+ """
+ 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 000000000000 -r 5376fbd79ead fubar-galaxytoolfactory-8cc3f3c0e539/rgToolFactory.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fubar-galaxytoolfactory-8cc3f3c0e539/rgToolFactory.xml Wed Jun 06 20:25:54 2012 -0400
@@ -0,0 +1,197 @@
+
+ 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
+
+
+
+
+
+
\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('