tool_factory_2: README.txt comparison

comparison README.txt @ 26:db35d39e1de9 draft

Passes planemo test Uses galaxyxml to generate new tool. More outputs will be added...

author	fubar
date	Thu, 30 Jul 2020 06:48:45 -0400
parents	d98f5a09137f
children

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 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*
+*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
+It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.
-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
+A test is generated using small sample test data inputs and parameter settings you supply.
-new Galaxy tool, effectively freezing the supplied script into a new,
+Once the test case outputs have been produced, they can be used to build a
-ordinary Galaxy tool that runs it over one or more input files selected by
+new Galaxy tool. The supplied script or executable is baked as a requirement
-the user. Generated tools are installed via a tool shed by an administrator
+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
-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
+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
 the Galaxy history add new data tool.
 <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
 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
-**Simple examples on the tool form**
-A simple Rscript "filter" showing how the command line parameters can be
-handled, takes an input file, does something (transpose in this case) and
-writes the results to a new tabular file::
-# transpose a tabular input file and write as a tabular output file
-ourargs = commandArgs(TRUE)
-inf = ourargs[1]
-outf = ourargs[2]
-inp = read.table(inf,head=F,row.names=NULL,sep='\t')
-outp = t(inp)
-write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
-Calculate a multiple test adjusted p value from a column of p values -
-for this script to be useful, it needs the right column for the input to be
-specified in the code for the given input file type(s) specified when the
-tool is generated ::
-# use p.adjust - assumes a HEADER row and column 1 - please fix for any
-real use
-column = 1 # adjust if necessary for some other kind of input
-fdrmeth = 'BH'
-ourargs = commandArgs(TRUE)
-inf = ourargs[1]
-outf = ourargs[2]
-inp = read.table(inf,head=T,row.names=NULL,sep='\t')
-p = inp[,column]
-q = p.adjust(p,method=fdrmeth)
-newval = paste(fdrmeth,'p-value',sep='_')
-q = data.frame(q)
-names(q) = newval
-outp = cbind(inp,newval=q)
-write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
-Another Rscript example without any input file - generates a random heatmap
-pdf - you must make sure the option to create an HTML output file is
-turned on for this to work. The heatmap will be presented as a thumbnail
-linked to the pdf in the resulting HTML page::
-# note this script takes NO input or output because it generates random data
-foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),
-e=runif(100),f=runif(100))
-bar = as.matrix(foo)
-pdf( "heattest.pdf" )
-heatmap(bar,main='Random Heatmap')
-dev.off()
-A Python example that reverses each row of a tabular file. You'll need
-to remove the leading spaces for this to work if cut and pasted into the
-script box. Note that you can already do this in Galaxy by setting up the
-cut columns tool with the correct number of columns in reverse order,but
-this script will work for any number of columns so is completely generic::
-# 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()
-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

Mercurial > repos > fubar > tool_factory_2

comparison README.txt @ 26:db35d39e1de9 draft