- """
- galhtmlattr = """
Galaxy Tool Factory Script Wrapper tool output %s run at %s
""" - galhtmlpostfix = """
\n"""
-
- flist = os.listdir(self.opts.output_dir)
- flist = [x for x in flist if x <> 'Rplots.pdf']
- flist.sort()
- html = [galhtmlprefix % progname,]
- html.append('Galaxy Tool Factory Script Wrapper tool output %s run at %s
""" - galhtmlpostfix = """
Galaxy %s outputs run at %s
\n' % (self.toolname,timenow())) - fhtml = [] - if len(flist) > 0: - html.append('
- ')
- fhtml.append('
') - html += fhtml # add all non-pdf files to the end of the display - else: - html.append('
### Error - %s returned no files - please confirm that parameters are sane' % self.opts.interpreter)
- html.append('%s log follows below
\n' % self.opts.interpreter)
- rlog = open(self.tlog,'r').readlines()
- html += rlog
- html.append('
%s CL = %s
\n' % (self.toolname,' '.join(sys.argv)))
- html.append('
\n')
- html.append(galhtmlattr % (progname,timenow()))
- 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):
- """
- """
- if self.opts.output_dir:
- sto = open(self.tlog,'w')
- p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
- else:
- p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)
- p.stdin.write(self.script)
- p.stdin.close()
- retval = p.wait()
- if self.opts.output_dir:
- sto.close()
- if self.opts.make_HTML:
- self.makeHtml()
- return retval
-
-
-def main():
- u = """
- This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
- rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
-
- """
- op = optparse.OptionParser()
- a = op.add_option
- a('--script_path',default=None)
- a('--tool_name',default=None)
- a('--interpreter',default=None)
- a('--output_dir',default=None)
- a('--output_html',default=None)
- a('--input_tab',default="None")
- a('--output_tab',default="None")
- a('--user_email',default=None)
- 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)
- opts, args = op.parse_args()
- assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin to add their ID to admin_users in universe_wsgi.ini' % (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()
- if retcode:
- sys.exit(retcode) # indicate failure to job runner
-
-
-if __name__ == "__main__":
- main()
-
-
diff -r f82dd90a8c9e -r ab0148be2111 fubar-galaxytoolfactory-8cc3f3c0e539/rgToolFactory.xml
--- a/fubar-galaxytoolfactory-8cc3f3c0e539/rgToolFactory.xml Wed Jun 06 22:43:47 2012 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,197 +0,0 @@
-
- Makes scripts into tools
-
-#if ( $__user_email__ not in $__admin_users__ ):
- rgToolFactory.py --bad_user $__user_email__
- #else:
- rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
- --tool_name "$tool_name"
- #if $make_TAB.value=="yes":
- --output_tab "$tab_file"
- #end if
- #if $makeMode.make_Tool=="yes":
- --make_Tool "$makeMode.make_Tool"
- --help_text "$helpme"
- --tool_desc "tool_desc"
- --new_tool "$new_tool"
- #end if
- #if $make_HTML.value=="yes":
- --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
- #end if
- #if $input1 != 'None':
- --input_tab "$input1"
- #end if
-#end if
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- make_TAB=="yes"
-
-
-
-
- make_HTML == "yes"
-
-
- makeMode['make_Tool'] == "yes"
-
-
-
-
-${dynScript}
-
-
-
-#if $makeMode.make_Tool == "yes":
-${makeMode.help_text}
-#end if
-
-
-
-
-.. class:: warningmark
-
-**Local Admins ONLY** Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
-
-**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.
-
-.. 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.
-
-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.
-
-.. class:: warningmark
-
-**Use on public servers** is STRONGLY discouraged for obvious reasons
-
-**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.
-
-**Simple examples**
-
-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::
-
- # 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')
- outp = t(inp)
- write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
-
-A more complex Rscript example takes no input file but generates a random heatmap pdf - you must make sure the option to create an HTML output file is
-turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page::
-
- # note this script takes NO input or output because it generates random data
- 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( "heattest.pdf" )
- 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()
-
-
-**Attribution** 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
-
-
-
-
-
-
diff -r f82dd90a8c9e -r ab0148be2111 inkblotheatmap/inkblotheatmap.Rscript
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/inkblotheatmap/inkblotheatmap.Rscript Wed Jun 06 23:04:16 2012 -0400
@@ -0,0 +1,7 @@
+
+# note this script takes NO input or output because it generates random data
+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( "heattest.pdf" )
+heatmap(bar,main='Random Heatmap')
+dev.off()
diff -r f82dd90a8c9e -r ab0148be2111 inkblotheatmap/inkblotheatmap.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/inkblotheatmap/inkblotheatmap.py Wed Jun 06 23:04:16 2012 -0400
@@ -0,0 +1,428 @@
+# rgToolFactory.py
+# https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+# this is a tool factory for simple scripts in python, R or whatever ails ye.
+# 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 binds 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.
+#
+
+#
+# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
+#
+# all rights reserved
+# Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+import sys
+import shutil
+import subprocess
+import os
+import time
+import tempfile
+import optparse
+import tarfile
+import re
+import shutil
+
+progname = os.path.split(sys.argv[0])[1]
+myversion = 'V000.1 May 2012'
+verbose = False
+debug = False
+
+
+def timenow():
+ """return current time as a string
+ """
+ return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+# characters that are allowed but need to be escaped
+
+class ScriptRunner:
+ """class is a wrapper for an arbitrary script
+ """
+
+ def __init__(self,opts=None):
+ """
+ cleanup inputs, setup some outputs
+
+ """
+ if opts.output_dir: # simplify for the tool tarball
+ os.chdir(opts.output_dir)
+ self.thumbformat = 'jpg'
+ self.opts = opts
+ self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name)
+ self.toolid = self.toolname
+ s = open(self.opts.script_path,'r').read()
+ self.script = s
+ 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
+ self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
+ if opts.output_dir: # may not want these complexities
+ self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
+ artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname)
+ artifact = open(artifactpath,'w')
+ artifact.write(self.script)
+ artifact.write('\n')
+ artifact.close()
+ if opts.make_Tool: # need this code and the user script for the tarball
+ localscript = open(self.sfile,'w')
+ localscript.write(self.script)
+ localscript.close()
+ shutil.copyfile(self.myname,'%s.py' % self.toolname) # for tool and for user
+ self.cl = []
+ self.html = []
+ a = self.cl.append
+ a(opts.interpreter)
+ a('-') # use stdin
+ a(opts.input_tab)
+ a(opts.output_tab)
+ self.outFormats = 'tabular' # TODO make this an option at tool generation time
+ self.inputFormats = 'tabular' # TODO make this an option at tool generation time
+ self.test1Input = 'test1_input.xls'
+ self.test1Output = 'test1_output.xls'
+ self.test1HTML = 'test1_output.html'
+
+ 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
+
+
+ a tabular file
+
+ reverse.py --script_path "$runMe" --interpreter "python"
+ --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
+
+
+
+
+
+
+
+
+
+
+
+**What it Does**
+
+Reverse the columns in a tabular file
+
+
+
+
+
+# reverse order of columns in a tabular file
+import sys
+inp = sys.argv[1]
+outp = sys.argv[2]
+i = open(inp,'r')
+o = open(outp,'w')
+for row in i:
+ rs = row.rstrip().split('\t')
+ rs.reverse()
+ o.write('\t'.join(rs))
+ o.write('\n')
+i.close()
+o.close()
+
+
+
+
+
+
+ """
+ newXML="""
+ %(tooldesc)s
+ %(command)s
+
+ %(inputs)s
+
+
+ %(outputs)s
+
+
+ %(help)s
+
+
+
+ %(script)s
+
+
+ """ # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
+
+ newCommand="""
+ %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
+ --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
+ """ # may NOT be an input or htmlout
+ tooltests = """
+
+
+
+ """
+ xdict = {}
+ xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
+ if self.opts.help_text:
+ xdict['help'] = open(self.opts.help_text,'r').read()
+ else:
+ xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
+ if self.opts.tool_desc:
+ xdict['tooldesc'] = '%s ' % self.opts.tool_desc
+ else:
+ xdict['tooldesc'] = ''
+ xdict['command_outputs'] = ''
+ xdict['outputs'] = ''
+ if self.opts.input_tab <> 'None':
+ xdict['command_inputs'] = '--input_tab "$input1"'
+ xdict['inputs'] = '' % self.inputFormats
+ else:
+ xdict['command_inputs'] = '' # assume no input - eg a random data generator
+ xdict['inputs'] = ''
+ xdict['inputs'] += '\n' % self.toolname
+ xdict['toolname'] = self.toolname
+ xdict['toolid'] = self.toolid
+ xdict['interpreter'] = self.opts.interpreter
+ xdict['scriptname'] = self.sfile
+ if self.opts.make_HTML:
+ xdict['command_outputs'] += '--output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
+ xdict['outputs'] += '\n'
+ if self.opts.output_tab <> 'None':
+ xdict['command_outputs'] += '--output_tab "$tab_file"'
+ xdict['outputs'] += '\n' % self.outFormats
+ xdict['command'] = newCommand % xdict
+ xmls = newXML % xdict
+ xf = open(self.xmlfile,'w')
+ xf.write(xmls)
+ xf.write('\n')
+ xf.close()
+ # ready for the tarball
+
+
+ def makeTooltar(self):
+ """
+ a tool is a gz tarball with eg
+ /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
+ """
+ retval = self.run()
+ if retval:
+ print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
+ sys.exit(1)
+ self.makeXML()
+ tdir = self.toolname
+ os.mkdir(tdir)
+ if self.opts.input_tab <> 'None': # we may have test data?
+ 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'))
+ shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
+ shutil.copyfile(self.pyfile,os.path.join(tdir,'%s.py' % self.toolname))
+ shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
+ tarpath = "%s.gz" % self.toolname
+ tar = tarfile.open(tarpath, "w:gz")
+ tar.add(tdir,arcname=self.toolname)
+ tar.close()
+ shutil.copy(tarpath,self.opts.new_tool)
+ shutil.rmtree(tdir)
+ ## TODO: replace with optional direct upload to local toolshed?
+ return retval
+
+ def compressPDF(self,inpdf=None,thumbformat='png'):
+ """need absolute path to pdf
+ """
+ assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
+ hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
+ sto = open(hlog,'w')
+ outpdf = '%s_compressed' % inpdf
+ cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
+ x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
+ retval1 = x.wait()
+ if retval1 == 0:
+ os.unlink(inpdf)
+ shutil.move(outpdf,inpdf)
+ outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
+ cl2 = ['convert', inpdf, outpng]
+ x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
+ retval2 = x.wait()
+ sto.close()
+ retval = retval1 or retval2
+ return retval
+
+
+ def getfSize(self,fpath,outpath):
+ """
+ format a nice file size string
+ """
+ size = ''
+ fp = os.path.join(outpath,fpath)
+ if os.path.isfile(fp):
+ 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 artefacts found in the output_dir
+ """
+
+ galhtmlprefix = """
+
+
+
+
+
Galaxy Tool Factory Script Wrapper tool output %s run at %s
"""
+ galhtmlpostfix = """\n"""
+
+ flist = os.listdir(self.opts.output_dir)
+ flist = [x for x in flist if x <> 'Rplots.pdf']
+ flist.sort()
+ html = [galhtmlprefix % progname,]
+ html.append('Galaxy %s outputs run at %s
\n' % (self.toolname,timenow()))
+ fhtml = []
+ if len(flist) > 0:
+ html.append('\n')
+ for fname in 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:
+ s= '
%s %s ' % (fname,fname,sfsize))
+ else:
+ fhtml.append('%s %s ' % (fname,fname,sfsize))
+ html.append('
\n')
+ if len(fhtml) > 0:
+ fhtml.insert(0,'')
+ fhtml.append('
')
+ html += fhtml # add all non-pdf files to the end of the display
+ else:
+ html.append('### Error - %s returned no files - please confirm that parameters are sane' % self.opts.interpreter)
+ html.append('%s log follows below
\n' % self.opts.interpreter)
+ rlog = open(self.tlog,'r').readlines()
+ html += rlog
+ html.append('
%s CL = %s
\n' % (self.toolname,' '.join(sys.argv)))
+ html.append('
\n')
+ html.append(galhtmlattr % (progname,timenow()))
+ 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):
+ """
+ """
+ if self.opts.output_dir:
+ sto = open(self.tlog,'w')
+ p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
+ else:
+ p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)
+ p.stdin.write(self.script)
+ p.stdin.close()
+ retval = p.wait()
+ if self.opts.output_dir:
+ sto.close()
+ if self.opts.make_HTML:
+ self.makeHtml()
+ return retval
+
+
+def main():
+ u = """
+ This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
+ rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
+
+ """
+ op = optparse.OptionParser()
+ a = op.add_option
+ a('--script_path',default=None)
+ a('--tool_name',default=None)
+ a('--interpreter',default=None)
+ a('--output_dir',default=None)
+ a('--output_html',default=None)
+ a('--input_tab',default="None")
+ a('--output_tab',default="None")
+ a('--user_email',default=None)
+ a('--bad_user',default=None)
+ a('--make_Tool',default=None)
+ a('--make_HTML',default=None)
+ a('--help_text',default=None)
+ a('--tool_desc',default=None)
+ a('--new_tool',default=None)
+ opts, args = op.parse_args()
+ assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin to add their ID to admin_users in universe_wsgi.ini' % (opts.bad_user)
+ assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
+ assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
+ assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
+ if opts.output_dir:
+ try:
+ os.makedirs(opts.output_dir)
+ except:
+ pass
+ r = ScriptRunner(opts)
+ if opts.make_Tool:
+ retcode = r.makeTooltar()
+ else:
+ retcode = r.run()
+ if retcode:
+ sys.exit(retcode) # indicate failure to job runner
+
+
+if __name__ == "__main__":
+ main()
+
+
diff -r f82dd90a8c9e -r ab0148be2111 inkblotheatmap/inkblotheatmap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/inkblotheatmap/inkblotheatmap.xml Wed Jun 06 23:04:16 2012 -0400
@@ -0,0 +1,32 @@
+
+ tool_desc
+
+ inkblotheatmap.py --script_path "$runMe" --interpreter "Rscript"
+ --tool_name "inkblotheatmap" --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
+
+
+
+
+
+
+
+
+
+
+
+**What it Does**
+
+
+
+
+
+# note this script takes NO input or output because it generates random data
+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( "heattest.pdf" )
+heatmap(bar,main='Random Heatmap')
+dev.off()
+
+
+
+
\n' % self.opts.interpreter) - rlog = open(self.tlog,'r').readlines() - html += rlog - html.append('
%s CL = %s
\n' % (self.toolname,' '.join(sys.argv))) - html.append('
+ """
+ galhtmlattr = """
Galaxy Tool Factory Script Wrapper tool output %s run at %s
""" + galhtmlpostfix = """
\n"""
+
+ flist = os.listdir(self.opts.output_dir)
+ flist = [x for x in flist if x <> 'Rplots.pdf']
+ flist.sort()
+ html = [galhtmlprefix % progname,]
+ html.append('Galaxy Tool Factory Script Wrapper tool output %s run at %s
""" + galhtmlpostfix = """
Galaxy %s outputs run at %s
\n' % (self.toolname,timenow())) + fhtml = [] + if len(flist) > 0: + html.append('
- ')
+ fhtml.append('
') + html += fhtml # add all non-pdf files to the end of the display + else: + html.append('
### Error - %s returned no files - please confirm that parameters are sane' % self.opts.interpreter)
+ html.append('%s log follows below
\n' % self.opts.interpreter)
+ rlog = open(self.tlog,'r').readlines()
+ html += rlog
+ html.append('
%s CL = %s
\n' % (self.toolname,' '.join(sys.argv)))
+ html.append('
\n')
+ html.append(galhtmlattr % (progname,timenow()))
+ 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):
+ """
+ """
+ if self.opts.output_dir:
+ sto = open(self.tlog,'w')
+ p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
+ else:
+ p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)
+ p.stdin.write(self.script)
+ p.stdin.close()
+ retval = p.wait()
+ if self.opts.output_dir:
+ sto.close()
+ if self.opts.make_HTML:
+ self.makeHtml()
+ return retval
+
+
+def main():
+ u = """
+ This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
+ rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
+
+ """
+ op = optparse.OptionParser()
+ a = op.add_option
+ a('--script_path',default=None)
+ a('--tool_name',default=None)
+ a('--interpreter',default=None)
+ a('--output_dir',default=None)
+ a('--output_html',default=None)
+ a('--input_tab',default="None")
+ a('--output_tab',default="None")
+ a('--user_email',default=None)
+ a('--bad_user',default=None)
+ a('--make_Tool',default=None)
+ a('--make_HTML',default=None)
+ a('--help_text',default=None)
+ a('--tool_desc',default=None)
+ a('--new_tool',default=None)
+ opts, args = op.parse_args()
+ assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin to add their ID to admin_users in universe_wsgi.ini' % (opts.bad_user)
+ assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
+ assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
+ assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
+ if opts.output_dir:
+ try:
+ os.makedirs(opts.output_dir)
+ except:
+ pass
+ r = ScriptRunner(opts)
+ if opts.make_Tool:
+ retcode = r.makeTooltar()
+ else:
+ retcode = r.run()
+ if retcode:
+ sys.exit(retcode) # indicate failure to job runner
+
+
+if __name__ == "__main__":
+ main()
+
+
diff -r f82dd90a8c9e -r ab0148be2111 inkblotheatmap/inkblotheatmap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/inkblotheatmap/inkblotheatmap.xml Wed Jun 06 23:04:16 2012 -0400
@@ -0,0 +1,32 @@
+
+ tool_desc
+
+ inkblotheatmap.py --script_path "$runMe" --interpreter "Rscript"
+ --tool_name "inkblotheatmap" --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
+
+
+
+
+
+
+
+
+
+
+
+**What it Does**
+
+
+
+
+
+# note this script takes NO input or output because it generates random data
+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( "heattest.pdf" )
+heatmap(bar,main='Random Heatmap')
+dev.off()
+
+
+
+
\n' % self.opts.interpreter) + rlog = open(self.tlog,'r').readlines() + html += rlog + html.append('
%s CL = %s
\n' % (self.toolname,' '.join(sys.argv))) + html.append('