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README.txt tool_dependencies.xml |
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rgToolFactory.py rgToolFactory.xml |
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| diff -r 71b85c322600 -r 4e3aa95ed3ac README.txt --- a/README.txt Thu Feb 12 17:22:24 2015 -0500 +++ b/README.txt Mon Mar 02 05:14:05 2015 -0500 |
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| b'@@ -1,226 +1,177 @@\n-\xef\xbb\xbf# WARNING before you start\n+# WARNING before you start\n # Install this tool on a private Galaxy ONLY\n # Please NEVER on a public or production instance\n # updated august 2014 by John Chilton adding citation support\n #\n # updated august 8 2014 to fix bugs reported by Marius van den Beek\n-# please cite the resource at\n-http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref\n+# please cite the resource at http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref \n # if you use this tool in your published work.\n \n *Short Story*\n \n This is an unusual Galaxy tool capable of generating new Galaxy tools.\n-It works by exposing *unrestricted* and therefore extremely dangerous scripting\n-to all designated administrators of the host Galaxy server, allowing them to\n-run scripts in R, python, sh and perl over multiple selected input data sets,\n-writing a single new data set as output.\n-\n-*Differences between TF2 and the original Tool Factory*\n-\n-1. TF2 (this one) allows any number of either fixed or user-editable parameters to be defined\n-for the new tool. If these are editable, the user can change them but otherwise, they are passed\n-as fixed and invisible parameters for each execution. Obviously, there are substantial security\n-implications with editable parameters, but these are always sanitized by Galaxy\'s inbuilt \n-parameter sanitization so you may need to "unsanitize" characters - eg translate all "__lt__" \n-into "<" for certain parameters where that is needed. Please practise safe toolshed.\n-\n-2. Any number of (the same datatype) of input files may be defined.\n-\n-These changes substantially complicate the way your supplied script is supplied with\n-all the new and variable parameters. Examples in each scripting language are shown\n-in the tool help\n+It works by exposing *unrestricted* and therefore extremely dangerous\n+scripting to all designated administrators of the host Galaxy server, allowing them to run scripts \n+in R, python, sh and perl over multiple selected input data sets, writing a single new data set as output.\n \n *Automated outputs in named sections*\n \n-If your script writes to the current directory path, arbitrary mix of (eg)\n-pdfs, tabular analysis results and run logs,the tool factory can optionally\n-auto-generate a linked Html page with separate sections showing a thumbnail\n-grid for all pdfs and the log text, grouping all artifacts sharing a file\n-name and log name prefix::\n+If your script writes to the current directory path, arbitrary mix of (eg) pdfs, tabular analysis results and run logs,\n+the tool factory can optionally auto-generate a linked Html page with separate sections showing a thumbnail grid\n+for all pdfs and the log text, grouping all artifacts sharing a file name and log name prefix::\n \n- eg: if "foo.log" is emitted then *all* other outputs matching foo_* will\n- all be grouped together - eg\n+ eg: if "foo.log" is emitted then *all* other outputs matching foo_* will all be grouped together - eg\n foo_baz.pdf\n foo_bar.pdf and\n foo_zot.xls\n- would all be displayed and linked in the same section with foo.log\'s contents\n- - to form the "Foo" section of the Html page. Sections appear in alphabetic\n- order and there are no limits on the number of files or sections.\n+ would all be displayed and linked in the same section with foo.log\'s contents - to form the "Foo" section of the Html page.\n+ Sections appear in alphabetic order and there are no limits on the number of files or sections.\n \n-*Automated generation of new Galaxy tools for installation into any Galaxy*\n+*Automated generation of new Galaxy tool shed tools for installation into any Galaxy*\n \n-Once a script is working correctly, this tool optionally generates a\n-new Galaxy tool, effectively freezing the supplied script into a new,\n-ordinary Galaxy tool that runs it over one or more input files selected by\n-the user. Generated tools are installed via a to'..b"op Galaxy API scripts and you like to live dangerously, please read on.\n \n Galaxy as an IDE?\n-Amazingly enough, blend-lib API scripts run perfectly well *inside*\n-Galaxy when pasted into a Tool Factory form. No need to generate a new\n-tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously,\n-it is actually quite useable.\n+Amazingly enough, blend-lib API scripts run perfectly well *inside* Galaxy when pasted into a Tool Factory form. No need to generate a new tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously, it is actually quite useable.\n \n Why bother - what's wrong with Eclipse\n-Nothing. But, compared with developing API scripts in the usual way outside\n-Galaxy, you get persistence and other framework benefits plus at absolutely\n-no extra charge, a ginormous security problem if you share the history or\n-any outputs because they contain the api script with key so development\n-servers only please!\n+Nothing. But, compared with developing API scripts in the usual way outside Galaxy, you get persistence and other framework benefits plus at absolutely no extra charge, a ginormous security problem if you share the history or any outputs because they contain the api script with key so development servers only please!\n \n Workflow\n Fire up the Tool Factory in Galaxy.\n \n-Leave the input box empty, set the interpreter to python, paste and run an\n-api script - eg working example (substitute the url and key) below.\n+Leave the input box empty, set the interpreter to python, paste and run an api script - eg working example (substitute the url and key) below.\n \n-It took me a few iterations to develop the example below because I know\n-almost nothing about the API. I started with very simple code from one of the\n-samples and after each run, the (edited..) api script is conveniently recreated\n-using the redo button on the history output item. So each successive version\n-of the developing api script you run is persisted - ready to be edited and\n-rerun easily. It is ''very'' handy to be able to add a line of code to the\n-script and run it, then view the output to (eg) inspect dicts returned by\n-API calls to help move progressively deeper iteratively.\n+It took me a few iterations to develop the example below because I know almost nothing about the API. I started with very simple code from one of the samples and after each run, the (edited..) api script is conveniently recreated using the redo button on the history output item. So each successive version of the developing api script you run is persisted - ready to be edited and rerun easily. It is ''very'' handy to be able to add a line of code to the script and run it, then view the output to (eg) inspect dicts returned by API calls to help move progressively deeper iteratively.\n \n-Give the below a whirl on a private clone (install the tool factory from\n-the main toolshed) and try adding complexity with few rerun/edit/rerun cycles.\n+Give the below a whirl on a private clone (install the tool factory from the main toolshed) and try adding complexity with few rerun/edit/rerun cycles.\n \n Eg tool factory api script\n import sys\n@@ -331,17 +258,16 @@\n libs = gi.libraries.get_libraries()\n res = []\n # libs looks like\n-# u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id':\n-u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data',\n-for lib in libs:\n+# u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data',\n+for lib in libs: \n res.append('%s:\\n' % lib['name'])\n res.append(str(gi.libraries.show_library(lib['id'],contents=True)))\n outf=open(sys.argv[2],'w')\n outf.write('\\n'.join(res))\n outf.close()\n \n-**Attribution**\n-Creating re-usable tools from scripts: The Galaxy Tool Factory\n+**Attribution** \n+Creating re-usable tools from scripts: The Galaxy Tool Factory \n Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team\n Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n \n" |
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| diff -r 71b85c322600 -r 4e3aa95ed3ac rgToolFactory.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgToolFactory.py Mon Mar 02 05:14:05 2015 -0500 |
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| b'@@ -0,0 +1,738 @@\n+# rgToolFactory.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+# August 2014 \n+# merged John Chilton\'s citation addition and ideas from Marius van den Beek to enable arbitrary\n+# data types for input and output - thanks!\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.\n+# Ugly but really inexpensive.\n+# \n+# Patches appreciated please. \n+#\n+#\n+# long route to June 2012 product\n+# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them\n+# derived from an integrated script model \n+# called rgBaseScriptWrapper.py\n+# Note to the unwary:\n+# This tool allows arbitrary scripting on your Galaxy as the Galaxy user\n+# There is nothing stopping a malicious user doing whatever they choose\n+# Extremely dangerous!!\n+# Totally insecure. So, trusted users only\n+#\n+# preferred model is a developer using their throw away workstation instance - ie a private site.\n+# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.\n+#\n+\n+import sys \n+import shutil \n+import subprocess \n+import os \n+import time \n+import tempfile \n+import optparse\n+import tarfile\n+import re\n+import shutil\n+import math\n+\n+progname = os.path.split(sys.argv[0])[1] \n+myversion = \'V001.1 March 2014\' \n+verbose = False \n+debug = False\n+toolFactoryURL = \'https://bitbucket.org/fubar/galaxytoolfactory\'\n+\n+# if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated\n+# tool xml\n+toolhtmldepskel = """<?xml version="1.0"?>\n+<tool_dependency>\n+ <'..b'.interpreter)\n+ html.append(galhtmlpostfix)\n+ htmlf = file(self.opts.output_html,\'w\')\n+ htmlf.write(\'\\n\'.join(html))\n+ htmlf.write(\'\\n\')\n+ htmlf.close()\n+ self.html = html\n+\n+\n+ def run(self):\n+ """\n+ scripts must be small enough not to fill the pipe!\n+ """\n+ if self.treatbashSpecial and self.opts.interpreter in [\'bash\',\'sh\']:\n+ retval = self.runBash()\n+ else:\n+ if self.opts.output_dir:\n+ ste = open(self.elog,\'a\')\n+ sto = open(self.tlog,\'a\')\n+ sto.write(\'## Toolfactory generated command line = %s\\n\' % \' \'.join(self.cl))\n+ sto.flush()\n+ p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)\n+ else:\n+ p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)\n+ p.stdin.write(self.script)\n+ p.stdin.close()\n+ retval = p.wait()\n+ if self.opts.output_dir:\n+ sto.close()\n+ ste.close()\n+ err = open(self.elog,\'r\').readlines()\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+ def runBash(self):\n+ """\n+ cannot use - for bash so use self.sfile\n+ """\n+ if self.opts.output_dir:\n+ s = \'## Toolfactory generated command line = %s\\n\' % \' \'.join(self.cl)\n+ sto = open(self.tlog,\'w\')\n+ sto.write(s)\n+ sto.flush()\n+ p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)\n+ else:\n+ p = subprocess.Popen(self.cl,shell=False) \n+ retval = p.wait()\n+ if self.opts.output_dir:\n+ sto.close()\n+ if self.opts.make_HTML:\n+ self.makeHtml()\n+ return retval\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="None")\n+ a(\'--input_formats\',default="tabular,text")\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(\'--citations\',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+ 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+ 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' |
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| diff -r 71b85c322600 -r 4e3aa95ed3ac rgToolFactory.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgToolFactory.xml Mon Mar 02 05:14:05 2015 -0500 |
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| b'@@ -0,0 +1,360 @@\n+<tool id="rgTF" name="Tool Factory" version="1.12">\n+ <description>Makes scripts into tools</description>\n+ <requirements>\n+ <requirement type="package" version="9.10">ghostscript</requirement>\n+ <requirement type="package" version="1.3.20">graphicsmagick</requirement>\n+ </requirements>\n+ <command interpreter="python">\n+#if ( $__user_email__ not in $__admin_users__ ):\n+ rgToolFactory.py --bad_user $__user_email__\n+#else:\n+ rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" \n+ --tool_name "$tool_name" --user_email "$__user_email__"\n+ #if str($make_TAB)=="yes":\n+ --output_tab "$tab_file"\n+ --output_format "$output_format"\n+ #end if\n+ #if str($makeMode.make_Tool) == "yes":\n+ --make_Tool "yes"\n+ --tool_desc "$makeMode.tool_desc"\n+ --tool_version "$makeMode.tool_version"\n+ --new_tool "$new_tool"\n+ --help_text "$helpme"\n+ --citations "$citeme"\n+ --include_dependencies "yes"\n+ #end if\n+\n+ #if str($make_HTML)=="yes":\n+ --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"\n+ #else:\n+ --output_dir "."\n+ #end if\n+ #if str($input1) != \'None\':\n+ --input_tab "$input1"\n+ --input_formats "$input_formats"\n+ #end if\n+#end if \n+ </command>\n+ <inputs>\n+ <param name="input1" type="data" label="Select an input file from your history" optional="true" size="120"\n+ help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>\n+ <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"\n+ help="If your datatype is not listed here, it has to be added in galaxy\'s datatypes_conf.xml">\n+ <options from_parameter="tool.app.datatypes_registry.upload_file_formats">\n+ <column name="value" index="0"/>\n+ </options>\n+ </param>\n+ <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60"\n+ help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.letters,string.digits"/>\n+ </sanitizer>\n+ </param>\n+ <conditional name="makeMode">\n+ <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!" size="60">\n+ <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>\n+ <option value="" selected="true">No. Just run the script please</option>\n+ </param>\n+ <when value = "yes">\n+ <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"\n+ help="If you change your script and regenerate the \'same\' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>\n+ <param name="tool_desc" label="Tool Description" type="text" value="" size="40" \n+ help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />\n+ <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" \n+ size="8x120" value="**What it Does**" \n+ help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" > \n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ <mapping initial="none"/>\n+ </sanitizer>\n+ </param>\n+ <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"\n+ help="If an H'..b'input to be specified in the code for the\n+given input file type(s) specified when the tool is generated ::\n+\n+ # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use\n+ column = 1 # adjust if necessary for some other kind of input\n+ ourargs = commandArgs(TRUE)\n+ inf = ourargs[1]\n+ outf = ourargs[2]\n+ inp = read.table(inf,head=T,row.names=NULL,sep=\'\\t\')\n+ p = inp[,column]\n+ q = p.adjust(p,method=\'BH\')\n+ outp = cbind(inp,\'BH Adjusted p-value\'=q)\n+ write.table(outp,outf, quote=FALSE, sep="\\t",row.names=F,col.names=T) \n+\n+\n+A demonstration Rscript example takes no input file but generates some random data based pdf images\n+You must make sure the option to create an HTML output file is\n+turned on for this to work. Images (pdf) are linked via thumbnails and\n+all files have a link on the resulting HTML page::\n+\n+ # note this script takes NO input or output because it generates random data\n+ for (i in 1:10) {\n+ foo = runif(100)\n+ bar = rnorm(100)\n+ bar = foo + 0.05*bar\n+ pdf(paste(\'yet\',i,"anotherplot.pdf",sep=\'_\'))\n+ plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)\n+ dev.off()\n+ foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))\n+ bar = as.matrix(foo)\n+ pdf(paste(\'yet\',i,"anotherheatmap.pdf",sep=\'_\'))\n+ heatmap(bar,main=\'Random Heatmap\')\n+ dev.off()\n+ }\n+\n+A slight variation taking an input tabular file from which we read the first number as nreps::\n+\n+ # note this script takes a single parameter\n+ # number of replicates\n+ ourargs = commandArgs(TRUE)\n+ infname = ourargs[1]\n+ nreps = read.table(infname,head=F)\n+ nreps = unlist(nreps)[1]\n+ nreps = max(c(1,nreps))\n+ nreps = min(c(20,nreps))\n+ print(paste("Using nreps=",nreps))\n+ for (i in 1:nreps) {\n+ foo = runif(100)\n+ bar = rnorm(100)\n+ bar = foo + 0.2*bar\n+ pdf(paste("yet",i,"anotherplot.pdf",sep="_"))\n+ plot(foo,bar,main=paste("Foo by Bar plot ",i),col="maroon", pch=3,cex=0.6)\n+ dev.off()\n+ foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))\n+ bar = as.matrix(foo)\n+ pdf(paste("yet",i,"anotherheatmap.pdf",sep="_"))\n+ heatmap(bar,main="Random Heatmap")\n+ dev.off()\n+ }\n+\n+A Python example that reverses each row of a tabular file (you\'ll need to remove the leading spaces \n+for this to work if cut and pasted into the script box)::\n+\n+ # reverse order of columns in a tabular file\n+ import sys\n+ inp = sys.argv[1]\n+ outp = sys.argv[2]\n+ i = open(inp,\'r\')\n+ o = open(outp,\'w\')\n+ for row in i:\n+ rs = row.rstrip().split(\'\\t\')\n+ rs.reverse()\n+ o.write(\'\\t\'.join(rs))\n+ o.write(\'\\n\')\n+ i.close()\n+ o.close()\n+ \n+A trivial shell script example to show that it works::\n+\n+ #!/bin/bash\n+ INF=$1\n+ OUTF=$2\n+ cut -c2,4,6,8,10,12 $INF > $OUTF \n+\n+A trivial perl script example to show that even perl works::\n+\n+ #\n+ # change all occurances of a string in a file to another string\n+ #\n+ $oldfile = $ARGV[0];\n+ $newfile = $ARGV[1];\n+ $old = "gene";\n+ $new = "foo";\n+ open(OF, $oldfile);\n+ open(NF, ">$newfile");\n+ # read in each line of the file\n+ while ($line = <OF>) {\n+ $line =~ s/$old/$new/;\n+ print NF $line;\n+ }\n+ close(OF);\n+ close(NF);\n+\n+]]>\n+\n+\n+**Citation**\n+\n+\n+Paper_ :\n+\n+Creating re-usable tools from scripts: The Galaxy Tool Factory\n+Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team\n+Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n+\n+\n+**Licensing** \n+\n+Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012\n+All rights reserved.\n+Licensed under the LGPL_\n+\n+.. _LGPL: http://www.gnu.org/copyleft/lesser.html\n+.. _GTF: https://bitbucket.org/fubar/galaxytoolfactory\n+.. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues\n+.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref\n+\n+\n+</help>\n+<citations>\n+ <citation type="doi">10.1093/bioinformatics/bts573</citation>\n+</citations>\n+</tool>\n+\n+\n' |
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| diff -r 71b85c322600 -r 4e3aa95ed3ac tool_dependencies.xml --- a/tool_dependencies.xml Thu Feb 12 17:22:24 2015 -0500 +++ b/tool_dependencies.xml Mon Mar 02 05:14:05 2015 -0500 |
| b |
| @@ -1,10 +1,10 @@ <?xml version="1.0"?> <tool_dependency> <package name="ghostscript" version="9.10"> - <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/" /> </package> <package name="graphicsmagick" version="1.3.20"> - <repository changeset_revision="d87c457bbbc2" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d87c457bbbc2" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu/" /> </package> <readme> Only Admins can use this tool generator but please do NOT install on a public facing Galaxy as it exposes unrestricted scripting as your Galaxy user |