Mercurial > repos > hspitia > rpkm_values
changeset 0:888cb13321fa draft default tip
Uploaded
| author | hspitia |
|---|---|
| date | Sun, 07 Sep 2014 02:02:23 -0400 |
| parents | |
| children | |
| files | GetRPKMvalues/GetRPKMvalues.py GetRPKMvalues/GetRPKMvalues.xml GetRPKMvalues/test-data/GetRPKMvalues_test1_input.xls GetRPKMvalues/test-data/GetRPKMvalues_test1_output.xls GetRPKMvalues/test-data/test1_out.log |
| diffstat | 5 files changed, 934 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GetRPKMvalues/GetRPKMvalues.py Sun Sep 07 02:02:23 2014 -0400 @@ -0,0 +1,742 @@ +# GetRPKMvalues/GetRPKMvalues.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py +# to make a new Galaxy tool called GetRPKMvalues +# User hfespitia@cenicana.org at 06/09/2014 23:41:54 +# rgToolFactory.py +# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home +# +# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 +# +# all rights reserved +# Licensed under the LGPL +# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home +# +# August 2014 +# merged John Chilton's citation addition and ideas from Marius van den Beek to enable arbitrary +# data types for input and output - thanks! +# +# march 2014 +# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript +# grrrrr - night before a demo +# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable +# +# added ghostscript and graphicsmagick as dependencies +# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp +# errors ensued +# +# august 2013 +# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn +# +# july 2013 +# added ability to combine images and individual log files into html output +# just make sure there's a log file foo.log and it will be output +# together with all images named like "foo_*.pdf +# otherwise old format for html +# +# January 2013 +# problem pointed out by Carlos Borroto +# added escaping for <>$ - thought I did that ages ago... +# +# August 11 2012 +# changed to use shell=False and cl as a sequence + +# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye. +# It also serves as the wrapper for the new tool. +# +# you paste and run your script +# Only works for simple scripts that read one input from the history. +# Optionally can write one new history dataset, +# and optionally collect any number of outputs into links on an autogenerated HTML page. + +# DO NOT install on a public or important site - please. + +# installed generated tools are fine if the script is safe. +# They just run normally and their user cannot do anything unusually insecure +# but please, practice safe toolshed. +# Read the fucking code before you install any tool +# especially this one + +# After you get the script working on some test data, you can +# optionally generate a toolshed compatible gzip file +# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for +# safe and largely automated installation in a production Galaxy. + +# If you opt for an HTML output, you get all the script outputs arranged +# as a single Html history item - all output files are linked, thumbnails for all the pdfs. +# Ugly but really inexpensive. +# +# Patches appreciated please. +# +# +# long route to June 2012 product +# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them +# derived from an integrated script model +# called rgBaseScriptWrapper.py +# Note to the unwary: +# This tool allows arbitrary scripting on your Galaxy as the Galaxy user +# There is nothing stopping a malicious user doing whatever they choose +# Extremely dangerous!! +# Totally insecure. So, trusted users only +# +# preferred model is a developer using their throw away workstation instance - ie a private site. +# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool. +# + +import sys +import shutil +import subprocess +import os +import time +import tempfile +import optparse +import tarfile +import re +import shutil +import math + +progname = os.path.split(sys.argv[0])[1] +myversion = 'V001.1 March 2014' +verbose = False +debug = False +toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory' + +# if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated +# tool xml +toolhtmldepskel = """<?xml version="1.0"?> +<tool_dependency> + <package name="ghostscript" version="9.10"> + <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" /> + </package> + <package name="graphicsmagick" version="1.3.18"> + <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" /> + </package> + <readme> + %s + </readme> +</tool_dependency> +""" + +protorequirements = """<requirements> + <requirement type="package" version="9.10">ghostscript</requirement> + <requirement type="package" version="1.3.18">graphicsmagick</requirement> + </requirements>""" + +def timenow(): + """return current time as a string + """ + return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) + +html_escape_table = { + "&": "&", + ">": ">", + "<": "<", + "$": "\$" + } + +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 + + +def parse_citations(citations_text): + """ + """ + citations = [c for c in citations_text.split("**ENTRY**") if c.strip()] + citation_tuples = [] + for citation in citations: + if citation.startswith("doi"): + citation_tuples.append( ("doi", citation[len("doi"):].strip() ) ) + else: + citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) ) + return citation_tuples + + +class ScriptRunner: + """class is a wrapper for an arbitrary script + """ + + def __init__(self,opts=None,treatbashSpecial=True): + """ + cleanup inputs, setup some outputs + + """ + self.useGM = cmd_exists('gm') + self.useIM = cmd_exists('convert') + self.useGS = cmd_exists('gs') + self.temp_warned = False # we want only one warning if $TMP not set + self.treatbashSpecial = treatbashSpecial + if opts.output_dir: # simplify for the tool tarball + os.chdir(opts.output_dir) + self.thumbformat = 'png' + self.opts = opts + self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but.. + self.toolid = self.toolname + self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later + self.pyfile = self.myname # crude but efficient - the cruft won't hurt much + self.xmlfile = '%s.xml' % self.toolname + 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' % html_escape(x) for x in s]) # for restructured text in help + self.escapedScript = '\n'.join([html_escape(x) for x in s]) + self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname) + if opts.output_dir: # may not want these complexities + self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname) + art = '%s.%s' % (self.toolname,opts.interpreter) + artpath = os.path.join(self.opts.output_dir,art) # need full path + artifact = open(artpath,'w') # use self.sfile as script source for Popen + artifact.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.outputFormat = self.opts.output_format + self.inputFormats = self.opts.input_formats + 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="${job_name}"/> + + </outputs> + <help> + +**What it Does** + +Reverse the columns in a tabular file + + </help> + <configfiles> + <configfile name="runMe"> + +# reverse order of columns in a tabular file +import sys +inp = sys.argv[1] +outp = sys.argv[2] +i = open(inp,'r') +o = open(outp,'w') +for row in i: + rs = row.rstrip().split('\t') + rs.reverse() + o.write('\t'.join(rs)) + o.write('\n') +i.close() +o.close() + + + </configfile> + </configfiles> + </tool> + + """ + newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s"> +%(tooldesc)s +%(requirements)s +<command interpreter="python"> +%(command)s +</command> +<inputs> +%(inputs)s +</inputs> +<outputs> +%(outputs)s +</outputs> +<configfiles> +<configfile name="runMe"> +%(script)s +</configfile> +</configfiles> + +%(tooltests)s + +<help> + +%(help)s + +</help> +<citations> + %(citations)s + <citation type="doi">10.1093/bioinformatics/bts573</citation> +</citations> +</tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto + + newCommand=""" + %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" + --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """ + # may NOT be an input or htmlout - appended later + tooltestsTabOnly = """ + <tests> + <test> + <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/> + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="tab_file" file="%(test1Output)s" ftype="%(outputFormat)s"/> + </test> + </tests> + """ + tooltestsHTMLOnly = """ + <tests> + <test> + <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/> + <param name="job_name" value="test1"/> + <param name="runMe" value="$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="%(inputFormats)s"/> + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="tab_file" file="%(test1Output)s" ftype="%(outputFormat)s" /> + <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/> + </test> + </tests> + """ + xdict = {} + xdict['outputFormat'] = self.outputFormat + xdict['inputFormats'] = self.inputFormats + xdict['requirements'] = '' + if self.opts.make_HTML: + if self.opts.include_dependencies == "yes": + xdict['requirements'] = protorequirements + 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: + helptext = open(self.opts.help_text,'r').readlines() + helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek + xdict['help'] = ''.join([x for x in helptext]) + else: + xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email) + if self.opts.citations: + citationstext = open(self.opts.citations,'r').read() + citation_tuples = parse_citations(citationstext) + citations_xml = "" + for citation_type, citation_content in citation_tuples: + citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content)) + citations_xml += citation_xml + xdict['citations'] = citations_xml + else: + xdict['citations'] = "" + coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::'] + coda.append('\n') + coda.append(self.indentedScript) + coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow())) + coda.append('See %s for details of that project' % (toolFactoryURL)) + coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ') + coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n') + xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda)) + if self.opts.tool_desc: + xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc + else: + xdict['tooldesc'] = '' + xdict['command_outputs'] = '' + xdict['outputs'] = '' + if self.opts.input_tab <> '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' + else: + xdict['command_outputs'] += ' --output_dir "./"' + 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.outputFormat + 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) + tdir = self.toolname + os.mkdir(tdir) + self.makeXML() + if self.opts.make_HTML: + if self.opts.help_text: + hlp = open(self.opts.help_text,'r').read() + else: + hlp = 'Please ask the tool author for help as none was supplied at tool generation\n' + if self.opts.include_dependencies: + tooldepcontent = toolhtmldepskel % hlp + depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w') + depf.write(tooldepcontent) + depf.write('\n') + depf.close() + 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')) + outpif = '%s.py' % self.toolname # new name + outpiname = os.path.join(tdir,outpif) # path for the tool tarball + pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM) + notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),] + notes.append('# to make a new Galaxy tool called %s\n' % self.toolname) + notes.append('# User %s at %s\n' % (self.opts.user_email,timenow())) + pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm + notes += pi + outpi = open(outpiname,'w') + outpi.write(''.join(notes)) + outpi.write('\n') + outpi.close() + stname = os.path.join(tdir,self.sfile) + if not os.path.exists(stname): + shutil.copyfile(self.sfile, stname) + xtname = os.path.join(tdir,self.xmlfile) + if not os.path.exists(xtname): + shutil.copyfile(self.xmlfile,xtname) + tarpath = "%s.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 + note that GS gets confoozled if no $TMP or $TEMP + so we set it + """ + assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) + hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'a') + our_env = os.environ.copy() + our_tmp = our_env.get('TMP',None) + if not our_tmp: + our_tmp = our_env.get('TEMP',None) + if not (our_tmp and os.path.exists(our_tmp)): + newtmp = os.path.join(self.opts.output_dir,'tmp') + try: + os.mkdir(newtmp) + except: + sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp) + our_env['TEMP'] = newtmp + if not self.temp_warned: + sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp) + self.temp_warned = True + outpdf = '%s_compressed' % inpdf + cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf] + x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval1 = x.wait() + sto.close() + if retval1 == 0: + os.unlink(inpdf) + shutil.move(outpdf,inpdf) + os.unlink(hlog) + hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf)) + sto = open(hlog,'w') + outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) + if self.useGM: + cl2 = ['gm', 'convert', inpdf, outpng] + else: # assume imagemagick + cl2 = ['convert', inpdf, outpng] + x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env) + retval2 = x.wait() + sto.close() + if retval2 == 0: + os.unlink(hlog) + retval = retval1 or retval2 + return retval + + + def getfSize(self,fpath,outpath): + """ + format a nice file size string + """ + size = '' + fp = os.path.join(outpath,fpath) + if os.path.isfile(fp): + size = '0 B' + n = float(os.path.getsize(fp)) + if n > 2**20: + size = '%1.1f MB' % (n/2**20) + elif n > 2**10: + size = '%1.1f KB' % (n/2**10) + elif n > 0: + size = '%d B' % (int(n)) + return size + + def makeHtml(self): + """ Create an HTML file content to list all the artifacts found in the output_dir + """ + + galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="toolFormBody"> + """ + galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" + galhtmlpostfix = """</div></body></html>\n""" + + flist = os.listdir(self.opts.output_dir) + flist = [x for x in flist if x <> 'Rplots.pdf'] + flist.sort() + html = [] + html.append(galhtmlprefix % progname) + html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow())) + fhtml = [] + if len(flist) > 0: + logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections + logfiles.sort() + logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)] + logfiles.append(os.path.abspath(self.tlog)) # make it the last one + pdflist = [] + npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) + for rownum,fname in enumerate(flist): + dname,e = os.path.splitext(fname) + sfsize = self.getfSize(fname,self.opts.output_dir) + if e.lower() == '.pdf' : # compress and make a thumbnail + thumb = '%s.%s' % (dname,self.thumbformat) + pdff = os.path.join(self.opts.output_dir,fname) + retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) + if retval == 0: + pdflist.append((fname,thumb)) + else: + pdflist.append((fname,fname)) + if (rownum+1) % 2 == 0: + fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) + else: + fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) + for logfname in logfiles: # expect at least tlog - if more + if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later + sectionname = 'All tool run' + if (len(logfiles) > 1): + sectionname = 'Other' + ourpdfs = pdflist + else: + realname = os.path.basename(logfname) + sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log + ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname] + pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove + nacross = 1 + npdf = len(ourpdfs) + + if npdf > 0: + nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2))) + if int(nacross)**2 != npdf: + nacross += 1 + nacross = int(nacross) + width = min(400,int(1200/nacross)) + html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname) + html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>') + ntogo = nacross # counter for table row padding with empty cells + html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>') + for i,paths in enumerate(ourpdfs): + fname,thumb = paths + s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" + alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname) + if ((i+1) % nacross == 0): + s += '</tr>\n' + ntogo = 0 + if i < (npdf - 1): # more to come + s += '<tr>' + ntogo = nacross + else: + ntogo -= 1 + html.append(s) + if html[-1].strip().endswith('</tr>'): + html.append('</table></div>\n') + else: + if ntogo > 0: # pad + html.append('<td> </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: + ste = open(self.elog,'w') + sto = open(self.tlog,'w') + sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) + sto.flush() + p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,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() + ste.close() + err = open(self.elog,'r').readlines() + if retval <> 0 and err: # problem + print >> sys.stderr,err + if self.opts.make_HTML: + self.makeHtml() + return retval + + def runBash(self): + """ + cannot use - for bash so use self.sfile + """ + if self.opts.output_dir: + s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl) + sto = open(self.tlog,'w') + sto.write(s) + sto.flush() + p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir) + else: + p = subprocess.Popen(self.cl,shell=False) + retval = p.wait() + if self.opts.output_dir: + sto.close() + if self.opts.make_HTML: + self.makeHtml() + return retval + + +def main(): + u = """ + This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: + <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" + </command> + """ + op = optparse.OptionParser() + a = op.add_option + a('--script_path',default=None) + a('--tool_name',default=None) + a('--interpreter',default=None) + a('--output_dir',default='./') + a('--output_html',default=None) + a('--input_tab',default="None") + a('--input_formats',default="tabular,text") + a('--output_tab',default="None") + a('--output_format',default="tabular") + a('--user_email',default='Unknown') + a('--bad_user',default=None) + a('--make_Tool',default=None) + a('--make_HTML',default=None) + a('--help_text',default=None) + a('--citations',default=None) + a('--tool_desc',default=None) + a('--new_tool',default=None) + a('--tool_version',default=None) + a('--include_dependencies',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/GetRPKMvalues/GetRPKMvalues.xml Sun Sep 07 02:02:23 2014 -0400 @@ -0,0 +1,189 @@ +<tool id="GetRPKMvalues" name="GetRPKMvalues" version="0.01"> +<description> from BAM file</description> + +<command interpreter="python"> + + GetRPKMvalues.py --script_path "$runMe" --interpreter "Rscript" + --tool_name "GetRPKMvalues" --input_tab "$input1" --output_dir "./" --output_tab "$tab_file" +</command> +<inputs> +<param name="input1" type="data" format="bam" label="Select a suitable input file from your history"/> +<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="GetRPKMvalues"/> + +</inputs> +<outputs> + <data format="tabular" name="tab_file" label="${job_name}"/> + +</outputs> +<configfiles> +<configfile name="runMe"> +#!/usr/bin/Rscript + +# source("http://bioconductor.org/biocLite.R") +# biocLite("Rsamtools") + +ourargs = commandArgs(trailingOnly = TRUE) +inf = ourargs[1] +outf = ourargs[2] + + +library(Rsamtools) +library(foreach) + +GetMappedReadsFreqs = function(bam.file){ + require(Rsamtools) + mapped.flag = scanBamFlag(isUnmappedQuery = FALSE) # Get all mapped reads + mapped.param = ScanBamParam(flag = mapped.flag, what = c("rname")) # Get only the reference name to which reads were mapped + bam.index.file = indexBam(bam.file) + mapped.scan.res = scanBam(param = mapped.param, file = bam.file, index = bam.index.file) + mapped = as.data.frame(table(mapped.scan.res[[1]]\$rname)) + colnames(mapped) = c("ref.sequence", "mapped.reads") + mapped +} + +GetRefSeqsLengths = function(bam.file){ + require(Rsamtools) + header = scanBamHeader(files = bam.file) + ref.seqs.data = as.data.frame(header[[1]]\$targets) + data.frame(length = header[[1]]\$targets, row.names = names(header[[1]]\$targets)) +} + +GetIdxStats = function(bam.file) { + mapped = GetMappedReadsFreqs(bam.file = bam.file) + ref.seqs.lengths = GetRefSeqsLengths(bam.file = bam.file) + merge(x = mapped, y = ref.seqs.lengths, + by.x = "ref.sequence", by.y = "row.names") +} + +GetRPKMValues = function(bam.file) { + bam.stats = GetIdxStats(bam.file = bam.file) + total.mapped = sum(bam.stats\$mapped.reads) + mapped.factor = total.mapped / 10^9 + + bam.stats\$RPKM = (bam.stats\$mapped.reads / (bam.stats\$length * mapped.factor)) + data.frame(RPKM = bam.stats\$RPKM, row.names = bam.stats\$ref.sequence) +} + +bam.files = inf + +if(any(!file.exists(bam.files))){ + not.found = bam.files[!file.exists(bam.files)] + out.names = paste(not.found, collapse = "\n ") + stop(paste("One or more files does not exist:\n", out.names)) +} else { + rpkm.data = foreach(c.bam.file = bam.files, .combine = "cbind") %do% { + GetRPKMValues(bam.file = c.bam.file) + } + colnames(rpkm.data) = sapply(bam.files, basename) + out.data = cbind(ref.sequence = rownames(rpkm.data), rpkm.data) + write.table(out.data, quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE, + file = outf) +} +</configfile> +</configfiles> + + + <tests> + <test> + <param name="input1" value="GetRPKMvalues_test1_input.xls" ftype="bam"/> + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="tab_file" file="GetRPKMvalues_test1_output.xls" ftype="tabular"/> + </test> + </tests> + + +<help> + + +This tool computes the RPKM values from a given BAM file. + +This tool is a R script and requires Rsamtools and foreach packages. + +The output is a tabular file with two columns: +1. ref.sequence: which contains the names of reference sequences (genes/transcripts), and + +2. dataset_#.dat: which referes to the name of input dataset (BAM file specified) and contains the RPKM values for each reference sequence. The symbol # represents a consecutive number automatically assigned by Galaxy. + +**Script** +Pressing execute will run the following code over your input file and generate some outputs in your history:: + + + #!/usr/bin/Rscript + + # source("http://bioconductor.org/biocLite.R") + # biocLite("Rsamtools") + + ourargs = commandArgs(trailingOnly = TRUE) + inf = ourargs[1] + outf = ourargs[2] + + + library(Rsamtools) + library(foreach) + + GetMappedReadsFreqs = function(bam.file){ + require(Rsamtools) + mapped.flag = scanBamFlag(isUnmappedQuery = FALSE) # Get all mapped reads + mapped.param = ScanBamParam(flag = mapped.flag, what = c("rname")) # Get only the reference name to which reads were mapped + bam.index.file = indexBam(bam.file) + mapped.scan.res = scanBam(param = mapped.param, file = bam.file, index = bam.index.file) + mapped = as.data.frame(table(mapped.scan.res[[1]]\$rname)) + colnames(mapped) = c("ref.sequence", "mapped.reads") + mapped + } + + GetRefSeqsLengths = function(bam.file){ + require(Rsamtools) + header = scanBamHeader(files = bam.file) + ref.seqs.data = as.data.frame(header[[1]]\$targets) + data.frame(length = header[[1]]\$targets, row.names = names(header[[1]]\$targets)) + } + + GetIdxStats = function(bam.file) { + mapped = GetMappedReadsFreqs(bam.file = bam.file) + ref.seqs.lengths = GetRefSeqsLengths(bam.file = bam.file) + merge(x = mapped, y = ref.seqs.lengths, + by.x = "ref.sequence", by.y = "row.names") + } + + GetRPKMValues = function(bam.file) { + bam.stats = GetIdxStats(bam.file = bam.file) + total.mapped = sum(bam.stats\$mapped.reads) + mapped.factor = total.mapped / 10^9 + + bam.stats\$RPKM = (bam.stats\$mapped.reads / (bam.stats\$length * mapped.factor)) + data.frame(RPKM = bam.stats\$RPKM, row.names = bam.stats\$ref.sequence) + } + + bam.files = inf + + if(any(!file.exists(bam.files))){ + not.found = bam.files[!file.exists(bam.files)] + out.names = paste(not.found, collapse = "\n ") + stop(paste("One or more files does not exist:\n", out.names)) + } else { + rpkm.data = foreach(c.bam.file = bam.files, .combine = "cbind") %do% { + GetRPKMValues(bam.file = c.bam.file) + } + colnames(rpkm.data) = sapply(bam.files, basename) + out.data = cbind(ref.sequence = rownames(rpkm.data), rpkm.data) + write.table(out.data, quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE, + file = outf) + } + +**Attribution** +This Galaxy tool was created by hfespitia@cenicana.org at 06/09/2014 23:41:54 +using the Galaxy Tool Factory. + +See https://bitbucket.org/fubar/galaxytoolfactory for details of that project +Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + + +</help> +<citations> + + <citation type="doi">10.1093/bioinformatics/bts573</citation> +</citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GetRPKMvalues/test-data/GetRPKMvalues_test1_output.xls Sun Sep 07 02:02:23 2014 -0400 @@ -0,0 +1,2 @@ +ref.sequence dataset_19.dat +gi|9626243|ref|NC_001416.1| 20617.7064863305
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GetRPKMvalues/test-data/test1_out.log Sun Sep 07 02:02:23 2014 -0400 @@ -0,0 +1,1 @@ +## Toolfactory generated command line = Rscript - /opt/biotools/galaxy/galaxy-dist/database/files/000/dataset_19.dat /opt/biotools/galaxy/galaxy-dist/database/files/000/dataset_26.dat