skunkworks: fubar-galaxytoolfactory-58871556de57/rgToolFactory.py annotate

annotate fubar-galaxytoolfactory-58871556de57/rgToolFactory.py @ 6:cb4937b0c21d draft

This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.

author	fubar
date	Sun, 24 Feb 2013 17:15:29 -0500
parents
children

rev	line source
6 cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	1 # rgToolFactory.py
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	3 #
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	5 #
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	6 # all rights reserved
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	7 # Licensed under the LGPL
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	9 #
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	10 # January 2013
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	11 # problem pointed out by Carlos Borroto
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	12 # added escaping for <>$ - thought I did that ages ago...
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	13 #
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	14 # August 11 2012
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	15 # changed to use shell=False and cl as a sequence
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	16
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	17 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	18 # It also serves as the wrapper for the new tool.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	19 #
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	20 # you paste and run your script
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	21 # Only works for simple scripts that read one input from the history.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	22 # Optionally can write one new history dataset,
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	23 # and optionally collect any number of outputs into links on an autogenerated HTML page.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	24
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	25 # DO NOT install on a public or important site - please.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	26
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	27 # installed generated tools are fine if the script is safe.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	28 # They just run normally and their user cannot do anything unusually insecure
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	29 # but please, practice safe toolshed.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	30 # Read the fucking code before you install any tool
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	31 # especially this one
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	32
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	33 # After you get the script working on some test data, you can
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	34 # optionally generate a toolshed compatible gzip file
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	35 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	36 # safe and largely automated installation in a production Galaxy.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	37
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	38 # If you opt for an HTML output, you get all the script outputs arranged
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	39 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	40 # Ugly but really inexpensive.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	41 #
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	42 # Patches appreciated please.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	43 #
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	44 #
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	45 # long route to June 2012 product
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	46 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	47 # derived from an integrated script model
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	48 # called rgBaseScriptWrapper.py
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	49 # Note to the unwary:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	50 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	51 # There is nothing stopping a malicious user doing whatever they choose
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	52 # Extremely dangerous!!
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	53 # Totally insecure. So, trusted users only
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	54 #
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	55 # preferred model is a developer using their throw away workstation instance - ie a private site.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	56 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	57 #
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	58
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	59 import sys
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	60 import shutil
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	61 import subprocess
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	62 import os
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	63 import time
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	64 import tempfile
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	65 import optparse
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	66 import tarfile
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	67 import re
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	68 import shutil
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	69 import math
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	70
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	71 progname = os.path.split(sys.argv[0])[1]
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	72 myversion = 'V000.2 June 2012'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	73 verbose = False
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	74 debug = False
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	75 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	76
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	77 def timenow():
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	78 """return current time as a string
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	79 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	80 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	81
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	82 cheetah_escape_table = {
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	83 "$": "\$"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	84 }
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	85
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	86 cheetah_unescape_table = {
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	87 "\$": "$"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	88 }
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	89
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	90 def html_escape(t):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	91 """Unescape \$ first in case already done
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	92 cheetah barfs if any $ without \
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	93 xml parsing is controlled with <![CDATA[...]]>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	94 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	95 text = t
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	96 for k in cheetah_unescape_table.keys():
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	97 text = text.replace(k,cheetah_unescape_table[k])
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	98 for k in cheetah_escape_table.keys():
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	99 text = text.replace(k,cheetah_escape_table[k])
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	100 return text
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	101
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	102
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	103 class ScriptRunner:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	104 """class is a wrapper for an arbitrary script
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	105 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	106
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	107 def __init__(self,opts=None,treatbashSpecial=True):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	108 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	109 cleanup inputs, setup some outputs
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	110
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	111 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	112 self.treatbashSpecial = treatbashSpecial
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	113 if opts.output_dir: # simplify for the tool tarball
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	114 os.chdir(opts.output_dir)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	115 self.thumbformat = 'jpg'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	116 self.opts = opts
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	117 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	118 self.toolid = self.toolname
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	119 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	120 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	121 self.xmlfile = '%s.xml' % self.toolname
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	122 s = open(self.opts.script_path,'r').readlines()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	123 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	124 self.script = '\n'.join(s)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	125 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	126 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	127 tscript.write(self.script)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	128 tscript.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	129 self.escapedS = [html_escape(x) for x in s] # for restructured text in help
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	130 self.escapedScript = '\n'.join(self.escapedS)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	131 self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	132 if opts.output_dir: # may not want these complexities
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	133 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	134 art = '%s.%s' % (self.toolname,opts.interpreter)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	135 artpath = os.path.join(self.opts.output_dir,art) # need full path
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	136 artifact = open(artpath,'w') # use self.sfile as script source for Popen
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	137 artifact.write(self.script)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	138 artifact.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	139 self.cl = []
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	140 self.html = []
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	141 a = self.cl.append
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	142 a(opts.interpreter)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	143 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	144 a(self.sfile)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	145 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	146 a('-') # stdin
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	147 a(opts.input_tab)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	148 a(opts.output_tab)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	149 self.outFormats = 'tabular' # TODO make this an option at tool generation time
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	150 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	151 self.test1Input = '%s_test1_input.xls' % self.toolname
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	152 self.test1Output = '%s_test1_output.xls' % self.toolname
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	153 self.test1HTML = '%s_test1_output.html' % self.toolname
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	154
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	155 def makeXML(self):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	156 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	157 Create a Galaxy xml tool wrapper for the new script as a string to write out
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	158 fixme - use templating or something less fugly than this example of what we produce
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	159
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	160 <tool id="reverse" name="reverse" version="0.01">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	161 <description>a tabular file</description>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	162 <command interpreter="python">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	163 reverse.py --script_path "$runMe" --interpreter "python"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	164 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	165 </command>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	166 <inputs>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	167 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	168
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	169 </inputs>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	170 <outputs>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	171 <data format="tabular" name="tab_file" label="${job_name}"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	172
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	173 </outputs>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	174 <help>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	175
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	176 What it Does
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	177
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	178 Reverse the columns in a tabular file
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	179
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	180 </help>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	181 <configfiles>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	182 <configfile name="runMe">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	183
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	184 # reverse order of columns in a tabular file
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	185 import sys
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	186 inp = sys.argv[1]
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	187 outp = sys.argv[2]
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	188 i = open(inp,'r')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	189 o = open(outp,'w')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	190 for row in i:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	191 rs = row.rstrip().split('\t')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	192 rs.reverse()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	193 o.write('\t'.join(rs))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	194 o.write('\n')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	195 i.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	196 o.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	197
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	198
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	199 </configfile>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	200 </configfiles>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	201 </tool>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	202
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	203 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	204 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	205 %(tooldesc)s
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	206 %(command)s
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	207 <inputs>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	208 %(inputs)s
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	209 </inputs>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	210 <outputs>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	211 %(outputs)s
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	212 </outputs>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	213 <configfiles>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	214 <configfile name="runMe">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	215 <![CDATA[
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	216 %(script)s
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	217 ]]>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	218 </configfile>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	219 </configfiles>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	220 %(tooltests)s
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	221 <help>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	222 <![CDATA[
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	223 %(help)s
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	224 ]]>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	225
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	226 </help>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	227 </tool>"""
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	228 # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	229
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	230 newCommand="""<command interpreter="python">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	231 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	232 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	233 </command>""" # may NOT be an input or htmlout
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	234 tooltestsTabOnly = """<tests><test>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	235 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	236 <param name="job_name" value="test1"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	237 <param name="runMe" value="$runMe"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	238 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	239 </test></tests>"""
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	240 tooltestsHTMLOnly = """<tests><test>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	241 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	242 <param name="job_name" value="test1"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	243 <param name="runMe" value="$runMe"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	244 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	245 </test></tests>"""
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	246 tooltestsBoth = """<tests><test>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	247 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	248 <param name="job_name" value="test1"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	249 <param name="runMe" value="$runMe"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	250 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	251 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	252 </test></tests>"""
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	253 xdict = {}
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	254 xdict['tool_version'] = self.opts.tool_version
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	255 xdict['test1Input'] = self.test1Input
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	256 xdict['test1HTML'] = self.test1HTML
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	257 xdict['test1Output'] = self.test1Output
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	258 if self.opts.make_HTML and self.opts.output_tab <> 'None':
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	259 xdict['tooltests'] = tooltestsBoth % xdict
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	260 elif self.opts.make_HTML:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	261 xdict['tooltests'] = tooltestsHTMLOnly % xdict
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	262 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	263 xdict['tooltests'] = tooltestsTabOnly % xdict
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	264 xdict['script'] = self.escapedScript
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	265 # configfile is least painful way to embed script to avoid external dependencies
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	266 # but requires escaping of <, > and $ to avoid Mako parsing
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	267 if self.opts.help_text:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	268 xdict['help'] = open(self.opts.help_text,'r').read()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	269 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	270 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation\n'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	271 coda = ['Script','Pressing execute will run the following code over your input file and generate some outputs in your history::\n']
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	272 coda.append(self.indentedScript)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	273 coda.append('\n\n')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	274 coda.append('Attribution This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	275 coda.append('See %s for details of that project' % (toolFactoryURL))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	276 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	277 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	278 xdict['help'] = '%s\n\n%s\n\n' % (xdict['help'],'\n'.join(coda))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	279 if self.opts.tool_desc:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	280 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	281 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	282 xdict['tooldesc'] = ''
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	283 xdict['command_outputs'] = ''
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	284 xdict['outputs'] = ''
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	285 if self.opts.input_tab <> 'None':
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	286 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	287 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	288 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	289 xdict['command_inputs'] = '' # assume no input - eg a random data generator
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	290 xdict['inputs'] = ''
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	291 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
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	292 xdict['toolname'] = self.toolname
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	293 xdict['toolid'] = self.toolid
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	294 xdict['interpreter'] = self.opts.interpreter
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	295 xdict['scriptname'] = self.sfile
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	296 if self.opts.make_HTML:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	297 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	298 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	299 if self.opts.output_tab <> 'None':
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	300 xdict['command_outputs'] += ' --output_tab "$tab_file"'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	301 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	302 xdict['command'] = newCommand % xdict
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	303 xmls = newXML % xdict
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	304 xf = open(self.xmlfile,'w')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	305 xf.write(xmls)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	306 xf.write('\n')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	307 xf.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	308 # ready for the tarball
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	309
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	310
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	311 def makeTooltar(self):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	312 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	313 a tool is a gz tarball with eg
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	314 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	315 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	316 retval = self.run()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	317 if retval:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	318 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	319 sys.exit(1)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	320 self.makeXML()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	321 tdir = self.toolname
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	322 os.mkdir(tdir)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	323 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	324 testdir = os.path.join(tdir,'test-data')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	325 os.mkdir(testdir) # make tests directory
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	326 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	327 if self.opts.output_tab <> 'None':
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	328 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	329 if self.opts.make_HTML:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	330 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	331 if self.opts.output_dir:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	332 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	333 op = '%s.py' % self.toolname # new name
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	334 outpiname = os.path.join(tdir,op) # path for the tool tarball
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	335 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	336 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	337 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	338 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	339 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	340 notes += pi
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	341 outpi = open(outpiname,'w')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	342 outpi.write(''.join(notes))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	343 outpi.write('\n')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	344 outpi.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	345 stname = os.path.join(tdir,self.sfile)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	346 if not os.path.exists(stname):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	347 shutil.copyfile(self.sfile, stname)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	348 xtname = os.path.join(tdir,self.xmlfile)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	349 if not os.path.exists(xtname):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	350 shutil.copyfile(self.xmlfile,xtname)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	351 tarpath = "%s.gz" % self.toolname
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	352 tar = tarfile.open(tarpath, "w:gz")
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	353 tar.add(tdir,arcname=self.toolname)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	354 tar.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	355 shutil.copyfile(tarpath,self.opts.new_tool)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	356 shutil.rmtree(tdir)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	357 ## TODO: replace with optional direct upload to local toolshed?
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	358 return retval
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	359
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	360 def compressPDF(self,inpdf=None,thumbformat='png'):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	361 """need absolute path to pdf
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	362 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	363 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	364 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	365 sto = open(hlog,'w')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	366 outpdf = '%s_compressed' % inpdf
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	367 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	368 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	369 retval1 = x.wait()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	370 if retval1 == 0:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	371 os.unlink(inpdf)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	372 shutil.move(outpdf,inpdf)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	373 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	374 cl2 = ['convert', inpdf, outpng]
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	375 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	376 retval2 = x.wait()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	377 sto.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	378 retval = retval1 or retval2
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	379 return retval
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	380
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	381
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	382 def getfSize(self,fpath,outpath):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	383 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	384 format a nice file size string
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	385 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	386 size = ''
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	387 fp = os.path.join(outpath,fpath)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	388 if os.path.isfile(fp):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	389 size = '0 B'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	390 n = float(os.path.getsize(fp))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	391 if n > 2**20:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	392 size = '%1.1f MB' % (n/2**20)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	393 elif n > 2**10:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	394 size = '%1.1f KB)' % (n/2**10)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	395 elif n > 0:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	396 size = '%d B' % (int(n))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	397 return size
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	398
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	399 def makeHtml(self):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	400 """ Create an HTML file content to list all the artifacts found in the output_dir
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	401 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	402
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	403 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	404 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	405 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	406 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	407 <title></title>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	408 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	409 </head>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	410 <body>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	411 <div class="toolFormBody">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	412 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	413 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/>"""
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	414 galhtmlpostfix = """</div></body></html>\n"""
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	415
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	416 flist = os.listdir(self.opts.output_dir)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	417 flist = [x for x in flist if x <> 'Rplots.pdf']
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	418 flist.sort()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	419 html = []
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	420 html.append(galhtmlprefix % progname)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	421 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	422 fhtml = []
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	423 if len(flist) > 0:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	424 pdflist = []
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	425 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	426 nacross = 1
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	427 if npdf > 0:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	428 nacross = int(round(math.log(npdf,2)))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	429 nacross = max(1,nacross)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	430 width = min(400,int(1200/nacross))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	431 for rownum,fname in enumerate(flist):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	432 dname,e = os.path.splitext(fname)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	433 sfsize = self.getfSize(fname,self.opts.output_dir)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	434 if e.lower() == '.pdf' : # compress and make a thumbnail
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	435 thumb = '%s.%s' % (dname,self.thumbformat)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	436 pdff = os.path.join(self.opts.output_dir,fname)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	437 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	438 if retval == 0:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	439 pdflist.append((fname,thumb))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	440 if (rownum+1) % 2 == 0:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	441 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	442 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	443 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	444 ntogo = nacross # counter for table row padding with empty cells
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	445 if len(pdflist) > 0:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	446 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	447 for i,paths in enumerate(pdflist):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	448 fname,thumb = paths
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	449 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	450 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	451 if ((i+1) % nacross == 0):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	452 s += '</tr>\n'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	453 ntogo = 0
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	454 if i < (npdf - 1): # more to come
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	455 s += '<tr>'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	456 ntogo = nacross
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	457 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	458 ntogo -= 1
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	459 html.append(s)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	460 if html[-1].strip().endswith('</tr>'):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	461 html.append('</table></div>\n')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	462 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	463 if ntogo > 0: # pad
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	464 html.append('<td> </td>'*ntogo)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	465 html.append('</tr></table></div>\n')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	466 if len(fhtml) > 0:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	467 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')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	468 fhtml.append('</table></div><br/>')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	469 html += fhtml # add all non-pdf files to the end of the display
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	470 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	471 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	472 rlog = open(self.tlog,'r').readlines()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	473 rlog = [x for x in rlog if x.strip() > '']
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	474 if len(rlog) > 1:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	475 html.append('<div class="toolFormTitle">%s log</div><pre>\n' % self.opts.interpreter)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	476 html += rlog
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	477 html.append('</pre>\n')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	478 html.append(galhtmlattr % (self.toolname))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	479 html.append(galhtmlpostfix)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	480 htmlf = file(self.opts.output_html,'w')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	481 htmlf.write('\n'.join(html))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	482 htmlf.write('\n')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	483 htmlf.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	484 self.html = html
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	485
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	486
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	487 def run(self):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	488 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	489 scripts must be small enough not to fill the pipe!
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	490 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	491 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	492 retval = self.runBash()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	493 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	494 if self.opts.output_dir:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	495 sto = open(self.tlog,'w')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	496 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	497 sto.flush()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	498 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	499 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	500 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	501 p.stdin.write(self.script)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	502 p.stdin.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	503 retval = p.wait()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	504 if self.opts.output_dir:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	505 sto.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	506 if self.opts.make_HTML:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	507 self.makeHtml()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	508 return retval
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	509
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	510 def runBash(self):
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	511 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	512 cannot use - for bash so use self.sfile
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	513 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	514 if self.opts.output_dir:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	515 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	516 sto = open(self.tlog,'w')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	517 sto.write(s)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	518 sto.flush()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	519 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	520 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	521 p = subprocess.Popen(self.cl,shell=False)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	522 retval = p.wait()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	523 if self.opts.output_dir:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	524 sto.close()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	525 if self.opts.make_HTML:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	526 self.makeHtml()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	527 return retval
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	528
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	529
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	530 def main():
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	531 u = """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	532 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	533 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	534 </command>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	535 """
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	536 op = optparse.OptionParser()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	537 a = op.add_option
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	538 a('--script_path',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	539 a('--tool_name',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	540 a('--interpreter',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	541 a('--output_dir',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	542 a('--output_html',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	543 a('--input_tab',default="None")
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	544 a('--output_tab',default="None")
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	545 a('--user_email',default='Unknown')
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	546 a('--bad_user',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	547 a('--make_Tool',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	548 a('--make_HTML',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	549 a('--help_text',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	550 a('--tool_desc',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	551 a('--new_tool',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	552 a('--tool_version',default=None)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	553 opts, args = op.parse_args()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	554 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)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	555 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	556 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	557 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	558 if opts.output_dir:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	559 try:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	560 os.makedirs(opts.output_dir)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	561 except:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	562 pass
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	563 r = ScriptRunner(opts)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	564 if opts.make_Tool:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	565 retcode = r.makeTooltar()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	566 else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	567 retcode = r.run()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	568 os.unlink(r.sfile)
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	569 if retcode:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	570 sys.exit(retcode) # indicate failure to job runner
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	571
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	572
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	573 if __name__ == "__main__":
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	574 main()
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	575
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now. fubar parents: diff changeset	576

Mercurial > repos > fubar > toolfactory

annotate fubar-galaxytoolfactory-58871556de57/rgToolFactory.py @ 6:cb4937b0c21d draft