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+toolfactory_2
+=============
+
+This is an upgrade to the tool factory but with added parameters 
+(optionally editable in the generated tool form - otherwise fixed) and 
+multiple input files.
+
+Specify any number of parameters - well at 
+least up to the limit of your patience with repeat groups.
+
+Parameter values supplied at tool generation time are defaults and 
+can be optionally editable by the user - names cannot be changed once
+a tool has been generated.
+
+If not editable, they act as hidden parameters passed to the script 
+and are not editable on the tool form.
+
+Note! There will be Galaxy default sanitization for all 
+user input parameters which your script may need to dance around.
+
+Any number of input files can be passed to your script, but of course it
+has to deal with them. Both path and metadata name are supplied either in the environment 
+(bash/sh) or as command line parameters (python,perl,rscript) that need to be parsed and
+dealt with in the script. This is complicated by the common use case of needing file names
+for (eg) column headers, as well as paths. Try the examples are show on the tool factory 
+form to see how Galaxy file and user supplied parameter values can be recovered in each 
+of the 4 scripting environments supported.
+
+Best way to deal with multiple outputs is to let the tool factory generate an HTML
+page for your users. It automagically lays out pdf images as thumbnail galleries
+and can have separate results sections gathering all similarly prefixed files, such as
+a Foo section taking text and results from text (foo_whatever.log) and 
+artifacts (eg foo_MDS_plot.pdf) file names. All artifacts are linked for download.
+A copy of the actual script is provided for provenance - be warned, it exposes
+real file paths.
+
+
+tldr;
+
+```
+
+# WARNING before you start
+# Install this tool on a private Galaxy ONLY
+# Please NEVER on a public or production instance
+# updated august 2014 by John Chilton adding citation support
+#
+# updated august 8 2014 to fix bugs reported by Marius van den Beek
+# please cite the resource at
+http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
+# if you use this tool in your published work.
+
+*Short Story*
+
+This is an unusual Galaxy tool capable of generating new Galaxy tools.
+It works by exposing *unrestricted* and therefore extremely dangerous scripting
+to all designated administrators of the host Galaxy server, allowing them to
+run scripts in R, python, sh and perl over multiple selected input data sets,
+writing a single new data set as output.
+
+*Differences between TF2 and the original Tool Factory*
+
+1. TF2 (this one) allows any number of either fixed or user-editable parameters to be defined
+for the new tool. If these are editable, the user can change them but otherwise, they are passed
+as fixed and invisible parameters for each execution. Obviously, there are substantial security
+implications with editable parameters, but these are always sanitized by Galaxy's inbuilt 
+parameter sanitization so you may need to "unsanitize" characters - eg translate all "__lt__" 
+into "<" for certain parameters where that is needed. Please practise safe toolshed.
+
+2. Any number of (the same datatype) of input files may be defined.
+
+These changes substantially complicate the way your supplied script is supplied with
+all the new and variable parameters. Examples in each scripting language are shown
+in the tool help
+
+*Automated outputs in named sections*
+
+If your script writes to the current directory path, arbitrary mix of (eg)
+pdfs, tabular analysis results and run logs,the tool factory can optionally
+auto-generate a linked Html page with separate sections showing a thumbnail
+grid for all pdfs and the log text, grouping all artifacts sharing a file
+name and log name prefix::
+
+ eg: if "foo.log" is emitted then *all* other outputs matching foo_* will
+ all be grouped together - eg
+ foo_baz.pdf
+ foo_bar.pdf and
+ foo_zot.xls
+ would all be displayed and linked in the same section with foo.log's contents
+ - to form the "Foo" section of the Html page.  Sections appear in alphabetic
+ order and there are no limits on the number of files or sections.
+
+*Automated generation of new Galaxy tools for installation into any Galaxy*
+
+Once a script is working correctly, this tool optionally generates a
+new Galaxy tool, effectively freezing the supplied script into a new,
+ordinary Galaxy tool that runs it over one or more input files selected by
+the user. Generated tools are installed via a tool shed by an administrator
+and work exactly like all other Galaxy tools for your users.
+
+If you use the Html output option, please ensure that sanitize_all_html is
+set to False and uncommented in universe_wsgi.ini - it should show::
+
+ # By default, all tool output served as 'text/html' will be sanitized
+ sanitize_all_html = False
+
+This opens potential security risks and may not be acceptable for public
+sites where the lack of stylesheets may make Html pages damage onlookers'
+eyeballs but should still be correct.
+
+
+*More Detail*
+
+To use the ToolFactory, you should have prepared a script to paste into a
+text box, and a small test input example ready to select from your history
+to test your new script.
+
+There is an example in each scripting language on the Tool Factory form. You
+can just cut and paste these to try it out - remember to select the right
+interpreter please. You'll also need to create a small test data set using
+the Galaxy history add new data tool.
+
+If the script fails somehow, use the "redo" button on the tool output in
+your history to recreate the form complete with broken script. Fix the bug
+and execute again. Rinse, wash, repeat.
+
+Once the script runs sucessfully, a new Galaxy tool that runs your script
+can be generated. Select the "generate" option and supply some help text and
+names. The new tool will be generated in the form of a new Galaxy datatype
+- toolshed.gz - as the name suggests, it's an archive ready to upload to a
+Galaxy ToolShed as a new tool repository.
+
+Once it's in a ToolShed, it can be installed into any local Galaxy server
+from the server administrative interface.
+
+Once the new tool is installed, local users can run it - each time, the script
+that was supplied when it was built will be executed with the input chosen
+from the user's history. In other words, the tools you generate with the
+ToolFactory run just like any other Galaxy tool,but run your script every time.
+
+Tool factory tools are perfect for workflow components. One input, one output,
+no variables.
+
+*To fully and safely exploit the awesome power* of this tool,
+Galaxy and the ToolShed, you should be a developer installing this
+tool on a private/personal/scratch local instance where you are an
+admin_user. Then, if you break it, you get to keep all the pieces see
+https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+** Installation **
+This is a Galaxy tool. You can install it most conveniently using the
+administrative "Search and browse tool sheds" link. Find the Galaxy Main
+toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
+repository. Open it and review the code and select the option to install it.
+
+(
+If you can't get the tool that way, the xml and py files here need to be
+copied into a new tools
+subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry
+pointing to the xml
+file - something like::
+
+  <section name="Tool building tools" id="toolbuilders">
+    <tool file="toolfactory/rgToolFactory.xml"/>
+  </section>
+
+If not already there (I just added it to datatypes_conf.xml.sample),
+please add:
+<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary"
+mimetype="multipart/x-gzip" subclass="True" />
+to your local data_types_conf.xml.
+)
+
+Of course, R, python, perl etc are needed on your path if you want to test
+scripts using those interpreters. Adding new ones to this tool code should
+be easy enough. Please make suggestions as bitbucket issues and code. The
+HTML file code automatically shrinks R's bloated pdfs, and depends on
+ghostscript. The thumbnails require imagemagick .
+
+* Restricted execution *
+The tool factory tool itself will then be usable ONLY by admin users -
+people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY
+admin_users can run this tool** Think about it for a moment. If allowed to
+run any arbitrary script on your Galaxy server, the only thing that would
+impede a miscreant bent on destroying all your Galaxy data would probably
+be lack of appropriate technical skills.
+
+*What it does* This is a tool factory for simple scripts in python, R and
+perl currently. Functional tests are automatically generated. How cool is that.
+
+LIMITED to 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 index page for the user to navigate -
+useful if the script writes images and output files - pdf outputs are shown
+as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and
+imagemagik need to be available.
+
+Generated tools can be edited and enhanced like any Galaxy tool, so start
+small and build up since a generated script gets you a serious leg up to a
+more complex one.
+
+*What you do* You paste and run your script, you fix the syntax errors and
+eventually it runs. You can use the redo button and edit the script before
+trying to rerun it as you debug - it works pretty well.
+
+Once the script works on some test data, you can generate a toolshed compatible
+gzip file containing your script ready to run as an ordinary Galaxy tool in
+a repository on your local toolshed. That means safe and largely automated
+installation in any production Galaxy configured to use your toolshed.
+
+*Generated tool Security* Once you install a generated tool, it's just
+another tool - assuming 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 -
+it is really scary.
+
+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 and suggestions welcome as bitbucket issues please?
+
+copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
+
+all rights reserved
+Licensed under the LGPL if you want to improve it, feel free
+https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+Material for our more enthusiastic and voracious readers continues below -
+we salute you.
+
+**Motivation** Simple transformation, filtering or reporting scripts get
+written, run and lost every day in most busy labs - even ours where Galaxy is
+in use. This 'dark script matter' is pervasive and generally not reproducible.
+
+**Benefits** For our group, this allows Galaxy to fill that important dark
+script gap - all those "small" bioinformatics tasks. Once a user has a working
+R (or python or perl) script that does something Galaxy cannot currently do
+(eg transpose a tabular file) and takes parameters the way Galaxy supplies
+them (see example below), they:
+
+1. Install the tool factory on a personal private instance
+
+2. Upload a small test data set
+
+3. Paste the script into the 'script' text box and iteratively run the
+insecure tool on test data until it works right - there is absolutely no
+reason to do this anywhere other than on a personal private instance.
+
+4. Once it works right, set the 'Generate toolshed gzip' option and run
+it again.
+
+5. A toolshed style gzip appears ready to upload and install like any other
+Toolshed entry.
+
+6. Upload the new tool to the toolshed
+
+7. Ask the local admin to check the new tool to confirm it's not evil and
+install it in the local production galaxy
+
+
+
+**Parameter passing and file inputs**
+
+Your script will receive up to 3 named parameters
+INPATHS is a comma separated list of input file paths
+INNAMES is a comma separated list of input file names in the same order
+OUTPATH is optional if a file is being generated, your script should write there
+Your script should open and write files in the provided working directory if you are using the Html
+automatic presentation option.
+
+Python script command lines will have --INPATHS and --additional_arguments etc. to make it easy to use argparse
+
+Rscript will need to use commandArgs(TRUE) - see the example below - additional arguments will
+appear as themselves - eg foo="bar" will mean that foo is defined as "bar" for the script.
+
+Bash and sh will see any additional parameters on their command lines and the 3 named parameters
+in their environment magically - well, using env on the CL
+
+***python***::
+
+ # argparse for 3 possible comma separated lists
+ # additional parameters need to be parsed !
+ # then echo parameters to the output file
+ import sys
+ import argparse
+ argp=argparse.ArgumentParser()
+ argp.add_argument('--INNAMES',default=None)
+ argp.add_argument('--INPATHS',default=None)
+ argp.add_argument('--OUTPATH',default=None)
+ argp.add_argument('--additional_parameters',default=[],action="append")
+ argp.add_argument('otherargs', nargs=argparse.REMAINDER)
+ args = argp.parse_args()
+ f= open(args.OUTPATH,'w')
+ s = '### args=%s\n' % str(args)
+ f.write(s)
+ s = 'sys.argv=%s\n' % sys.argv
+ f.write(s) 
+ f.close()
+
+
+
+***Rscript***::
+
+ # tool factory Rscript parser suggested by Forester
+ # http://www.r-bloggers.com/including-arguments-in-r-cmd-batch-mode/
+ # additional parameters will appear in the ls() below - they are available
+ # to your script
+ # echo parameters to the output file
+ ourargs = commandArgs(TRUE)
+ if(length(ourargs)==0){
+    print("No arguments supplied.")
+ }else{
+    for(i in 1:length(ourargs)){
+         eval(parse(text=ourargs[[i]]))
+    }
+ sink(OUTPATH)
+ cat('INPATHS=',INPATHS,'\n')
+ cat('INNAMES=',INNAMES,'\n')
+ cat('OUTPATH=',OUTPATH,'\n')
+ x=ls()
+ cat('all objects=',x,'\n')
+ sink()
+ }
+ sessionInfo()
+ print.noquote(date())
+
+
+***bash/sh***::
+
+ # tool factory sets up these environmental variables
+ # this example writes those to the output file
+ # additional params appear on command line
+ if [ ! -f "$OUTPATH" ] ; then
+    touch "$OUTPATH"
+ fi
+ echo "INPATHS=$INPATHS" >> "$OUTPATH"
+ echo "INNAMES=$INNAMES" >> "$OUTPATH"
+ echo "OUTPATH=$OUTPATH" >> "$OUTPATH"
+ echo "CL=$@" >> "$OUTPATH"
+
+***perl***::
+
+ (my $INPATHS,my $INNAMES,my $OUTPATH ) = @ARGV;
+ open(my $fh, '>', $OUTPATH) or die "Could not open file '$OUTPATH' $!";
+ print $fh "INPATHS=$INPATHS\n INNAMES=$INNAMES\n OUTPATH=$OUTPATH\n";
+ close $fh;
+ 
+
+
+Galaxy as an IDE for developing API scripts
+If you need to develop Galaxy API scripts and you like to live dangerously,
+please read on.
+
+Galaxy as an IDE?
+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.
+
+Why bother - what's wrong with Eclipse
+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!
+
+Workflow
+Fire up the Tool Factory in Galaxy.
+
+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.
+
+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.
+
+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.
+
+Eg tool factory api script
+import sys
+from blend.galaxy import GalaxyInstance
+ourGal = 'http://x.x.x.x:xxxx'
+ourKey = 'xxx'
+gi = GalaxyInstance(ourGal, key=ourKey)
+libs = gi.libraries.get_libraries()
+res = []
+# libs looks like
+# u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id':
+u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data',
+for lib in libs:
+    res.append('%s:\n' % lib['name'])
+    res.append(str(gi.libraries.show_library(lib['id'],contents=True)))
+outf=open(sys.argv[2],'w')
+outf.write('\n'.join(res))
+outf.close()
+
+**Attribution**
+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
+
+http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
+
+**Licensing**
+Copyright Ross Lazarus 2010
+ross lazarus at g mail period com
+
+All rights reserved.
+
+Licensed under the LGPL
+
+**Obligatory screenshot**
+
+http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
+
+
+```
+