Mercurial > repos > mvdbeek > demo_signature_tool_toolfactory
changeset 0:eb4ec3488f3a draft
Uploaded
| author | mvdbeek |
|---|---|
| date | Sat, 07 Feb 2015 07:56:18 -0500 |
| parents | |
| children | c79a1a37c689 |
| files | multiple_overlap_signatures/multiple_overlap_signatures.py multiple_overlap_signatures/multiple_overlap_signatures.xml multiple_overlap_signatures/test-data/multiple_overlap_signatures_test1_input.xls multiple_overlap_signatures/test-data/multiple_overlap_signatures_test1_output.html multiple_overlap_signatures/test-data/test1_out.log |
| diffstat | 5 files changed, 1078 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiple_overlap_signatures/multiple_overlap_signatures.py Sat Feb 07 07:56:18 2015 -0500 @@ -0,0 +1,728 @@ +# multiple_overlap_signatures/multiple_overlap_signatures.py - a self annotated version of DockerToolFactory.py generated by running DockerToolFactory.py +# to make a new Galaxy tool called multiple overlap signatures +# User m.vandenbeek@gmail.com at 07/02/2015 12:43:09 +# DockerToolFactory.py +# see https://bitbucket.org/mvdbeek/DockerToolFactory + +import sys +import shutil +import subprocess +import os +import time +import tempfile +import argparse +import tarfile +import re +import shutil +import math +import fileinput +from os.path import abspath + +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> + <container type="docker">toolfactory/custombuild:%s</container> +</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 edit_dockerfile(dockerfile): + '''we have to change the userid of galaxy inside the container to the id with which the tool is run, + otherwise we have a mismatch in the file permissions inside the container''' + uid=os.getuid() + for line in fileinput.FileInput(dockerfile, inplace=1): + sys.stdout.write(re.sub("RUN adduser galaxy.*", "RUN adduser galaxy -u {0}\n".format(uid), line)) + +def build_docker(dockerfile, docker_client, image_tag='base'): + '''Given the path to a dockerfile, and a docker_client, build the image, if it does not + exist yet.''' + image_id='toolfactory/custombuild:'+image_tag + existing_images=", ".join(["".join(d['RepoTags']) for d in docker_client.images()]) + if image_id in existing_images: + print 'docker container exists, skipping build' + return image_id + print "Building Docker image, using Dockerfile:{0}".format(dockerfile) + build_process=docker_client.build(fileobj=open(dockerfile, 'r'), tag=image_id) + print "succesfully dispatched docker build process, building now" + build_log=[line for line in build_process] #will block until image is built. + return image_id + +def construct_bind(host_path, container_path=False, binds=None, ro=True): + #TODO remove container_path if it's alwyas going to be the same as host_path + '''build or extend binds dictionary with container path. binds is used + to mount all files using the docker-py client.''' + if not binds: + binds={} + if isinstance(host_path, list): + for k,v in enumerate(host_path): + if not container_path: + container_path=host_path[k] + binds[host_path[k]]={'bind':container_path, 'ro':ro} + container_path=False #could be more elegant + return binds + else: + if not container_path: + container_path=host_path + binds[host_path]={'bind':container_path, 'ro':ro} + return binds + +def switch_to_docker(opts): + import docker #need local import, as container does not have docker-py + docker_client=docker.Client() + toolfactory_path=abspath(sys.argv[0]) + dockerfile=os.path.dirname(toolfactory_path)+'/Dockerfile' + edit_dockerfile(dockerfile) + image_id=build_docker(dockerfile, docker_client) + binds=construct_bind(host_path=opts.script_path, ro=False) + binds=construct_bind(binds=binds, host_path=abspath(opts.output_dir), ro=False) + if len(opts.input_tab)>0: + binds=construct_bind(binds=binds, host_path=opts.input_tab, ro=True) + if not opts.output_tab == 'None': + binds=construct_bind(binds=binds, host_path=opts.output_tab, ro=False) + if opts.make_HTML: + binds=construct_bind(binds=binds, host_path=opts.output_html, ro=False) + if opts.make_Tool: + binds=construct_bind(binds=binds, host_path=opts.new_tool, ro=False) + binds=construct_bind(binds=binds, host_path=opts.help_text, ro=True) + binds=construct_bind(binds=binds, host_path=toolfactory_path) + volumes=binds.keys() + sys.argv=[abspath(opts.output_dir) if sys.argv[i-1]=='--output_dir' else arg for i,arg in enumerate(sys.argv)] ##inject absolute path of working_dir + cmd=['python', '-u']+sys.argv+['--dockerized', '1'] + container=docker_client.create_container( + image=image_id, + user='galaxy', + volumes=volumes, + command=cmd + ) + docker_client.start(container=container[u'Id'], binds=binds) + docker_client.wait(container=container[u'Id']) + logs=docker_client.logs(container=container[u'Id']) + print "".join([log for log in logs]) + +class ScriptRunner: + """class is a wrapper for an arbitrary script + """ + + def __init__(self,opts=None,treatbashSpecial=True, image_tag='base'): + """ + cleanup inputs, setup some outputs + + """ + self.opts = opts + 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 + self.image_tag = image_tag + os.chdir(abspath(opts.output_dir)) + self.thumbformat = 'png' + self.toolname_sanitized = re.sub('[^a-zA-Z0-9_]+', '_', opts.tool_name) # a sanitizer now does this but.. + self.toolname = opts.tool_name + 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_sanitized + 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_sanitized,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_sanitized) + if opts.output_dir: # may not want these complexities + self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname_sanitized) + art = '%s.%s' % (self.toolname_sanitized,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 + for input in opts.input_tab: + a(input) + if opts.output_tab == 'None': #If tool generates only HTML, set output name to toolname + a(str(self.toolname_sanitized)+'.out') + a(opts.output_tab) + for param in opts.additional_parameters: + param, value=param.split(',') + a('--'+param) + a(value) + #print self.cl + self.outFormats = opts.output_format + self.inputFormats = [formats for formats in opts.input_formats] + self.test1Input = '%s_test1_input.xls' % self.toolname_sanitized + self.test1Output = '%s_test1_output.xls' % self.toolname_sanitized + self.test1HTML = '%s_test1_output.html' % self.toolname_sanitized + + 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"/> + + </inputs> + <outputs> + <data format=opts.output_format name="tab_file"/> + + </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> +</tool>""" # needs a dict with toolname, toolname_sanitized, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto + + newCommand=""" + %(toolname_sanitized)s.py --script_path "$runMe" --interpreter "%(interpreter)s" + --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """ + # may NOT be an input or htmlout - appended later + tooltestsTabOnly = """ + <tests> + <test> + <param name="input1" value="%(test1Input)s" ftype="tabular"/> + <param name="runMe" value="$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="runMe" value="$runMe"/> + <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/> + </test> + </tests> + """ + tooltestsBoth = """<tests> + <test> + <param name="input1" value="%(test1Input)s" ftype="tabular"/> + <param name="runMe" value="$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: + xdict['requirements'] = protorequirements % self.image_tag + 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) + 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' + xdict['inputs']='' + for i,input in enumerate(self.inputFormats): + xdict['inputs' ]+='<param name="input{0}" type="data" format="{1}" label="Select a suitable input file from your history"/> \n'.format(i+1, input) + xdict['command_inputs'] += ' $input{0}'.format(i+1) + else: + xdict['command_inputs'] = '' # assume no input - eg a random data generator + xdict['inputs'] = '' + # I find setting the job name not very logical. can be changed in workflows anyway. xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname + xdict['toolname'] = self.toolname + xdict['toolname_sanitized'] = self.toolname_sanitized + xdict['toolid'] = self.toolid + xdict['interpreter'] = self.opts.interpreter + xdict['scriptname'] = self.sfile + if self.opts.make_HTML: + xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"' + xdict['outputs'] += ' <data format="html" name="html_file"/>\n' + else: + xdict['command_outputs'] += ' --output_dir "./"' + #print self.opts.output_tab + if self.opts.output_tab!="None": + xdict['command_outputs'] += ' --output_tab "$tab_file"' + xdict['outputs'] += ' <data format="%s" name="tab_file"/>\n' % self.outFormats + xdict['command'] = newCommand % xdict + #print xdict['outputs'] + 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_sanitized/tool.xml /toolname_sanitized/tool.py /toolname_sanitized/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_sanitized + 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 + for i in self.opts.input_tab: + #print i + shutil.copyfile(i,os.path.join(testdir,self.test1Input)) + if not self.opts.output_tab: + 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_sanitized # 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=[line.replace('if False:', 'if False:') for line in open(self.pyfile)] #do not run docker in the generated tool + 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_sanitized + tar = tarfile.open(tarpath, "w:gz") + tar.add(tdir,arcname=self.toolname_sanitized) + 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 abspath(x) <> abspath(self.tlog)] + logfiles.append(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 abspath(logfname) == 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 #same problem, need to capture docker stdin/stdout + 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 = argparse.ArgumentParser() + a = op.add_argument + 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', nargs='*') + 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) + a('--include_dependencies',default=None) + a('--dockerized',default=0) + a('--output_format', default='tabular') + a('--input_format', dest='input_formats', action='append', default=[]) + a('--additional_parameters', dest='additional_parameters', action='append', default=[]) + opts = 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 + if False: + switch_to_docker(opts) + return + 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/multiple_overlap_signatures/multiple_overlap_signatures.xml Sat Feb 07 07:56:18 2015 -0500 @@ -0,0 +1,120 @@ +<tool id="multiple overlap signatures" name="multiple overlap signatures" version="0.01"> +<description>plot multiple overlap signatures</description> +<requirements> + <requirement type="package" version="9.10">ghostscript</requirement> + <requirement type="package" version="1.3.18">graphicsmagick</requirement> + <container type="docker">toolfactory/custombuild:base</container> +</requirements> +<command interpreter="python"> + + multiple_overlap_signatures.py --script_path "$runMe" --interpreter "Rscript" + --tool_name "multiple overlap signatures" --input_tab $input1 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" +</command> +<inputs> +<param name="input1" type="data" format="Any" label="Select a suitable input file from your history"/> + +</inputs> +<outputs> + <data format="html" name="html_file"/> + +</outputs> +<configfiles> +<configfile name="runMe"> +library(ggplot2) +library(reshape) +library(plyr) + +ourargs = commandArgs(TRUE) +inf = ourargs[1] + +df=read.delim(inf, header=T) +pdf('pairs_signature.pdf', height=10) + +g= ggplot(aes(x=overlap, y=num.of.pairs), data=df) +g + geom_line() + facet_wrap(~sample, ncol=2) + theme_bw() + ylab("Number of pairs") + + xlab("Overlap between pairs") + geom_vline(xintercept=10, colour="red", linetype = "longdash") + scale_x_continuous(breaks=seq(5,15)) + +dev.off() +samples=levels(df\$sample) +sample_mean=sapply(samples, function(x) mean(df[df\$sample==x,]\$num.of.pairs)) +sample_sd=sapply(samples, function(x) sd(df[df\$sample==x,]\$num.of.pairs)) +sample_z=sapply(names(sample_mean), function(x) (df[df\$sample==x,]\$num.of.pairs-sample_mean[x])/sample_sd[x]) + +z=melt(sample_z) +colnames(z)=c("overlap", "sample", "z_score") +z\$overlap=z\$overlap+min(df\$overlap)-1 +#df\$z_score=z\$value +df=join(df, z) + +pdf('z-signature.pdf', height=10) +g= ggplot(aes(x=overlap, y=z_score), data=df) +g + geom_line() + facet_wrap(~sample, ncol=2) + theme_bw() + ylab("Z score") + + xlab("Overlap between pairs") + geom_vline(xintercept=10, colour="red", linetype = "longdash") + scale_x_continuous(breaks=seq(5,15)) +dev.off() +</configfile> +</configfiles> + + + <tests> + <test> + <param name="input1" value="multiple_overlap_signatures_test1_input.xls" ftype="tabular"/> + <param name="runMe" value="$runMe"/> + <output name="html_file" file="multiple_overlap_signatures_test1_output.html" ftype="html" lines_diff="5"/> + </test> + </tests> + + +<help> + + +**What it Does** +Plots the piRNA signature for a tabular file with overlap, number of pairs, probability of overlap for a pair and library name. +This can be produced using the Small RNA Signatures tool (https://testtoolshed.g2.bx.psu.edu/view/drosofff/msp_sr_signature). + +**Script** +Pressing execute will run the following code over your input file and generate some outputs in your history:: + + + library(ggplot2) + library(reshape) + library(plyr) + + ourargs = commandArgs(TRUE) + inf = ourargs[1] + + df=read.delim(inf, header=T) + pdf('pairs_signature.pdf', height=10) + + g= ggplot(aes(x=overlap, y=num.of.pairs), data=df) + g + geom_line() + facet_wrap(~sample, ncol=2) + theme_bw() + ylab("Number of pairs") + + xlab("Overlap between pairs") + geom_vline(xintercept=10, colour="red", linetype = "longdash") + scale_x_continuous(breaks=seq(5,15)) + + dev.off() + samples=levels(df\$sample) + sample_mean=sapply(samples, function(x) mean(df[df\$sample==x,]\$num.of.pairs)) + sample_sd=sapply(samples, function(x) sd(df[df\$sample==x,]\$num.of.pairs)) + sample_z=sapply(names(sample_mean), function(x) (df[df\$sample==x,]\$num.of.pairs-sample_mean[x])/sample_sd[x]) + + z=melt(sample_z) + colnames(z)=c("overlap", "sample", "z_score") + z\$overlap=z\$overlap+min(df\$overlap)-1 + #df\$z_score=z\$value + df=join(df, z) + + pdf('z-signature.pdf', height=10) + g= ggplot(aes(x=overlap, y=z_score), data=df) + g + geom_line() + facet_wrap(~sample, ncol=2) + theme_bw() + ylab("Z score") + + xlab("Overlap between pairs") + geom_vline(xintercept=10, colour="red", linetype = "longdash") + scale_x_continuous(breaks=seq(5,15)) + dev.off() + +**Attribution** +This Galaxy tool was created by m.vandenbeek@gmail.com at 07/02/2015 12:43:09 +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> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiple_overlap_signatures/test-data/multiple_overlap_signatures_test1_input.xls Sat Feb 07 07:56:18 2015 -0500 @@ -0,0 +1,155 @@ +overlap num of pairs probability sample +5 0 0.000000 GKG16 +6 2 0.000019 GKG16 +7 1 0.000011 GKG16 +8 0 0.000000 GKG16 +9 0 0.000000 GKG16 +10 1 0.000006 GKG16 +11 1 0.000008 GKG16 +12 2 0.000010 GKG16 +13 3 0.000031 GKG16 +14 3 0.000132 GKG16 +15 1 0.000009 GKG16 +5 0 0.000000 GKG18 +6 0 0.000000 GKG18 +7 0 0.000000 GKG18 +8 0 0.000000 GKG18 +9 0 0.000000 GKG18 +10 0 0.000000 GKG18 +11 0 0.000000 GKG18 +12 0 0.000000 GKG18 +13 1 0.000017 GKG18 +14 0 0.000000 GKG18 +15 1 0.000017 GKG18 +5 1 0.000011 GKG47 +6 1 0.000011 GKG47 +7 1 0.000011 GKG47 +8 1 0.000011 GKG47 +9 1 0.000018 GKG47 +10 0 0.000000 GKG47 +11 0 0.000000 GKG47 +12 0 0.000000 GKG47 +13 0 0.000000 GKG47 +14 1 0.000014 GKG47 +15 3 0.000052 GKG47 +5 3 0.000043 GKG52 +6 0 0.000000 GKG52 +7 1 0.000084 GKG52 +8 2 0.000022 GKG52 +9 1 0.000008 GKG52 +10 0 0.000000 GKG52 +11 0 0.000000 GKG52 +12 3 0.000045 GKG52 +13 2 0.000026 GKG52 +14 0 0.000000 GKG52 +15 3 0.000033 GKG52 +5 1 0.000012 GNE4 +6 1 0.000030 GNE4 +7 1 0.000010 GNE4 +8 1 0.000010 GNE4 +9 1 0.000010 GNE4 +10 1 0.000010 GNE4 +11 1 0.000059 GNE4 +12 0 0.000000 GNE4 +13 0 0.000000 GNE4 +14 0 0.000000 GNE4 +15 0 0.000000 GNE4 +5 0 0.000000 GKG63 +6 0 0.000000 GKG63 +7 0 0.000000 GKG63 +8 0 0.000000 GKG63 +9 0 0.000000 GKG63 +10 0 0.000000 GKG63 +11 0 0.000000 GKG63 +12 0 0.000000 GKG63 +13 0 0.000000 GKG63 +14 0 0.000000 GKG63 +15 0 0.000000 GKG63 +5 0 0.000000 GKG66 +6 0 0.000000 GKG66 +7 0 0.000000 GKG66 +8 0 0.000000 GKG66 +9 0 0.000000 GKG66 +10 0 0.000000 GKG66 +11 0 0.000000 GKG66 +12 0 0.000000 GKG66 +13 0 0.000000 GKG66 +14 0 0.000000 GKG66 +15 0 0.000000 GKG66 +5 7 0.000053 GKG16 with testes reads +6 6 0.000028 GKG16 with testes reads +7 5 0.000028 GKG16 with testes reads +8 4 0.000022 GKG16 with testes reads +9 7 0.000096 GKG16 with testes reads +10 19 0.000284 GKG16 with testes reads +11 3 0.000016 GKG16 with testes reads +12 8 0.000054 GKG16 with testes reads +13 0 0.000000 GKG16 with testes reads +14 7 0.000036 GKG16 with testes reads +15 7 0.000048 GKG16 with testes reads +5 2 0.000030 GKG18 with testes reads +6 2 0.000026 GKG18 with testes reads +7 2 0.000024 GKG18 with testes reads +8 6 0.000087 GKG18 with testes reads +9 1 0.000011 GKG18 with testes reads +10 25 0.000468 GKG18 with testes reads +11 2 0.000026 GKG18 with testes reads +12 1 0.000009 GKG18 with testes reads +13 3 0.000063 GKG18 with testes reads +14 1 0.000015 GKG18 with testes reads +15 2 0.000026 GKG18 with testes reads +5 4 0.000054 GKG47 with testes reads +6 2 0.000026 GKG47 with testes reads +7 4 0.000047 GKG47 with testes reads +8 4 0.000053 GKG47 with testes reads +9 4 0.000055 GKG47 with testes reads +10 13 0.000358 GKG47 with testes reads +11 5 0.000079 GKG47 with testes reads +12 3 0.000039 GKG47 with testes reads +13 2 0.000022 GKG47 with testes reads +14 4 0.000052 GKG47 with testes reads +15 6 0.000085 GKG47 with testes reads +5 5 0.000055 GKG52 with testes reads +6 1 0.000010 GKG52 with testes reads +7 1 0.000083 GKG52 with testes reads +8 0 0.000000 GKG52 with testes reads +9 1 0.000013 GKG52 with testes reads +10 15 0.000266 GKG52 with testes reads +11 1 0.000013 GKG52 with testes reads +12 8 0.000093 GKG52 with testes reads +13 4 0.000049 GKG52 with testes reads +14 2 0.000022 GKG52 with testes reads +15 4 0.000050 GKG52 with testes reads +5 1 0.000017 GNE4 with testes reads +6 0 0.000000 GNE4 with testes reads +7 0 0.000000 GNE4 with testes reads +8 1 0.000017 GNE4 with testes reads +9 5 0.000108 GNE4 with testes reads +10 22 0.000422 GNE4 with testes reads +11 2 0.000048 GNE4 with testes reads +12 3 0.000045 GNE4 with testes reads +13 3 0.000044 GNE4 with testes reads +14 4 0.000049 GNE4 with testes reads +15 10 0.000174 GNE4 with testes reads +5 3 0.000091 GKG63 with testes reads +6 1 0.000030 GKG63 with testes reads +7 3 0.000091 GKG63 with testes reads +8 4 0.000121 GKG63 with testes reads +9 3 0.000083 GKG63 with testes reads +10 18 0.000596 GKG63 with testes reads +11 0 0.000000 GKG63 with testes reads +12 1 0.000030 GKG63 with testes reads +13 0 0.000000 GKG63 with testes reads +14 2 0.000060 GKG63 with testes reads +15 3 0.000106 GKG63 with testes reads +5 2 0.000037 GKG66 with testes reads +6 2 0.000032 GKG66 with testes reads +7 5 0.000075 GKG66 with testes reads +8 2 0.000024 GKG66 with testes reads +9 6 0.000152 GKG66 with testes reads +10 22 0.000595 GKG66 with testes reads +11 1 0.000008 GKG66 with testes reads +12 8 0.000146 GKG66 with testes reads +13 3 0.000075 GKG66 with testes reads +14 4 0.000088 GKG66 with testes reads +15 5 0.000124 GKG66 with testes reads
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiple_overlap_signatures/test-data/multiple_overlap_signatures_test1_output.html Sat Feb 07 07:56:18 2015 -0500 @@ -0,0 +1,70 @@ +<!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 DockerToolFactory.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 "multiple overlap signatures" run at 07/02/2015 12:43:09</div><br/> +<div class="toolFormTitle">multiple log output</div> + +<pre> + +Loading required package: methods + +Attaching package: 'plyr' + +The following objects are masked from 'package:reshape': + + rename, round_any + +Joining by: overlap, sample + + +</pre> + +<div class="toolFormTitle">Other images and outputs</div> +(Click on a thumbnail image to download the corresponding original PDF image)<br/> +<div><table class="simple" cellpadding="2" cellspacing="2"> +<tr> +<td><a href="pairs_signature.pdf"><img src="pairs_signature.png" title="Click to download a PDF of pairs_signature.pdf" hspace="5" width="400" + alt="Image called pairs_signature.pdf"/></a></td> + +<td><a href="z-signature.pdf"><img src="z-signature.png" title="Click to download a PDF of z-signature.pdf" hspace="5" width="400" + alt="Image called z-signature.pdf"/></a></td> +</tr> + +</table></div> + +<div class="toolFormTitle">Other log output</div> + +<pre> + +## Toolfactory generated command line = Rscript - /home/galaxy/galaxy-dist/database/files/008/dataset_8175.dat multiple_overlap_signatures.out None + +null device + + 1 + +null device + + 1 + + +</pre> + +<div class="toolFormTitle">All output files available for downloading</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="multiple_overlap_signatures.Rscript">multiple_overlap_signatures.Rscript</a></td><td>1.2 KB</td></tr> +<tr class="odd_row"><td><a href="multiple_overlap_signatures_error.log">multiple_overlap_signatures_error.log</a></td><td>171 B</td></tr> +<tr><td><a href="multiple_overlap_signatures_runner.log">multiple_overlap_signatures_runner.log</a></td><td>200 B</td></tr> +<tr class="odd_row"><td><a href="pairs_signature.pdf">pairs_signature.pdf</a></td><td>9.8 KB</td></tr> +<tr><td><a href="z-signature.pdf">z-signature.pdf</a></td><td>9.5 KB</td></tr> +</table></div><br/> +</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiple_overlap_signatures/test-data/test1_out.log Sat Feb 07 07:56:18 2015 -0500 @@ -0,0 +1,5 @@ +## Toolfactory generated command line = Rscript - /home/galaxy/galaxy-dist/database/files/008/dataset_8175.dat multiple_overlap_signatures.out None +null device + 1 +null device + 1