074-2</a>
+
+Mir24-2                                                                  127                                                             65                                                            140      3470             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'></a>Mir24-2</a>
+
+5430416N02Rik                                                             99                                                             79                                                            141       564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'></a>5430416N02Rik</a>
+
+[1] # 445 tags significant at adj p= 0.05
+
+[1] # deTags
+
+[1] "0610005C13Rik" "0610007N19Rik" "0610008F07Rik" "0610012G03Rik" "0610031O16Rik" "1110038B12Rik"
+
+# DESeq top 50
+
+               id     baseMean    baseMeanA    baseMeanB   foldChange log2FoldChange         pval         padj
+
+536       Mir122a  10112.31117 2.021162e+04 1.300527e+01 6.434550e-04     -10.601873 5.488369e-57 6.262229e-54
+
+645       Mir208a    616.76981 2.430915e-01 1.233297e+03 5.073385e+03      12.308733 6.046036e-53 3.449263e-50
+
+600        Mir192 271352.97636 5.385927e+05 4.113233e+03 7.637001e-03      -7.032778 1.311798e-38 4.989204e-36
+
+568        Mir149    810.35429 1.224267e+01 1.608466e+03 1.313819e+02       7.037623 7.073079e-37 2.017596e-34
+
+791        Mir490    220.99790 9.450198e-01 4.410508e+02 4.667107e+02       8.866385 1.354865e-36 3.091803e-34
+
+642        Mir204    347.57397 3.737736e+00 6.914102e+02 1.849810e+02       7.531234 8.058436e-36 1.532446e-33
+
+844        Mir802    166.83414 3.336683e+02 0.000000e+00 0.000000e+00           -Inf 3.255469e-35 5.306414e-33
+
+698       Mir3073     98.93199 1.978640e+02 0.000000e+00 0.000000e+00           -Inf 1.111351e-28 1.585065e-26
+
+646       Mir208b   1649.77924 1.445675e-01 3.299414e+03 2.282265e+04      14.478178 7.505934e-28 9.515857e-26
+
+614       Mir1948    263.89527 5.246983e+02 3.092210e+00 5.893310e-03      -7.406706 1.534188e-26 1.750509e-24
+
+608      Mir194-2    391.65678 7.637703e+02 1.954329e+01 2.558791e-02      -5.288394 1.622682e-24 1.683163e-22
+
+796        Mir499    712.45950 0.000000e+00 1.424919e+03          Inf            Inf 2.577318e-19 2.450600e-17
+
+585       Mir181c   2765.96510 3.955399e+02 5.136390e+03 1.298577e+01       3.698860 1.942959e-17 1.705320e-15
+
+631       Mir199b     47.84725 1.818862e+00 9.387565e+01 5.161231e+01       5.689643 4.012622e-15 3.270287e-13
+
+530        Mir10b  27820.40551 1.501200e+03 5.413961e+04 3.606421e+01       5.172496 3.069912e-14 2.335180e-12
+
+586       Mir181d    275.22797 4.254569e+01 5.079103e+02 1.193800e+01       3.577489 5.204519e-14 3.711473e-12
+
+602        Mir193     45.70861 8.913819e+01 2.279021e+00 2.556728e-02      -5.289558 1.657854e-13 1.112713e-11
+
+637       Mir200a     27.09009 5.402561e+01 1.545578e-01 2.860824e-03      -8.449354 2.466964e-13 1.563781e-11
+
+722        Mir322    899.53469 1.797868e+02 1.619283e+03 9.006682e+00       3.170996 1.359804e-12 8.165978e-11
+
+756        Mir378    483.21548 1.056050e+02 8.608260e+02 8.151374e+00       3.027043 2.046396e-12 1.160965e-10
+
+523       Mir101b   6846.19683 1.280838e+04 8.840090e+02 6.901800e-02      -3.856884 2.136745e-12 1.160965e-10
+
+552       Mir133b     19.46050 0.000000e+00 3.892101e+01          Inf            Inf 2.388227e-12 1.238621e-10
+
+663        Mir23a   1289.18043 2.671574e+02 2.311203e+03 8.651093e+00       3.112882 3.093049e-12 1.534421e-10
+
+671        Mir27a   2788.72629 6.066392e+02 4.970813e+03 8.194019e+00       3.034571 5.970859e-12 2.838646e-10
+
+616        Mir195    519.86200 1.038507e+02 9.358733e+02 9.011721e+00       3.171803 6.245320e-12 2.850364e-10
+
+607      Mir194-1     71.10636 1.325374e+02 9.675354e+00 7.300095e-02      -3.775941 1.405195e-11 6.166645e-10
+
+344        Dnm3os    179.61643 3.285433e+01 3.263785e+02 9.934110e+00       3.312391 1.503324e-11 6.352936e-10
+
+590        Mir184     32.23796 1.645700e+00 6.283021e+01 3.817841e+01       5.254685 1.644760e-11 6.702396e-10
+
+582     Mir181a-2    347.82506 8.313904e+01 6.125111e+02 7.367310e+00       2.881138 2.735424e-11 1.076248e-09
+
+541     Mir125b-2    493.08516 1.122867e+02 8.738836e+02 7.782608e+00       2.960254 5.662328e-11 2.153572e-09
+
+573        Mir155     57.66182 7.341434e+00 1.079822e+02 1.470860e+01       3.878588 6.173765e-11 2.272344e-09
+
+464        Gm5441     20.24317 2.430915e-01 4.024325e+01 1.655478e+02       7.371104 6.503611e-11 2.318944e-09
+
+571        Mir153     19.90411 2.430915e-01 3.956513e+01 1.627582e+02       7.346586 8.675688e-11 2.999685e-09
+
+649         Mir21  26121.31011 4.639963e+04 5.842995e+03 1.259276e-01      -2.989333 1.048681e-10 3.519252e-09
+
+654        Mir214    134.69038 2.546966e+01 2.439111e+02 9.576536e+00       3.259504 1.338023e-10 4.361954e-09
+
+638       Mir200b     87.13638 1.725548e+02 1.717931e+00 9.955853e-03      -6.650239 2.397950e-10 7.600169e-09
+
+666       Mir24-2    424.48288 1.104079e+02 7.385578e+02 6.689355e+00       2.741867 4.542021e-10 1.363802e-08
+
+700     Mir3074-2    424.48288 1.104079e+02 7.385578e+02 6.689355e+00       2.741867 4.542021e-10 1.363802e-08
+
+845        Mir871     33.03360 6.461640e+01 1.450790e+00 2.245235e-02      -5.476990 5.839129e-10 1.708320e-08
+
+767        Mir429     49.75018 9.677270e+01 2.727653e+00 2.818618e-02      -5.148868 6.903556e-10 1.969239e-08
+
+655        Mir215    152.78082 3.329953e+01 2.722621e+02 8.176156e+00       3.031423 8.994273e-10 2.503040e-08
+
+566       Mir148a 118994.46955 2.065090e+05 3.147993e+04 1.524386e-01      -2.713700 1.022762e-09 2.772155e-08
+
+569        Mir150    553.20599 1.318948e+02 9.745171e+02 7.388592e+00       2.885299 1.044721e-09 2.772155e-08
+
+628       Mir1983     14.04997 0.000000e+00 2.809994e+01          Inf            Inf 2.859722e-09 7.415778e-08
+
+581     Mir181a-1     59.53826 1.179305e+01 1.072835e+02 9.097179e+00       3.185419 3.537731e-09 8.970115e-08
+
+784        Mir470     18.37716 3.608521e+01 6.691037e-01 1.854232e-02      -5.753034 7.467127e-09 1.852172e-07
+
+630     Mir199a-2     44.84878 7.384673e+00 8.231288e+01 1.114645e+01       3.478512 8.433815e-09 2.047443e-07
+
+550        Mir132    106.46062 2.691980e+01 1.860014e+02 6.909467e+00       2.788574 1.329950e-08 3.161402e-07
+
+76  2610203C20Rik     79.17666 1.649993e+01 1.418534e+02 8.597210e+00       3.103869 1.594438e-08 3.712764e-07
+
+540     Mir125b-1     79.01988 1.649993e+01 1.415398e+02 8.578206e+00       3.100676 1.650666e-08 3.766821e-07
+
+# VOOM top 50
+
+                ID      logFC    AveExpr          t      P.Value    adj.P.Val         B
+
+600         Mir192  -6.948883 14.6763803 -42.722954 2.301199e-16 2.625668e-13 27.266471
+
+536        Mir122a -10.426125  8.1698641 -21.722912 2.859682e-12 1.087633e-09 17.760171
+
+568         Mir149   7.030463  6.3160807  20.883835 4.915491e-12 1.402144e-09 17.277609
+
+645        Mir208a  11.015018  3.9395538  23.252407 1.118938e-12 6.383542e-10 17.208662
+
+530         Mir10b   5.130915 12.2628672  18.242023 3.124991e-11 4.963978e-09 16.221503
+
+561       Mir143hg   2.249221 16.2444825  18.082481 3.521739e-11 4.963978e-09 16.026695
+
+560         Mir143   2.251067 16.2358599  18.081481 3.524391e-11 4.963978e-09 16.026084
+
+646        Mir208b  12.433228  4.6076218  19.592458 1.179199e-11 2.690931e-09 15.683666
+
+523        Mir101b  -3.765722 10.8508440 -16.538566 1.180419e-10 1.036045e-08 14.900027
+
+796         Mir499  11.567529  3.7874598  17.942086 3.915496e-11 4.963978e-09 14.821741
+
+566        Mir148a  -2.638213 15.4435820 -16.548188 1.171186e-10 1.036045e-08 14.814792
+
+844         Mir802  -9.158434  2.9157675 -17.316522 6.338616e-11 7.232360e-09 14.381577
+
+698        Mir3073  -8.420542  2.5457189 -16.702657 1.033066e-10 1.036045e-08 13.985845
+
+649          Mir21  -2.938537 13.1642917 -15.375404 3.148335e-10 2.394833e-08 13.867698
+
+585        Mir181c   3.742560  9.6295577  15.242361 3.537063e-10 2.522368e-08 13.810405
+
+791         Mir490   8.474378  3.7506957  16.259650 1.484816e-10 1.210125e-08 13.424617
+
+663         Mir23a   3.165768  8.7896592  14.631179 6.110682e-10 3.873493e-08 13.269174
+
+586        Mir181d   3.636211  6.3713218  14.317073 8.157508e-10 4.898798e-08 12.956333
+
+642         Mir204   7.684425  4.7751735  15.033484 4.254268e-10 2.855364e-08 12.822427
+
+671         Mir27a   3.106935  9.9255796  13.838251 1.281011e-09 6.960160e-08 12.513086
+
+552        Mir133b   6.493549  1.2544862  13.969968 1.129934e-09 6.446275e-08 11.982684
+
+608       Mir194-2  -5.264136  6.0897615 -13.044012 2.792884e-09 1.448491e-07 11.715753
+
+616         Mir195   3.216595  7.4509350  12.869478 3.332788e-09 1.653353e-07 11.587523
+
+756         Mir378   3.097393  7.3832049  11.684163 1.171371e-08 5.346138e-07 10.329692
+
+672         Mir27b   1.976376 15.0957731  11.756036 1.082197e-08 5.144946e-07 10.127719
+
+1017      Snord104  -2.337374 10.6109024 -11.495675 1.444482e-08 6.339052e-07 10.023395
+
+722         Mir322   3.296618  8.2153415  11.415362 1.580762e-08 6.441605e-07 10.008472
+
+655         Mir215   3.045873  5.7544234  11.148134 2.141822e-08 8.082459e-07  9.753268
+
+628        Mir1983   5.895500  0.9931851  11.445812 1.527548e-08 6.441605e-07  9.749260
+
+344         Dnm3os   3.363344  5.8607432  11.092261 2.283960e-08 8.082459e-07  9.689496
+
+637        Mir200a  -6.191561  1.7981309 -11.322172 1.756229e-08 6.909853e-07  9.662295
+
+587         Mir182  -4.903995  7.1511683 -11.074468 2.331304e-08 8.082459e-07  9.658842
+
+582      Mir181a-2   3.048298  6.9414651  11.072128 2.337609e-08 8.082459e-07  9.644017
+
+614        Mir1948  -7.195525  4.5513493 -11.005492 2.524936e-08 8.473388e-07  9.341794
+
+654         Mir214   3.280874  5.4784451  10.768257 3.332555e-08 1.086413e-06  9.318504
+
+571         Mir153   5.963803  1.4386315  10.727082 3.498742e-08 1.093990e-06  9.035569
+
+318        Cyp3a25  -6.318200  1.4888933 -10.698226 3.620443e-08 1.093990e-06  9.024973
+
+464         Gm5441   5.982176  1.4484953  10.692891 3.643436e-08 1.093990e-06  9.000362
+
+541      Mir125b-2   3.077678  7.4316058  10.446668 4.893073e-08 1.431538e-06  8.884250
+
+551      Mir133a-1   5.144671  0.5903264  10.358205 5.447229e-08 1.553822e-06  8.575535
+
+550         Mir132   2.847559  5.3211839  10.110952 7.380297e-08 2.004981e-06  8.531491
+
+13   1110038B12Rik  -2.226702 10.8487089 -10.194609 6.655312e-08 1.852125e-06  8.439308
+
+922        Rabggtb  -1.935779  9.9874171  -9.928995 9.262821e-08 2.457879e-06  8.133384
+
+569         Mir150   2.938531  7.6297870   9.842102 1.033602e-07 2.620755e-06  8.116464
+
+800         Mir504   5.256127  0.6221088   9.892894 9.693595e-08 2.513725e-06  8.068853
+
+573         Mir155   3.906600  3.9899000   9.732173 1.188627e-07 2.712448e-06  8.046518
+
+666        Mir24-2   2.833979  7.3083691   9.767192 1.136724e-07 2.646944e-06  8.030550
+
+700      Mir3074-2   2.833979  7.3083691   9.767192 1.136724e-07 2.646944e-06  8.030550
+
+664         Mir23b   2.124129  9.8141190   9.806316 1.081569e-07 2.625681e-06  7.979464
+
+631        Mir199b   5.752816  2.8805143   9.823920 1.057683e-07 2.623514e-06  7.979387
+
+Warning messages:
+
+1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group ==  :
+
+  Outlier (-Inf) in boxplot 5 is not drawn
+
+2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group ==  :
+
+  Outlier (-Inf) in boxplot 7 is not drawn
+
+3: In bxp(list(stats = c(-Inf, -Inf, -0.158608221176912, 0.826586442285183,  :
+
+  some notches went outside hinges ('box'): maybe set notch=FALSE
+
+4: In par(defpar) : calling par(new=TRUE) with no plot
+
+R version 2.15.1 (2012-06-22)
+
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+locale:
+
+ [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8     LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8    LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
+
+attached base packages:
+
+[1] methods   grid      stats     graphics  grDevices utils     datasets  base     
+
+other attached packages:
+
+ [1] edgeR_3.0.8        limma_3.14.4       DESeq_1.10.1       lattice_0.20-15    locfit_1.5-9.1     Biobase_2.18.0     BiocGenerics_0.4.0 gplots_2.11.0      MASS_7.3-23        KernSmooth_2.23-10 caTools_1.14       gdata_2.12.0.2     gtools_2.7.1       stringr_0.6.2     
+
+loaded via a namespace (and not attached):
+
+ [1] annotate_1.36.0      AnnotationDbi_1.20.7 bitops_1.0-5         DBI_0.2-7            genefilter_1.40.0    geneplotter_1.36.0   IRanges_1.16.6       parallel_2.15.1      RColorBrewer_1.0-5   RSQLite_0.11.3       splines_2.15.1       stats4_2.15.1        survival_2.37-4      XML_3.96-1.1         xtable_1.7-1        
+
+</pre>
+
+<hr/><div class="infomessage">This tool (edgeR) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>
+</div></body></html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/test-data/edgeRtest1out.xls	Fri Jul 26 23:50:59 2013 -0400
@@ -0,0 +1,1142 @@
+Name	logFC	logCPM	LR	PValue	adj.p.value	Dispersion	totreads	case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam	control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam	case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam	control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam
+Mir122a	-10.6613482198735	12.5379487184339	445.912028851371	5.59474310450852e-99	6.38360188224422e-96	0.102055096028295	90428	6.64466912039531	2.86464823551992	20.1236936368881	4.75652253016081	20841.6623198401	16818.9531619257	7242.55663282834	8468.31297344994	12	7	27	8	29767	24233	11911	24463
+Mir192	-7.10901851688288	17.2474145508888	366.131659138235	1.3015583263717e-81	7.42539025195057e-79	0.0776548700185199	2325567	1779.66387941254	1294.41176699279	4493.54625691845	1933.52640851037	463599.032378899	340312.253828562	383591.60517699	182292.180510107	3214	3163	6029	3252	662133	490327	630849	526600
+Mir208b	13.4237202575152	9.82233816515324	355.417815392181	2.80129611458365e-79	1.06542628891331e-76	0.124440587141633	14756	1245.90702213628	570.139045385768	4930.34448733332	881.902421077918	0.74532198655141	0	0	0	2049	1647	8904	2155	1	0	0	0
+Mir208a	11.9775863683342	8.38828977985358	348.815401742963	7.675450754893e-78	2.18942232783323e-75	0.0993679816515115	4638	433.789589950159	712.527819143148	1006.59908044528	649.748467524829	0	0	0	0.553722426699609	1060	956	1693	928	0	0	0	1
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+Mir5129	0.0957314088382215	-0.822204343190538	0.00662119867327871	0.935147111451955	0.956095747461183	0.470649185108855	8	0	0.553722426699609	0.409235462217131	1.49064397310282	0	0.700159986556928	0.694051630500793	1.2161122714849	0	1	1	2	0	1	1	2
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+2010320M18Rik	-0.0135816064033237	-0.577688977281378	9.37664770823687e-05	0.992273957831848	0.994889794276045	0.436705588816395	10	0	0	1.03850463640395	1.10744485339922	0.409235462217131	1.49064397310282	0.594565316270102	0.700159986556928	0	0	3	2	1	2	1	1
+2310001K24Rik	0.00612441798475525	-1.86264950933858	6.95515125732626e-05	0.993345915420738	0.995090157590046	0.638146949527696	4	0	0	0.594565316270102	0.700159986556928	0	0.608056135742452	0.34616821213465	0	0	0	1	1	0	1	1	0
+Mir1966	0.000918355090882732	-0.94191710317151	1.38947096530728e-05	0.997025843661245	0.997900427734632	0.449008936327196	8	0	0.34616821213465	1.66116728009883	0	1.49064397310282	0.594565316270102	0.700159986556928	0	0	1	3	0	2	1	1	0
+Mir376b	-0.00136357255892604	1.39148339025352	2.78221370209053e-06	0.998669131632702	0.998669131632702	0.592374698826143	42	1.49064397310282	2.37826126508041	7.70175985212621	2.08215489150238	9.72889817187923	1.73084106067325	0.553722426699609	0	2	4	11	3	16	5	1	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/test-data/gentestdata.sh	Fri Jul 26 23:50:59 2013 -0400
@@ -0,0 +1,9 @@
+#!/bin/bash
+# generate test data for rgGSEA
+# ross lazarus June 2013 
+# adjust gseajar_path !
+GSEAJAR_PATH=/home/rlazarus/galaxy-central/tool_dependency_dir/gsea_jar/2.0.12/fubar/rg_gsea_test/8e291f464aa0/jars/gsea2-2.0.12.jar
+python ../rgGSEA.py --input_tab "gsea_test_DGE.xls"  --adjpvalcol "5" --signcol "2" --idcol "1" --outhtml "gseatestout.html" --input_name "gsea_test" --setMax "500" --setMin "15" --nPerm "10" --plotTop "20" --gsea_jar "$GSEAJAR_PATH" --output_dir "gseatestout" --mode "Max_probe" 
+--title "GSEA test" --builtin_gmt "gseatestdata.gmt"
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/test-data/test_bams2mx.xls	Fri Jul 26 23:50:59 2013 -0400
@@ -0,0 +1,3243 @@
+Contigname	11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam	11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam	11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam	11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam	11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam	11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam	11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam	11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam
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+Snord68	1644	460	353	1060	1295	805	1310	376
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+Zfp133-ps	0	0	0	0	0	0	0	0
+Zfp207	5	0	2	0	0	9	1	2
+Zfp326	7	2	1	1	0	4	4	0
+Zfp389	0	0	0	0	0	0	0	0
+Zfp410	10	0	2	0	0	6	2	0
+Zfp414	1	0	0	0	0	4	0	0
+Zfp57	0	0	0	0	0	0	0	0
+Zfp572	0	0	0	0	0	0	0	0
+Zfp672	0	0	0	0	0	2	0	0
+Zfp783	0	0	0	0	0	0	0	0
+Zfp809	7	1	0	0	0	4	2	0
+Zfp821	0	0	0	2	2	0	0	0
+Zfp862	4	0	0	0	0	10	2	0
+Zim3	0	0	0	0	0	0	0	0
+Zmynd8	3	5	4	4	3	8	2	1
+Znf41-ps	0	0	0	0	0	0	0	0
+Zp4-ps	0	0	0	0	0	0	0	0
+Zscan4a	0	0	0	0	0	0	0	0
+Zxda	0	0	0	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgedgeR/tool_dependencies.xml	Fri Jul 26 23:50:59 2013 -0400
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="r3" version="3.0.1">
+        <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    </package>
+    <package name="biocbasics" version="2.12">
+        <install version="1.0"> 
+            <actions>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <package name="r3" version="3.0.1" />
+                    </repository>
+                </action>
+                <action type="make_directory">$INSTALL_DIR</action>
+                <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T)" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>                
+                <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
+            </actions>
+        </install>
+        <readme>Installs some basic bioc packages for the edgeR wrapper 
+        It's clunky but this is the only way I could get anything installed into the package_r3 R
+       </readme>
+    </package>
+</tool_dependency>