Mercurial > repos > fubar > toolfactory
changeset 33:ca60c96f0beb draft
Deleted selected files
| author | fubar |
|---|---|
| date | Thu, 28 Aug 2014 02:27:03 -0400 |
| parents | 4162896b29bd |
| children | c6fdf2c6d0f4 |
| files | rgToolFactoryMultIn.py rgToolFactoryMultIn.xml |
| diffstat | 2 files changed, 0 insertions(+), 1079 deletions(-) [+] |
line wrap: on
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--- a/rgToolFactoryMultIn.py Thu Aug 28 02:25:07 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,736 +0,0 @@ -# rgToolFactoryMultIn.py -# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home -# -# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 -# -# all rights reserved -# Licensed under the LGPL -# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home -# -# august 2014 -# Allows arbitrary number of input files -# NOTE positional parameters are now passed to script -# and output (may be "None") is *before* arbitrary number of inputs -# -# march 2014 -# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript -# grrrrr - night before a demo -# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable -# -# added ghostscript and graphicsmagick as dependencies -# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp -# errors ensued -# -# august 2013 -# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn -# -# july 2013 -# added ability to combine images and individual log files into html output -# just make sure there's a log file foo.log and it will be output -# together with all images named like "foo_*.pdf -# otherwise old format for html -# -# January 2013 -# problem pointed out by Carlos Borroto -# added escaping for <>$ - thought I did that ages ago... -# -# August 11 2012 -# changed to use shell=False and cl as a sequence - -# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye. -# It also serves as the wrapper for the new tool. -# -# you paste and run your script -# Only works for simple scripts that read one input from the history. -# Optionally can write one new history dataset, -# and optionally collect any number of outputs into links on an autogenerated HTML page. - -# DO NOT install on a public or important site - please. - -# installed generated tools are fine if the script is safe. -# They just run normally and their user cannot do anything unusually insecure -# but please, practice safe toolshed. -# Read the fucking code before you install any tool -# especially this one - -# After you get the script working on some test data, you can -# optionally generate a toolshed compatible gzip file -# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for -# safe and largely automated installation in a production Galaxy. - -# If you opt for an HTML output, you get all the script outputs arranged -# as a single Html history item - all output files are linked, thumbnails for all the pdfs. -# Ugly but really inexpensive. -# -# Patches appreciated please. -# -# -# long route to June 2012 product -# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them -# derived from an integrated script model -# called rgBaseScriptWrapper.py -# Note to the unwary: -# This tool allows arbitrary scripting on your Galaxy as the Galaxy user -# There is nothing stopping a malicious user doing whatever they choose -# Extremely dangerous!! -# Totally insecure. So, trusted users only -# -# preferred model is a developer using their throw away workstation instance - ie a private site. -# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool. -# - -import sys -import shutil -import subprocess -import os -import time -import tempfile -import optparse -import tarfile -import re -import shutil -import math - -progname = os.path.split(sys.argv[0])[1] -myversion = 'V001.1 March 2014' -verbose = False -debug = False -toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory' - -# if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated -# tool xml -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 - - -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 = [] - self.test1Inputs = [] # now a list - a = self.cl.append - a(opts.interpreter) - if self.treatbashSpecial and opts.interpreter in ['bash','sh']: - a(self.sfile) - else: - a('-') # stdin - # if multiple inputs - positional or need to distinguish them with cl params - if opts.output_tab: - a('%s' % opts.output_tab) - if opts.input_tab: - tests = [] - for i,intab in enumerate(opts.input_tab): # if multiple, make tests - if intab.find(',') <> -1: - (gpath,uname) = intab.split(',') - else: - gpath = uname = intab - a('"%s"' % (intab)) - tests.append(os.path.basename(gpath)) - self.test1Inputs = '<param name="input_tab" value="%s" />' % (','.join(tests)) - else: - self.test1Inputs = '' - self.outFormats = opts.output_format - self.inputFormats = opts.input_formats - self.test1Output = '%s_test1_output.xls' % self.toolname - self.test1HTML = '%s_test1_output.html' % self.toolname - - def makeXML(self): - """ - Create a Galaxy xml tool wrapper for the new script as a string to write out - fixme - use templating or something less fugly than this example of what we produce - - <tool id="reverse" name="reverse" version="0.01"> - <description>a tabular file</description> - <command interpreter="python"> - reverse.py --script_path "$runMe" --interpreter "python" - --tool_name "reverse" --input_tab "$input1" --output_tab "$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="${job_name}"/> - - </outputs> - <help> - -**What it Does** - -Reverse the columns in a tabular file - - </help> - <configfiles> - <configfile name="runMe"> - -# reverse order of columns in a tabular file -import sys -inp = sys.argv[1] -outp = sys.argv[2] -i = open(inp,'r') -o = open(outp,'w') -for row in i: - rs = row.rstrip().split('\t') - rs.reverse() - o.write('\t'.join(rs)) - o.write('\n') -i.close() -o.close() - - - </configfile> - </configfiles> - </tool> - - """ - newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s"> -%(tooldesc)s -%(requirements)s -<command interpreter="python"> -%(command)s -</command> -<inputs> -%(inputs)s -</inputs> -<outputs> -%(outputs)s -</outputs> -<configfiles> -<configfile name="runMe"> -%(script)s -</configfile> -</configfiles> -<tests> -%(tooltests)s -</tests> -<help> - -%(help)s - -</help> -</tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto - - newCommand=""" - %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" - --tool_name "%(toolname)s" - %(command_inputs)s - %(command_outputs)s - """ - # may NOT be an input or htmlout - appended later - tooltestsTabOnly = """ - <test> - %(test1Inputs)s - <param name="job_name" value="test1"/> - <param name="runMe" value="$runMe"/> - <output name="tab_file" file="%(test1Output)s" ftype="tabular"/> - </test> - </tests> - """ - tooltestsHTMLOnly = """ - <test> - %(test1Inputs)s - <param name="job_name" value="test1"/> - <param name="runMe" value="$runMe"/> - <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/> - </test> - </tests> - """ - tooltestsBoth = """ - <test> - %(test1Inputs)s - <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['requirements'] = '' - if self.opts.make_HTML: - if self.opts.include_dependencies == "yes": - xdict['requirements'] = protorequirements - xdict['tool_version'] = self.opts.tool_version - xdict['test1HTML'] = self.test1HTML - xdict['test1Output'] = self.test1Output - xdict['test1Inputs'] = self.test1Inputs - if self.opts.make_HTML and self.opts.output_tab <> '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) - 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': - cins = ['\n',] - cins.append('#for intab in $input1:') - cins.append('--input_tab "$intab"') - cins.append('#end for\n') - xdict['command_inputs'] = '\n'.join(cins) - xdict['inputs'] = '''<param name="input1" multiple="true" type="data" format="%s" label="Select a suitable input file from your history" - help="Multiple inputs may be selected if the script can deal with them..."/> \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.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) - 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 == "yes": - 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 - for i,intab in enumerate(self.opts.input_tab): - si = self.opts.input_tab[i] - if si.find(',') <> -1: - s = si.split(',')[0] - si = s - dest = os.path.join(testdir,os.path.basename(si)) - if si <> dest: - shutil.copyfile(si,dest) - if self.opts.output_tab <> '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=[], action="append") - a("--input_formats",default="tabular") - a('--output_tab',default="None") - a('--output_format',default='tabular') - a('--user_email',default='Unknown') - a('--bad_user',default=None) - a('--make_Tool',default=None) - a('--make_HTML',default=None) - a('--help_text',default=None) - a('--tool_desc',default=None) - a('--new_tool',default=None) - a('--tool_version',default=None) - a('--include_dependencies',default=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 - opts.input_tab = [x.replace('"','').replace("'",'') for x in opts.input_tab] - r = ScriptRunner(opts) - if opts.make_Tool: - retcode = r.makeTooltar() - else: - retcode = r.run() - os.unlink(r.sfile) - if retcode: - sys.exit(retcode) # indicate failure to job runner - - -if __name__ == "__main__": - main() - -
--- a/rgToolFactoryMultIn.xml Thu Aug 28 02:25:07 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,343 +0,0 @@ -<tool id="rgTFM" name="Tool Factory Multiple Inputs" version="1.12"> - <description>Makes scripts into tools</description> - <requirements> - <requirement type="package" version="9.10">ghostscript</requirement> - <requirement type="package" version="1.3.18">graphicsmagick</requirement> - </requirements> - <command interpreter="python"> -#if ( $__user_email__ not in $__admin_users__ ): - rgToolFactoryMultIn.py --bad_user $__user_email__ -#else: - rgToolFactoryMultIn.py --script_path "$runme" --interpreter "$interpreter" - --tool_name "$tool_name" --user_email "$__user_email__" - #if $make_TAB.value=="yes": - --output_tab "$output1" - --output_format "$output_format" - #end if - #if $makeMode.make_Tool=="yes": - --make_Tool "$makeMode.make_Tool" - --tool_desc "$makeMode.tool_desc" - --tool_version "$makeMode.tool_version" - --new_tool "$new_tool" - --help_text "$helpme" - #if $make_HTML.value=="yes": - #if $makeMode.include_deps.value=="yes": - --include_dependencies "yes" - #end if - #end if - #end if - #if $make_HTML.value=="yes": - --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" - #else: - --output_dir "." - #end if - #if $input1 != 'None': - --input_formats "$input_formats" - #for intab in $input1: - #if $add_names.value == "yes": - --input_tab "$intab,$intab.name" - #else: - --input_tab "$intab" - #end if - #end for - --input_formats = "$input_formats" - #end if -#end if - </command> - <inputs> - <param name="input1" type="data" label="Select an input file from your history" optional="true" size="120" multiple="true" - help="Use the multiple input widget (above/right of input box) for multiple inputs - your script MUST be ready to parse the command line right - see samples below"/> - <param name="input_formats" type="text" value="tabular" label="Select allowable Galaxy input formats for your inputs passed to your script - default is tabular" - help="Multiple input formats are allowed as a comma separated list (eg 'tabular,txt'), but your script must be able to deal with whatever is passed in!"> - <sanitizer invalid_char=""> - <valid initial="string.letters"> - <add value=","/> - <add value=" "/> - </valid> - </sanitizer> - </param> - <param name="add_names" type="select" label="Pass input file(s) as path,name - useful if you need the user supplied Galaxy name for your data sets" - help="Your script is responsible for parsing and dealing with these comma separated values!"> - <option value="yes">Pass inputs as comma separated path,name values on the script command line</option> - <option value="" selected="true">Pass input parameters as path only - do not include the user supplied name</option> - </param> - <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60" - help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"> - <add value="_"/> - </valid> - </sanitizer> - </param> - <conditional name="makeMode"> - <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!" size="60"> - <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option> - <option value="" selected="true">No. Just run the script please</option> - </param> - <when value = "yes"> - <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01" - help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/> - <param name="tool_desc" label="Tool Description" type="text" value="" size="40" - help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" /> - <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" - size="8x120" value="**What it Does**" - help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" > - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60" - help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect"> - <option value="">Rely on system ghostscript and graphicsmagick rather than include these as dependencies</option> - <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option> - </param> - - </when> - <when value = ""> - </when> - </conditional> - <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60" - help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output"> - <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option> - <option value="" selected="true">No, no HTML output file thanks</option> - </param> - <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an HTML file specified above" - help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes"> - <option value="yes" selected="true">My script writes to a new history output</option> - <option value="">I do not want a new history output file</option> - </param> - <param name="output_format" type="select" label="Galaxy datatype for your tool's output file if any" help="You may need to edit the xml to extend this list"> - <option value="tabular" selected="true">Tabular</option> - <option value="text">text</option> - <option value="interval">Interval</option> - <option value="gz">gz</option> - </param> - <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host"> - <option value="Rscript" selected="true">Rscript</option> - <option value="python">python</option> - <option value="perl">perl</option> - <option value="sh">sh</option> - </param> - <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120" - help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None')."> - <sanitizer> - <valid initial="string.printable"> - </valid> - <mapping initial="none"/> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="tabular" name="output1" label="${tool_name}.${output_format}"> - <filter>make_TAB=="yes"</filter> - <change_format> - <when input="output_format" value="interval" format="interval" /> - <when input="output_format" value="gz" format="gz" /> - <when input="output_format" value="text" format="text" /> - </change_format> - </data> - <data format="html" name="html_file" label="${tool_name}.html"> - <filter>make_HTML == "yes"</filter> - </data> - <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz"> - <filter>makeMode['make_Tool'] == "yes"</filter> - </data> - </outputs> -<configfiles> -<configfile name="runme">$dynScript</configfile> -<configfile name="helpme"> -#if $makeMode.make_Tool == "yes": -${makeMode.help_text} -#end if -</configfile> -</configfiles> -<help> - -.. class:: warningmark - -**Details and attribution** GTF_ - -**Local Admins ONLY** Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool. - -**If you find a bug** please raise an issue at the bitbucket repository GTFI_ - -**What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy. - -**Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history. - -**Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs, -a new HTML report linking all the files and images created by the script can be automatically generated. - -**Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file -ready to upload to your local toolshed for sharing and installation. Provide a small sample input when you run generate the tool because -it will become the input for the generated functional test. - -.. class:: warningmark - -**Note to system administrators** This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances. -Admin_users will have the power to do anything they want as the Galaxy user if you install this tool. - -.. class:: warningmark - -**Use on public servers** is STRONGLY discouraged for obvious reasons - -The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation. -We recommend that you follow the good code hygiene practices associated with safe toolshed. - -**Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not select one, and the path to the optional -output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below. -Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output. -This can be handy for complex scripts creating lots of output. - -**Examples** -<![CDATA[ - -Each of these following trivial examples can be cut and pasted into the script box for testing. -Please make sure you choose the appropriate interpreter and upload and select a suitable small matching test data input - -A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and -writes the results to a new tabular file. Note the use of colClasses to ensure that no fiddling takes place with numeric values by treating everything -as a string:: - - # transpose a tabular input file and write as a tabular output file - ourargs = commandArgs(TRUE) - inf = ourargs[1] - outf = ourargs[2] - inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character") - outp = t(inp) - write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F) - -Calculate a multiple test adjusted p value from a column of p values - for this script to be useful, it needs the right column for the input to be specified in the code for the -given input file type(s) specified when the tool is generated :: - - # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use - column = 1 # adjust if necessary for some other kind of input - ourargs = commandArgs(TRUE) - inf = ourargs[1] - outf = ourargs[2] - inp = read.table(inf,head=T,row.names=NULL,sep='\t') - p = inp[,column] - q = p.adjust(p,method='BH') - outp = cbind(inp,'BH Adjusted p-value'=q) - write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T) - - -A demonstration Rscript example takes no input file but generates some random data based pdf images -You must make sure the option to create an HTML output file is -turned on for this to work. Images (pdf) are linked via thumbnails and -all files have a link on the resulting HTML page:: - - # note this script takes NO input or output because it generates random data - for (i in 1:10) { - foo = runif(100) - bar = rnorm(100) - bar = foo + 0.05*bar - pdf(paste('yet',i,"anotherplot.pdf",sep='_')) - plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6) - dev.off() - foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) - bar = as.matrix(foo) - pdf(paste('yet',i,"anotherheatmap.pdf",sep='_')) - heatmap(bar,main='Random Heatmap') - dev.off() - } - -A slight variation taking an input tabular file from which we read the first number as nreps - -# note this script takes a single parameter -# number of replicates -ourargs = commandArgs(TRUE) -infname = ourargs[1] -nreps = read.table(infname,head=F) -nreps = unlist(nreps)[1] -nreps = max(c(1,nreps)) -nreps = min(c(20,nreps)) -print(paste("Using nreps=",nreps)) -for (i in 1:nreps) { - foo = runif(100) - bar = rnorm(100) - bar = foo + 0.2*bar - pdf(paste("yet",i,"anotherplot.pdf",sep="_")) - plot(foo,bar,main=paste("Foo by Bar plot ",i),col="maroon", pch=3,cex=0.6) - dev.off() - foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) - bar = as.matrix(foo) - pdf(paste("yet",i,"anotherheatmap.pdf",sep="_")) - heatmap(bar,main="Random Heatmap") - dev.off() -} - -A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces -for this to work if cut and pasted into the script box):: - - # reverse order of columns in a tabular file - import sys - inp = sys.argv[1] - outp = sys.argv[2] - i = open(inp,'r') - o = open(outp,'w') - for row in i: - rs = row.rstrip().split('\t') - rs.reverse() - o.write('\t'.join(rs)) - o.write('\n') - i.close() - o.close() - -A trivial shell script example to show that it works:: - - #!/bin/bash - INF=$1 - OUTF=$2 - cut -c2,4,6,8,10,12 $INF > $OUTF - -A trivial perl script example to show that even perl works:: - - # - # change all occurances of a string in a file to another string - # - $oldfile = $ARGV[0]; - $newfile = $ARGV[1]; - $old = "gene"; - $new = "foo"; - open(OF, $oldfile); - open(NF, ">$newfile"); - # read in each line of the file - while ($line = <OF>) { - $line =~ s/$old/$new/; - print NF $line; - } - close(OF); - close(NF); - -]]> - -**Citation** - - -Paper_ : - -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 - - -**Licensing** - -Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012 -All rights reserved. -Licensed under the LGPL_ - -.. _LGPL: http://www.gnu.org/copyleft/lesser.html -.. _GTF: https://bitbucket.org/fubar/galaxytoolfactory -.. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues -.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref - - -</help> - -</tool> - -