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tool1/test-data/test1_out.log tool1/test-data/tool1_test1_output.xls tool1/tool1.py tool1/tool1.xml tool1/tool_dependencies.xml |
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| diff -r 000000000000 -r 9cc0f9a8912e tool1/test-data/test1_out.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool1/test-data/test1_out.log Thu Apr 21 06:45:57 2016 -0400 |
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| @@ -0,0 +1,2 @@ +## Executing Toolfactory generated command line = python /home/guest/Downloads/ngsap/database/tmp/tool1cCIHZo.python --outpath=/home/guest/Downloads/ngsap/database/files/000/dataset_82.dat +This is another line |
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| diff -r 000000000000 -r 9cc0f9a8912e tool1/tool1.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool1/tool1.py Thu Apr 21 06:45:57 2016 -0400 |
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| b'@@ -0,0 +1,966 @@\n+# tool1/tool1.py - a self annotated version of rgToolFactory2.py generated by running rgToolFactory2.py\n+# to make a new Galaxy tool called tool1\n+# User admin@ngsap.com at 13/04/2016 19:49:50\n+# rgToolFactoryMultIn.py\n+# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home\n+# \n+# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012\n+# \n+# all rights reserved\n+# Licensed under the LGPL\n+# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home\n+#\n+# January 2015\n+# unified all setups by passing the script on the cl rather than via a PIPE - no need for treat_bash_special so removed\n+#\n+# in the process of building a complex tool\n+# added ability to choose one of the current toolshed package_r or package_perl or package_python dependencies and source that package\n+# add that package to tool_dependencies\n+# Note that once the generated tool is loaded, it will have that package\'s env.sh loaded automagically so there is no\n+# --envshpath in the parameters for the generated tool and it uses the system one which will be first on the adjusted path.\n+#\n+# sept 2014 added additional params from\n+# https://bitbucket.org/mvdbeek/dockertoolfactory/src/d4863bcf7b521532c7e8c61b6333840ba5393f73/DockerToolFactory.py?at=default\n+# passing them is complex\n+# and they are restricted to NOT contain commas or double quotes to ensure that they can be safely passed together on \n+# the toolfactory command line as a comma delimited double quoted string for parsing and passing to the script\n+# see examples on this tool form\n+\n+# august 2014\n+\n+# Allows arbitrary number of input files\n+# NOTE positional parameters are now passed to script\n+# and output (may be "None") is *before* arbitrary number of inputs\n+#\n+# march 2014\n+# had to remove dependencies because cross toolshed dependencies are not possible - can\'t pre-specify a toolshed url for graphicsmagick and ghostscript\n+# grrrrr - night before a demo\n+# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable\n+#\n+# added ghostscript and graphicsmagick as dependencies \n+# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp\n+# errors ensued\n+#\n+# august 2013\n+# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn\n+#\n+# july 2013\n+# added ability to combine images and individual log files into html output\n+# just make sure there\'s a log file foo.log and it will be output\n+# together with all images named like "foo_*.pdf\n+# otherwise old format for html\n+#\n+# January 2013\n+# problem pointed out by Carlos Borroto\n+# added escaping for <>$ - thought I did that ages ago...\n+#\n+# August 11 2012 \n+# changed to use shell=False and cl as a sequence\n+\n+# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.\n+# It also serves as the wrapper for the new tool.\n+# \n+# you paste and run your script\n+# Only works for simple scripts that read one input from the history.\n+# Optionally can write one new history dataset,\n+# and optionally collect any number of outputs into links on an autogenerated HTML page.\n+\n+# DO NOT install on a public or important site - please.\n+\n+# installed generated tools are fine if the script is safe.\n+# They just run normally and their user cannot do anything unusually insecure\n+# but please, practice safe toolshed.\n+# Read the fucking code before you install any tool \n+# especially this one\n+\n+# After you get the script working on some test data, you can\n+# optionally generate a toolshed compatible gzip file\n+# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for\n+# safe and largely automated installation in a production Galaxy.\n+\n+# If you opt for an HTML output, you get all the script outputs arranged\n+# as a single Html history item - all output files are linked, thumbnails for all the pdfs'..b'o I\'m keeping with the faith\n+ Feel free to update. \n+ """\n+ if self.opts.envshpath != \'system\':\n+ shell_source(self.opts.envshpath)\n+ # this only happens at tool generation - the generated tool relies on the dependencies all being set up\n+ # at toolshed installation by sourcing local env.sh \n+ if self.opts.output_dir:\n+ ste = open(self.elog,\'wb\')\n+ sto = open(self.tlog,\'wb\')\n+ s = \' \'.join(self.cl)\n+ sto.write(\'## Executing Toolfactory generated command line = %s\\n\' % s)\n+ sto.flush()\n+ p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,cwd=self.opts.output_dir)\n+ retval = p.wait()\n+ sto.close()\n+ ste.close()\n+ tmp_stderr = open( self.elog, \'rb\' )\n+ err = \'\'\n+ buffsize = 1048576\n+ try:\n+ while True:\n+ err += tmp_stderr.read( buffsize )\n+ if not err or len( err ) % buffsize != 0:\n+ break\n+ except OverflowError:\n+ pass\n+ tmp_stderr.close()\n+ else:\n+ p = subprocess.Popen(self.cl,shell=False)\n+ retval = p.wait()\n+ if self.opts.output_dir:\n+ if retval != 0 and err: # problem\n+ print >> sys.stderr,err\n+ if self.opts.make_HTML:\n+ self.makeHtml()\n+ return retval\n+\n+ \n+\n+def main():\n+ u = """\n+ This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:\n+ <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"\n+ </command>\n+ """\n+ op = optparse.OptionParser()\n+ a = op.add_option\n+ a(\'--script_path\',default=None)\n+ a(\'--tool_name\',default=None)\n+ a(\'--interpreter\',default=None)\n+ a(\'--output_dir\',default=\'./\')\n+ a(\'--output_html\',default=None)\n+ a(\'--input_tab\',default=[], action="append") # these are "galaxypath,metadataname" pairs\n+ a("--input_formats",default="tabular")\n+ a(\'--output_tab\',default=None)\n+ a(\'--output_format\',default=\'tabular\')\n+ a(\'--user_email\',default=\'Unknown\')\n+ a(\'--bad_user\',default=None)\n+ a(\'--make_Tool\',default=None)\n+ a(\'--make_HTML\',default=None)\n+ a(\'--help_text\',default=None)\n+ a(\'--tool_desc\',default=None)\n+ a(\'--new_tool\',default=None)\n+ a(\'--tool_version\',default=None)\n+ a(\'--include_dependencies\',default=None) \n+ a(\'--citations\',default=None)\n+ a(\'--additional_parameters\', dest=\'additional_parameters\', action=\'append\', default=[])\n+ a(\'--edit_additional_parameters\', action="store_true", default=False)\n+ a(\'--envshpath\',default="system") \n+ opts, args = op.parse_args()\n+ 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)\n+ assert opts.tool_name,\'## Tool Factory expects a tool name - eg --tool_name=DESeq\'\n+ assert opts.interpreter,\'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript\'\n+ assert os.path.isfile(opts.script_path),\'## Tool Factory wrapper expects a script path - eg --script_path=foo.R\'\n+ if opts.output_dir:\n+ try:\n+ os.makedirs(opts.output_dir)\n+ except:\n+ pass\n+ opts.input_tab = [x.replace(\'"\',\'\').replace("\'",\'\') for x in opts.input_tab]\n+ for i,x in enumerate(opts.additional_parameters): # remove quotes we need to deal with spaces in CL params\n+ opts.additional_parameters[i] = opts.additional_parameters[i].replace(\'"\',\'\')\n+ r = ScriptRunner(opts)\n+ if opts.make_Tool:\n+ retcode = r.makeTooltar()\n+ else:\n+ retcode = r.run()\n+ os.unlink(r.sfile)\n+ if retcode:\n+ sys.exit(retcode) # indicate failure to job runner\n+\n+\n+if __name__ == "__main__":\n+ main()\n+\n+\n+\n' |
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| diff -r 000000000000 -r 9cc0f9a8912e tool1/tool1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool1/tool1.xml Thu Apr 21 06:45:57 2016 -0400 |
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| @@ -0,0 +1,74 @@ +<tool id="tool1" name="tool1" version="0.01"> +<description>grep command</description> + +<command interpreter="python"> + + tool1.py --script_path "$runMe" --interpreter "python" + --tool_name "tool1" + + --output_dir "./" --output_tab "$output1" + +</command> +<inputs> +<param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="tool1"/> + + +</inputs> +<outputs> + <data format="ab1" name="output1" label="${job_name}"/> + +</outputs> +<configfiles> +<configfile name="runMe"> + import re + hand = open('/home/guest/word.txt') + for line in hand: + line = line.rstrip() + if re.search('is', line) : + print line +</configfile> +</configfiles> +<tests> + + <test> + + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="output1="tool1_test1_output.xls" ftype="tabular"/> + + </test> + +</tests> +<help> + + +get the line. + +**Script** +Pressing execute will run the following code over your input file and generate some outputs in your history:: + + + import re + hand = open('/home/guest/word.txt') + for line in hand: + line = line.rstrip() + if re.search('is', line) : + print line + +**Attribution** +This Galaxy tool was created by admin@ngsap.com at 13/04/2016 19:49:50 +using the Galaxy Tool Factory. + +See https://bitbucket.org/fubar/galaxytoolfactory for details of that project +Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + + +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 +</help> +<citations> + + <citation type="doi">10.1093/bioinformatics/bts573</citation> +</citations> +</tool> |
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| diff -r 000000000000 -r 9cc0f9a8912e tool1/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool1/tool_dependencies.xml Thu Apr 21 06:45:57 2016 -0400 |
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| @@ -0,0 +1,10 @@ +<?xml version="1.0"?> + <tool_dependency> + <readme> + +get the line. + + This file was autogenerated by the Galaxy Tool Factory 2 + </readme> + </tool_dependency> + |