--- a/toolfactory/README.md	Fri Aug 07 07:55:35 2020 -0400
+++ b/toolfactory/README.md	Fri Aug 07 23:14:54 2020 -0400
@@ -1,49 +1,17 @@
-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.
+*WARNING before you start*
 
-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.
+ 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
 
-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.
+Updated august 8 2014 to fix bugs reported by Marius van den Beek
 
-**WARNING before you start**
-
-Install this tool on a private Galaxy ONLY
-Please NEVER on a public or production instance
 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*
+**Short Story**
 
 This is an unusual Galaxy tool capable of generating new Galaxy tools.
 It works by exposing *unrestricted* and therefore extremely dangerous scripting
@@ -51,60 +19,28 @@
 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*
+*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*
 
-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.
+It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.
 
-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.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**
 
-*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
+A test is generated using small sample test data inputs and parameter settings you supply.
+Once the test case outputs have been produced, they can be used to build a
+new Galaxy tool. The supplied script or executable is baked as a requirement
+into a new, ordinary Galaxy tool, fully workflow compatible out of the box.
+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
-Change ```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*
+**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
+text box, or have a package in mind and a small test input example ready to select from your history
 to test your new script.
 
+```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me
+
 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
@@ -117,7 +53,7 @@
 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
+*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
@@ -137,38 +73,31 @@
 admin_user. Then, if you break it, you get to keep all the pieces see
 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
 
-** Installation **
+**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::
 
-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),
+
+If not already there,
 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**
 
-* 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
@@ -176,7 +105,9 @@
 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
+**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
@@ -190,7 +121,9 @@
 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
+**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.
 
@@ -199,202 +132,19 @@
 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
+**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.
+Read the 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.
+**Send Code**
 
 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***::
+**Attribution**
 
- # 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
@@ -402,6 +152,7 @@
 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
 
 **Licensing**
+
 Copyright Ross Lazarus 2010
 ross lazarus at g mail period com
 
@@ -409,10 +160,7 @@
 
 Licensed under the LGPL
 
-**screenshot**
-
-![example run](/images/dynamicScriptTool.png)
+**Obligatory screenshot**
 
+http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
 
-```
-