# HG changeset patch
# User lucasfsilva
# Date 1426192582 14400
# Node ID a3d3dc004a88d7b8d155490e8927afc778a89c7b
Uploaded
diff -r 000000000000 -r a3d3dc004a88 teste_out/test-data/dataset_20.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/teste_out/test-data/dataset_20.dat Thu Mar 12 16:36:22 2015 -0400
@@ -0,0 +1,1 @@
+GSM686937_SAMPLE19.LNCAP-H3K27AC-DHT-SICTRL.REGIONS.HG19.BEDTESTE: MYDYNAMICSCRIPT.TXTTESTE: SAIDATESTE.TXTTESTE: MYDYNAMICSCRIPT.TXTTESTE: SAIDA_TESTE_2.TXTTESTE: MYDYNAMICSCRIPT.AB1TESTE: MYDYNAMICSCRIPT.AB1TESTE: MYDYNAMICSCRIPT.TXTTESTE: SAIDA_QUASE.TXTTESTE: MYDYNAMICSCRIPT.TXT
\ No newline at end of file
diff -r 000000000000 -r a3d3dc004a88 teste_out/test-data/dataset_22.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/teste_out/test-data/dataset_22.dat Thu Mar 12 16:36:22 2015 -0400
@@ -0,0 +1,1 @@
+GSM686937_SAMPLE19.LNCAP-H3K27AC-DHT-SICTRL.REGIONS.HG19.BEDTESTE: MYDYNAMICSCRIPT.TXTTESTE: SAIDATESTE.TXTTESTE: MYDYNAMICSCRIPT.TXTTESTE: SAIDA_TESTE_2.TXTTESTE: MYDYNAMICSCRIPT.AB1TESTE: MYDYNAMICSCRIPT.AB1TESTE: MYDYNAMICSCRIPT.TXTTESTE: SAIDA_QUASE.TXTTESTE: MYDYNAMICSCRIPT.TXT
\ No newline at end of file
diff -r 000000000000 -r a3d3dc004a88 teste_out/test-data/test1_out.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/teste_out/test-data/test1_out.log Thu Mar 12 16:36:22 2015 -0400
@@ -0,0 +1,1 @@
+## Executing Toolfactory generated command line = python /home/lucassilva/galaxy/galaxy-dist/database/tmp/teste_outXab0YS.python --inpaths=/home/lucassilva/galaxy/galaxy-dist/database/files/000/dataset_20.dat,/home/lucassilva/galaxy/galaxy-dist/database/files/000/dataset_22.dat --innames=lucas_teste.txt,lucas_teste.txt --outpath=/home/lucassilva/galaxy/galaxy-dist/database/files/000/dataset_24.dat
diff -r 000000000000 -r a3d3dc004a88 teste_out/test-data/teste_out_test1_output.xls
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/teste_out/test-data/teste_out_test1_output.xls Thu Mar 12 16:36:22 2015 -0400
@@ -0,0 +1,1 @@
+LUCAS_TESTE.TXTTESTE: LUCAS_TESTE.TXT
\ No newline at end of file
diff -r 000000000000 -r a3d3dc004a88 teste_out/teste_out.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/teste_out/teste_out.py Thu Mar 12 16:36:22 2015 -0400
@@ -0,0 +1,966 @@
+# teste_out/teste_out.py - a self annotated version of rgToolFactory2.py generated by running rgToolFactory2.py
+# to make a new Galaxy tool called teste_out
+# User bioinfolucas@gmail.com at 12/03/2015 17:34:22
+# rgToolFactoryMultIn.py
+# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+#
+# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
+#
+# all rights reserved
+# Licensed under the LGPL
+# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+#
+# January 2015
+# unified all setups by passing the script on the cl rather than via a PIPE - no need for treat_bash_special so removed
+#
+# in the process of building a complex tool
+# added ability to choose one of the current toolshed package_r or package_perl or package_python dependencies and source that package
+# add that package to tool_dependencies
+# Note that once the generated tool is loaded, it will have that package's env.sh loaded automagically so there is no
+# --envshpath in the parameters for the generated tool and it uses the system one which will be first on the adjusted path.
+#
+# sept 2014 added additional params from
+# https://bitbucket.org/mvdbeek/dockertoolfactory/src/d4863bcf7b521532c7e8c61b6333840ba5393f73/DockerToolFactory.py?at=default
+# passing them is complex
+# and they are restricted to NOT contain commas or double quotes to ensure that they can be safely passed together on
+# the toolfactory command line as a comma delimited double quoted string for parsing and passing to the script
+# see examples on this tool form
+
+# august 2014
+
+# Allows arbitrary number of input files
+# NOTE positional parameters are now passed to script
+# and output (may be "None") is *before* arbitrary number of inputs
+#
+# march 2014
+# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
+# grrrrr - night before a demo
+# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
+#
+# added ghostscript and graphicsmagick as dependencies
+# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
+# errors ensued
+#
+# august 2013
+# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
+#
+# july 2013
+# added ability to combine images and individual log files into html output
+# just make sure there's a log file foo.log and it will be output
+# together with all images named like "foo_*.pdf
+# otherwise old format for html
+#
+# January 2013
+# problem pointed out by Carlos Borroto
+# added escaping for <>$ - thought I did that ages ago...
+#
+# August 11 2012
+# changed to use shell=False and cl as a sequence
+
+# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
+# It also serves as the wrapper for the new tool.
+#
+# you paste and run your script
+# Only works for simple scripts that read one input from the history.
+# Optionally can write one new history dataset,
+# and optionally collect any number of outputs into links on an autogenerated HTML page.
+
+# DO NOT install on a public or important site - please.
+
+# installed generated tools are fine if the script is safe.
+# They just run normally and their user cannot do anything unusually insecure
+# but please, practice safe toolshed.
+# Read the fucking code before you install any tool
+# especially this one
+
+# After you get the script working on some test data, you can
+# optionally generate a toolshed compatible gzip file
+# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
+# safe and largely automated installation in a production Galaxy.
+
+# If you opt for an HTML output, you get all the script outputs arranged
+# as a single Html history item - all output files are linked, thumbnails for all the pdfs.
+# Ugly but really inexpensive.
+#
+# Patches appreciated please.
+#
+#
+# long route to June 2012 product
+# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
+# derived from an integrated script model
+# called rgBaseScriptWrapper.py
+# Note to the unwary:
+# This tool allows arbitrary scripting on your Galaxy as the Galaxy user
+# There is nothing stopping a malicious user doing whatever they choose
+# Extremely dangerous!!
+# Totally insecure. So, trusted users only
+#
+# preferred model is a developer using their throw away workstation instance - ie a private site.
+# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
+#
+
+import sys
+import shutil
+import subprocess
+import os
+import time
+import tempfile
+import optparse
+import tarfile
+import re
+import shutil
+import math
+
+progname = os.path.split(sys.argv[0])[1]
+myversion = 'V001.1 March 2014'
+verbose = False
+debug = False
+toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
+
+# if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
+# tool xml
+
+def timenow():
+ """return current time as a string
+ """
+ return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+def quote_non_numeric(s):
+ """return a prequoted string for non-numerics
+ useful for perl and Rscript parameter passing?
+ """
+ try:
+ res = float(s)
+ return s
+ except ValueError:
+ return '"%s"' % s
+
+html_escape_table = {
+ "&": "&",
+ ">": ">",
+ "<": "<",
+ "$": "\$"
+ }
+
+def html_escape(text):
+ """Produce entities within text."""
+ return "".join(html_escape_table.get(c,c) for c in text)
+
+
+def html_unescape(text):
+ """Revert entities within text."""
+ t = text.replace('&','&').replace('>','>').replace('<','<').replace('\$','$')
+ return t
+
+def cmd_exists(cmd):
+ return subprocess.call("type " + cmd, shell=True,
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
+
+def parse_citations(citations_text):
+ """
+ """
+ citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
+ citation_tuples = []
+ for citation in citations:
+ if citation.startswith("doi"):
+ citation_tuples.append( ("doi", citation[len("doi"):].strip() ) )
+ else:
+ citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
+ return citation_tuples
+
+def shell_source(script):
+ """need a way to source a Galaxy tool interpreter env.sh to point at the right dependency package
+ This based on the idea in http://pythonwise.blogspot.fr/2010/04/sourcing-shell-script.html
+ Note that we have to finesse any wierdly quoted newlines in automagic exports using nulls (env -0) as newlines"""
+ pipe = subprocess.Popen("env -i ; . %s ; env -0" % script, stdout=subprocess.PIPE, shell=True)
+ output = pipe.communicate()[0]
+ outl = output.split('\0')
+ outl = [x for x in outl if len(x.split("=")) == 2]
+ newenv = dict((line.split("=", 1) for line in outl))
+ os.environ.update(newenv)
+
+class ScriptRunner:
+ """class is a wrapper for an arbitrary script
+ note funky templating. this should all be done proper.
+ Problem is, this kludge developed quite naturally and seems to work ok with
+ little overhead...
+
+ """
+
+
+ def __init__(self,opts=None):
+ """
+ cleanup inputs, setup some outputs
+
+ """
+
+ self.toolhtmldepinterpskel = """
+
+
+
+
+
+
+
+
+
+
+
+
+ %(readme)s
+ This file was autogenerated by the Galaxy Tool Factory 2
+
+
+ """
+
+ self.toolhtmldepskel = """
+
+
+
+
+
+
+
+
+ %(readme)s
+ This file was autogenerated by the Galaxy Tool Factory 2
+
+
+ """
+
+ self.emptytoolhtmldepskel = """
+
+
+ %(readme)s
+ This file was autogenerated by the Galaxy Tool Factory 2
+
+
+ """
+
+ self.protorequirements = """
+ ghostscript
+ graphicsmagick
+ """
+
+ self.protorequirements_interpreter = """
+ ghostscript
+ graphicsmagick
+ %(interpreter_name)s
+ """
+
+
+ self.newCommand="""
+ %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
+ --tool_name "%(toolname)s"
+ %(command_inputs)s
+ %(command_outputs)s
+ """
+
+ self.tooltestsTabOnly = """
+
+ %(test1Inputs)s
+
+
+
+ %(additionalParams)s
+
+ """
+
+ self.tooltestsHTMLOnly = """
+
+ %(test1Inputs)s
+
+
+ %(additionalParams)s
+
+
+ """
+
+ self.tooltestsBoth = """
+
+ %(test1Inputs)s
+
+
+ %(additionalParams)s
+
+
+
+ """
+
+ self.newXML="""
+%(tooldesc)s
+%(requirements)s
+
+%(command)s
+
+
+%(inputs)s
+%(additionalInputs)s
+
+
+%(outputs)s
+
+
+
+%(script)s
+
+
+
+%(tooltests)s
+
+
+
+%(help)s
+
+This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
+https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2
+
+
+ %(citations)s
+ 10.1093/bioinformatics/bts573
+
+"""
+
+ self.useGM = cmd_exists('gm')
+ self.useIM = cmd_exists('convert')
+ self.useGS = cmd_exists('gs')
+ self.temp_warned = False # we want only one warning if $TMP not set
+ if opts.output_dir: # simplify for the tool tarball
+ os.chdir(opts.output_dir)
+ self.thumbformat = 'png'
+ self.opts = opts
+ self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
+ self.toolid = self.toolname
+ self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
+ self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
+ self.xmlfile = '%s.xml' % self.toolname
+ rx = open(self.opts.script_path,'r').readlines()
+ rx = [x.rstrip() for x in rx] # remove pesky dos line endings if needed
+ self.script = '\n'.join(rx)
+ fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
+ tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
+ tscript.write(self.script)
+ tscript.close()
+ self.indentedScript = " %s" % '\n'.join([' %s' % html_escape(x) for x in rx]) # for restructured text in help
+ self.escapedScript = "%s" % '\n'.join([' %s' % html_escape(x) for x in rx])
+ self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
+ if opts.output_dir: # may not want these complexities
+ self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
+ art = '%s.%s' % (self.toolname,opts.interpreter)
+ artpath = os.path.join(self.opts.output_dir,art) # need full path
+ artifact = open(artpath,'w') # use self.sfile as script source for Popen
+ artifact.write(self.script)
+ artifact.close()
+ self.cl = []
+ self.html = []
+ self.test1Inputs = [] # now a list
+ a = self.cl.append
+ a(opts.interpreter)
+ a(self.sfile)
+ # if multiple inputs - positional or need to distinguish them with cl params
+ if opts.input_tab:
+ tests = []
+ for i,intab in enumerate(opts.input_tab): # if multiple, make tests
+ if intab.find(',') <> -1:
+ (gpath,uname) = intab.split(',')
+ else:
+ gpath = uname = intab
+ tests.append(os.path.basename(gpath))
+ self.test1Inputs = '' % (','.join(tests))
+ else:
+ self.test1Inputs = ''
+ # we always pass path,name pairs in using python optparse append
+ # but the command line has to be different
+ self.infile_paths = ''
+ self.infile_names = ''
+ if self.opts.input_tab:
+ self.infile_paths = ','.join([x.split(',')[0].strip() for x in self.opts.input_tab])
+ self.infile_names = ','.join([x.split(',')[1].strip() for x in self.opts.input_tab])
+ if self.opts.interpreter == 'python':
+ # yes, this is how additional parameters are always passed in python - to the TF itself and to
+ # scripts to avoid having unknown parameter names (yes, they can be parsed but...) on the command line
+ if self.opts.input_tab:
+ a('--inpaths=%s' % (self.infile_paths))
+ a('--innames=%s' % (self.infile_names))
+ if self.opts.output_tab:
+ a('--outpath=%s' % self.opts.output_tab)
+ for p in opts.additional_parameters:
+ p = p.replace('"','')
+ psplit = p.split(',')
+ param = html_unescape(psplit[0])
+ value = html_unescape(psplit[1])
+ a('%s="%s"' % (param,value))
+ if (self.opts.interpreter == 'Rscript'):
+ # pass params on command line as expressions which the script evaluates - see sample
+ if self.opts.input_tab:
+ a('INPATHS="%s"' % self.infile_paths)
+ a('INNAMES="%s"' % self.infile_names)
+ if self.opts.output_tab:
+ a('OUTPATH="%s"' % self.opts.output_tab)
+ for p in opts.additional_parameters:
+ p = p.replace('"','')
+ psplit = p.split(',')
+ param = html_unescape(psplit[0])
+ value = html_unescape(psplit[1])
+ a('%s=%s' % (param,quote_non_numeric(value)))
+ if (self.opts.interpreter == 'perl'):
+ # pass positional params on command line - perl script needs to discombobulate the path/name lists
+ if self.opts.input_tab:
+ a('%s' % self.infile_paths)
+ a('%s' % self.infile_names)
+ if self.opts.output_tab:
+ a('%s' % self.opts.output_tab)
+ for p in opts.additional_parameters:
+ # followed by any additional name=value parameter pairs
+ p = p.replace('"','')
+ psplit = p.split(',')
+ param = html_unescape(psplit[0])
+ value = html_unescape(psplit[1])
+ a('%s=%s' % (param,quote_non_numeric(value)))
+ if self.opts.interpreter == 'sh' or self.opts.interpreter == 'bash':
+ # more is better - now move all params into environment AND drop on to command line.
+ self.cl.insert(0,'env')
+ if self.opts.input_tab:
+ self.cl.insert(1,'INPATHS=%s' % (self.infile_paths))
+ self.cl.insert(2,'INNAMES=%s' % (self.infile_names))
+ if self.opts.output_tab:
+ self.cl.insert(3,'OUTPATH=%s' % (self.opts.output_tab))
+ a('OUTPATH=%s' % (self.opts.output_tab))
+ # sets those environment variables for the script
+ # additional params appear in CL - yes, it's confusing
+ for i,p in enumerate(opts.additional_parameters):
+ psplit = p.split(',')
+ param = html_unescape(psplit[0])
+ value = html_unescape(psplit[1])
+ a('%s=%s' % (param,quote_non_numeric(value)))
+ self.cl.insert(4+i,'%s=%s' % (param,quote_non_numeric(value)))
+ self.interpreter_owner = 'SYSTEM'
+ self.interpreter_pack = 'SYSTEM'
+ self.interpreter_name = 'SYSTEM'
+ self.interpreter_version = 'SYSTEM'
+ self.interpreter_revision = 'SYSTEM'
+ if opts.envshpath <> 'system': # need to parse out details for our tool_dependency
+ try: # fragile - depends on common naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play
+ # this ONLY happens at tool generation by an admin - the generated tool always uses the default of system so path is from local env.sh
+ packdetails = opts.envshpath.split(os.path.sep)[-4:-1] # eg ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
+ self.interpreter_owner = packdetails[0]
+ self.interpreter_pack = packdetails[1]
+ self.interpreter_name = packdetails[1].split('_')[1].upper()
+ self.interpreter_revision = packdetails[2]
+ self.interpreter_version = '.'.join(packdetails[1].split('_')[2:])
+ except:
+ pass
+ self.outFormats = opts.output_format
+ self.inputFormats = opts.input_formats
+ self.test1Output = '%s_test1_output.xls' % self.toolname
+ self.test1HTML = '%s_test1_output.html' % self.toolname
+
+ def makeXML(self):
+ """
+ Create a Galaxy xml tool wrapper for the new script as a string to write out
+ fixme - use templating or something less fugly than this example of what we produce
+
+
+ a tabular file
+
+ reverse.py --script_path "$runMe" --interpreter "python"
+ --tool_name "reverse" --input_tab "$input1" --output_tab "$output1"
+
+
+
+
+
+
+
+
+
+
+
+**What it Does**
+
+Reverse the columns in a tabular file
+
+
+
+
+
+# reverse order of columns in a tabular file
+import sys
+inp = sys.argv[1]
+outp = sys.argv[2]
+i = open(inp,'r')
+o = open(outp,'w')
+for row in i:
+ rs = row.rstrip().split('\t')
+ rs.reverse()
+ o.write('\t'.join(rs))
+ o.write('\n')
+i.close()
+o.close()
+
+
+
+
+
+
+ """
+
+ # these templates need a dict with the right keys to match the parameters - outputs, help, code...
+
+ xdict = {}
+ xdict['additionalParams'] = ''
+ xdict['additionalInputs'] = ''
+ if self.opts.additional_parameters:
+ if self.opts.edit_additional_parameters: # add to new tool form with default value set to original value
+ xdict['additionalInputs'] = '\n'.join(['' % \
+ (x.split(',')[0],html_escape(x.split(',')[1]),html_escape(x.split(',')[2]),html_escape(x.split(',')[3]), x.split(',')[4]) for x in self.opts.additional_parameters])
+ xdict['additionalParams'] = '\n'.join(['' % (x.split(',')[0],html_escape(x.split(',')[1])) for x in self.opts.additional_parameters])
+ xdict['interpreter_owner'] = self.interpreter_owner
+ xdict['interpreter_version'] = self.interpreter_version
+ xdict['interpreter_pack'] = self.interpreter_pack
+ xdict['interpreter_name'] = self.interpreter_name
+ xdict['requirements'] = ''
+ if self.opts.include_dependencies == "yes":
+ if self.opts.envshpath <> 'system':
+ xdict['requirements'] = self.protorequirements_interpreter % xdict
+ else:
+ xdict['requirements'] = self.protorequirements
+ xdict['tool_version'] = self.opts.tool_version
+ xdict['test1HTML'] = self.test1HTML
+ xdict['test1Output'] = self.test1Output
+ xdict['test1Inputs'] = self.test1Inputs
+ if self.opts.make_HTML and self.opts.output_tab:
+ xdict['tooltests'] = self.tooltestsBoth % xdict
+ elif self.opts.make_HTML:
+ xdict['tooltests'] = self.tooltestsHTMLOnly % xdict
+ else:
+ xdict['tooltests'] = self.tooltestsTabOnly % xdict
+ xdict['script'] = self.escapedScript
+ # configfile is least painful way to embed script to avoid external dependencies
+ # but requires escaping of <, > and $ to avoid Mako parsing
+ if self.opts.help_text:
+ helptext = open(self.opts.help_text,'r').readlines()
+ helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
+ xdict['help'] = ''.join([x for x in helptext])
+ else:
+ xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
+ coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
+ coda.append('\n')
+ coda.append(self.indentedScript)
+ coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
+ coda.append('See %s for details of that project' % (toolFactoryURL))
+ coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
+ coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
+ xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
+ if self.opts.tool_desc:
+ xdict['tooldesc'] = '%s' % self.opts.tool_desc
+ else:
+ xdict['tooldesc'] = ''
+ xdict['command_outputs'] = ''
+ xdict['outputs'] = ''
+ if self.opts.input_tab:
+ cins = ['\n',]
+ cins.append('--input_formats %s' % self.opts.input_formats)
+ cins.append('#for intab in $input1:')
+ cins.append('--input_tab "${intab},${intab.name}"')
+ cins.append('#end for\n')
+ xdict['command_inputs'] = '\n'.join(cins)
+ xdict['inputs'] = ''' \n''' % (self.inputFormats,self.inputFormats)
+ else:
+ xdict['command_inputs'] = '' # assume no input - eg a random data generator
+ xdict['inputs'] = ''
+ if (len(self.opts.additional_parameters) > 0):
+ cins = ['\n',]
+ for params in self.opts.additional_parameters:
+ psplit = params.split(',') # name,value...
+ psplit[3] = html_escape(psplit[3])
+ if self.opts.edit_additional_parameters:
+ psplit[1] = '$%s' % psplit[0] # replace with form value
+ else:
+ psplit[1] = html_escape(psplit[1]) # leave prespecified value
+ cins.append('--additional_parameters """%s"""' % ','.join(psplit))
+ xdict['command_inputs'] = '%s\n%s' % (xdict['command_inputs'],'\n'.join(cins))
+ xdict['inputs'] += ' \n' % self.toolname
+ xdict['toolname'] = self.toolname
+ xdict['toolid'] = self.toolid
+ xdict['interpreter'] = self.opts.interpreter
+ xdict['scriptname'] = self.sfile
+ if self.opts.make_HTML:
+ xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
+ xdict['outputs'] += ' \n'
+ else:
+ xdict['command_outputs'] += ' --output_dir "./"'
+ if self.opts.output_tab:
+ xdict['command_outputs'] += ' --output_tab "$output1"'
+ xdict['outputs'] += ' \n' % self.outFormats
+ xdict['command'] = self.newCommand % xdict
+ if self.opts.citations:
+ citationstext = open(self.opts.citations,'r').read()
+ citation_tuples = parse_citations(citationstext)
+ citations_xml = ""
+ for citation_type, citation_content in citation_tuples:
+ citation_xml = """%s""" % (citation_type, html_escape(citation_content))
+ citations_xml += citation_xml
+ xdict['citations'] = citations_xml
+ else:
+ xdict['citations'] = ""
+ xmls = self.newXML % xdict
+ xf = open(self.xmlfile,'w')
+ xf.write(xmls)
+ xf.write('\n')
+ xf.close()
+ # ready for the tarball
+
+
+ def makeTooltar(self):
+ """
+ a tool is a gz tarball with eg
+ /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
+ """
+ retval = self.run()
+ if retval:
+ print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
+ sys.exit(1)
+ tdir = self.toolname
+ os.mkdir(tdir)
+ self.makeXML()
+ if self.opts.help_text:
+ hlp = open(self.opts.help_text,'r').read()
+ else:
+ hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
+ readme_dict = {'readme':hlp,'interpreter':self.opts.interpreter,'interpreter_version':self.interpreter_version,'interpreter_name':self.interpreter_name,
+ 'interpreter_owner':self.interpreter_owner,'interpreter_pack':self.interpreter_pack}
+ if self.opts.include_dependencies == "yes":
+ if self.opts.envshpath == 'system':
+ tooldepcontent = self.toolhtmldepskel % readme_dict
+ else:
+ tooldepcontent = self.toolhtmldepinterpskel % readme_dict
+ else:
+ tooldepcontent = self.emptytoolhtmldepskel % readme_dict
+ depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
+ depf.write(tooldepcontent)
+ depf.write('\n')
+ depf.close()
+ testdir = os.path.join(tdir,'test-data')
+ os.mkdir(testdir) # make tests directory
+ for i,intab in enumerate(self.opts.input_tab):
+ si = self.opts.input_tab[i]
+ if si.find(',') <> -1:
+ s = si.split(',')[0]
+ si = s
+ dest = os.path.join(testdir,os.path.basename(si))
+ if si <> dest:
+ shutil.copyfile(si,dest)
+ if self.opts.output_tab:
+ shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
+ if self.opts.make_HTML:
+ shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
+ if self.opts.output_dir:
+ shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
+ outpif = '%s.py' % self.toolname # new name
+ outpiname = os.path.join(tdir,outpif) # path for the tool tarball
+ pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
+ notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
+ notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
+ notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
+ pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
+ notes += pi
+ outpi = open(outpiname,'w')
+ outpi.write(''.join(notes))
+ outpi.write('\n')
+ outpi.close()
+ stname = os.path.join(tdir,self.sfile)
+ if not os.path.exists(stname):
+ shutil.copyfile(self.sfile, stname)
+ xtname = os.path.join(tdir,self.xmlfile)
+ if not os.path.exists(xtname):
+ shutil.copyfile(self.xmlfile,xtname)
+ tarpath = "%s.tar.gz" % self.toolname
+ tar = tarfile.open(tarpath, "w:gz")
+ tar.add(tdir,arcname='%s' % self.toolname)
+ tar.close()
+ shutil.copyfile(tarpath,self.opts.new_tool)
+ shutil.rmtree(tdir)
+ ## TODO: replace with optional direct upload to local toolshed?
+ return retval
+
+
+ def compressPDF(self,inpdf=None,thumbformat='png'):
+ """need absolute path to pdf
+ note that GS gets confoozled if no $TMP or $TEMP
+ so we set it
+ """
+ assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
+ hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
+ sto = open(hlog,'a')
+ our_env = os.environ.copy()
+ our_tmp = our_env.get('TMP',None)
+ if not our_tmp:
+ our_tmp = our_env.get('TEMP',None)
+ if not (our_tmp and os.path.exists(our_tmp)):
+ newtmp = os.path.join(self.opts.output_dir,'tmp')
+ try:
+ os.mkdir(newtmp)
+ except:
+ sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
+ our_env['TEMP'] = newtmp
+ if not self.temp_warned:
+ sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
+ self.temp_warned = True
+ outpdf = '%s_compressed' % inpdf
+ cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
+ x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
+ retval1 = x.wait()
+ sto.close()
+ if retval1 == 0:
+ os.unlink(inpdf)
+ shutil.move(outpdf,inpdf)
+ os.unlink(hlog)
+ hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
+ sto = open(hlog,'w')
+ outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
+ if self.useGM:
+ cl2 = ['gm', 'convert', inpdf, outpng]
+ else: # assume imagemagick
+ cl2 = ['convert', inpdf, outpng]
+ x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
+ retval2 = x.wait()
+ sto.close()
+ if retval2 == 0:
+ os.unlink(hlog)
+ retval = retval1 or retval2
+ return retval
+
+
+ def getfSize(self,fpath,outpath):
+ """
+ format a nice file size string
+ """
+ size = ''
+ fp = os.path.join(outpath,fpath)
+ if os.path.isfile(fp):
+ size = '0 B'
+ n = float(os.path.getsize(fp))
+ if n > 2**20:
+ size = '%1.1f MB' % (n/2**20)
+ elif n > 2**10:
+ size = '%1.1f KB' % (n/2**10)
+ elif n > 0:
+ size = '%d B' % (int(n))
+ return size
+
+ def makeHtml(self):
+ """ Create an HTML file content to list all the artifacts found in the output_dir
+ """
+
+ galhtmlprefix = """
+
+
+
+
+
+
+
+
\n"""
+
+ flist = os.listdir(self.opts.output_dir)
+ flist = [x for x in flist if x <> 'Rplots.pdf']
+ flist.sort()
+ html = []
+ html.append(galhtmlprefix % progname)
+ html.append('
Galaxy Tool "%s" run at %s
' % (self.toolname,timenow()))
+ fhtml = []
+ if len(flist) > 0:
+ logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
+ logfiles.sort()
+ logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
+ logfiles.append(os.path.abspath(self.tlog)) # make it the last one
+ pdflist = []
+ npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
+ for rownum,fname in enumerate(flist):
+ dname,e = os.path.splitext(fname)
+ sfsize = self.getfSize(fname,self.opts.output_dir)
+ if e.lower() == '.pdf' : # compress and make a thumbnail
+ thumb = '%s.%s' % (dname,self.thumbformat)
+ pdff = os.path.join(self.opts.output_dir,fname)
+ retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
+ if retval == 0:
+ pdflist.append((fname,thumb))
+ else:
+ pdflist.append((fname,fname))
+ if (rownum+1) % 2 == 0:
+ fhtml.append('
' % (fname,fname,sfsize))
+ for logfname in logfiles: # expect at least tlog - if more
+ if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
+ sectionname = 'All tool run'
+ if (len(logfiles) > 1):
+ sectionname = 'Other'
+ ourpdfs = pdflist
+ else:
+ realname = os.path.basename(logfname)
+ sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
+ ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
+ pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
+ nacross = 1
+ npdf = len(ourpdfs)
+
+ if npdf > 0:
+ nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
+ if int(nacross)**2 != npdf:
+ nacross += 1
+ nacross = int(nacross)
+ width = min(400,int(1200/nacross))
+ html.append('
%s images and outputs
' % sectionname)
+ html.append('(Click on a thumbnail image to download the corresponding original PDF image) ')
+ ntogo = nacross # counter for table row padding with empty cells
+ html.append('
\n
')
+ for i,paths in enumerate(ourpdfs):
+ fname,thumb = paths
+ s= """
\n""" % (fname,thumb,fname,width,fname)
+ if ((i+1) % nacross == 0):
+ s += '
\n'
+ ntogo = 0
+ if i < (npdf - 1): # more to come
+ s += '