changeset 20:d98f5a09137f draft

author fubar
date Mon, 02 Feb 2015 20:57:40 -0500
parents ff812453b1b3
children 71b85c322600
files LICENSE README.txt images/dynamicScriptTool.png rgToolFactory2.xml test-data/tf2_test.html test-data/tf2_test.toolshed.gz test-data/tf2_test_in.xls test-data/tf2_test_out.xls test-data/ tool_dependencies.xml
diffstat 12 files changed, 2403 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Mon Feb 02 20:57:40 2015 -0500
@@ -0,0 +1,504 @@
+                       Version 2.1, February 1999
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
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+ Everyone is permitted to copy and distribute verbatim copies
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+That's all there is to it!
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/	Mon Feb 02 20:57:40 2015 -0500
@@ -0,0 +1,16 @@
+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.
+Any number of  parameters up to the limit of your patience with repeat groups
+These are optionally editable by the user - names cannot be changed so 
+no overwriting $JAVA_HOME_DIR or else permanently fixed and not editable at run time.
+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.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Mon Feb 02 20:57:40 2015 -0500
@@ -0,0 +1,361 @@
+# 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
+# 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
+** 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 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
+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')
+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')
+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!
+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)))
+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
+Copyright Ross Lazarus 2010
+ross lazarus at g mail period com
+All rights reserved.
+Licensed under the LGPL
+**Obligatory screenshot**
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/	Mon Feb 02 20:57:40 2015 -0500
@@ -0,0 +1,53 @@
+import os
+import subprocess
+import sys
+def find_packages(prefix="package_r_"):
+    """
+    """
+    #locate | grep -i package_r_
+    #/data/extended/galaxyJune14_2014/tool_dependency/readline/6.2/devteam/package_r_2_15_0/8ab0d08a3da1/
+    #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/5f1b8d22140a/
+    #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/d9964efbfbe3/
+    #/data/home/rlazarus/galtest/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/63cdb9b2234c/
+    eprefix = prefix
+    if prefix.find('/') <> -1:
+        eprefix = prefix.replace('/','\/') # for grep
+    path = '.'
+    # fails on nitesh's recent mac - locate not working 
+    # cl = ['locate | grep -i %s' % eprefix,]
+    cl = ['find %s -iname "" | grep -i %s' % (path,eprefix),]
+    p = subprocess.Popen(cl, stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True)
+    out, err = p.communicate()
+    fpaths = out.split('\n')
+    fpaths = [x for x in fpaths if len(x) > 1]
+    fver = [x.split(os.path.sep)[-4:-1] for x in fpaths]
+    # >>> foo.split(os.path.sep)[-4:-1]
+    # ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
+    if len(fpaths) > 0:
+        res = [['%s rev %s owner %s' % (x[1],x[2],x[0]),fpaths[i],False] for i,x in enumerate(fver)]
+        res.insert(0,['Use default (system) interpreter','system',False])
+    else:
+        res = [['Use default (system) interpreter','system',False],
+        ['**WARNING** NO package files found - is the "locate" system command working? Are any interpreters installed?','system',True]]
+    if len(res) > 2:
+        res[1][2] = True # selected if more than one
+    # return a triplet - user_sees,value,selected - all unselected if False
+    return res
+def testapi():
+    host_url = 'http://localhost:8080'
+    new_path = [ os.path.join( os.getcwd(), "lib" ) ]
+    new_path.extend( sys.path[1:] ) # remove scripts/ from the path
+    sys.path = new_path
+    from galaxy import config
+    aconfig = config.Configuration( )
+    M_A_K = aconfig.master_api_key
+    tooldeps = aconfig.tool_dependency_dir
+    gi = GalaxyInstance(url=host_url, key=M_A_K)
+if __name__ == "__main__":
+    print find_packages()
Binary file images/dynamicScriptTool.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/	Mon Feb 02 20:57:40 2015 -0500
@@ -0,0 +1,962 @@
+# see
+# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
+# all rights reserved
+# Licensed under the LGPL
+# suggestions for improvement and bug fixes welcome at
+# January 2015
+# unified all setups by passing the script on the cl rather than via a PIPE - no need for treat_bash_special so removed
+# in the process of building a complex tool
+# added ability to choose one of the current toolshed package_r or package_perl or package_python dependencies and source that package
+# add that package to tool_dependencies
+# Note that once the generated tool is loaded, it will have that package's loaded automagically so there is no
+# --envshpath in the parameters for the generated tool and it uses the system one which will be first on the adjusted path.
+# sept 2014 added additional params from
+# passing them is complex
+# and they are restricted to NOT contain commas or double quotes to ensure that they can be safely passed together on 
+# the toolfactory command line as a comma delimited double quoted string for parsing and passing to the script
+# see examples on this tool form
+# august 2014
+# Allows arbitrary number of input files
+# NOTE positional parameters are now passed to script
+# and output (may be "None") is *before* arbitrary number of inputs
+# march 2014
+# had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
+# grrrrr - night before a demo
+# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
+# added ghostscript and graphicsmagick as dependencies 
+# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
+# errors ensued
+# august 2013
+# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
+# july 2013
+# added ability to combine images and individual log files into html output
+# just make sure there's a log file foo.log and it will be output
+# together with all images named like "foo_*.pdf
+# otherwise old format for html
+# January 2013
+# problem pointed out by Carlos Borroto
+# added escaping for <>$ - thought I did that ages ago...
+# August 11 2012 
+# changed to use shell=False and cl as a sequence
+# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
+# It also serves as the wrapper for the new tool.
+# you paste and run your script
+# Only works for 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 page.
+# DO NOT install on a public or important site - please.
+# installed generated tools are fine if 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
+# After you get the script working on some test data, you can
+# optionally generate a toolshed compatible gzip file
+# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
+# safe and largely automated installation in a production Galaxy.
+# 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 appreciated please. 
+# long route to June 2012 product
+# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
+# derived from an integrated script model  
+# called
+# Note to the unwary:
+#   This tool allows arbitrary scripting on your Galaxy as the Galaxy user
+#   There is nothing stopping a malicious user doing whatever they choose
+#   Extremely dangerous!!
+#   Totally insecure. So, trusted users only
+# preferred model is a developer using their throw away workstation instance - ie a private site.
+# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
+import sys 
+import shutil 
+import subprocess 
+import os 
+import time 
+import tempfile 
+import optparse
+import tarfile
+import re
+import shutil
+import math
+progname = os.path.split(sys.argv[0])[1] 
+myversion = 'V001.1 March 2014' 
+verbose = False 
+debug = False
+toolFactoryURL = ''
+# if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
+# tool xml
+def timenow():
+    """return current time as a string
+    """
+    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+def quote_non_numeric(s):
+    """return a prequoted string for non-numerics
+    useful for perl and Rscript parameter passing?
+    """
+    try:
+        res = float(s)
+        return s
+    except ValueError:
+        return '"%s"' % s
+html_escape_table = {
+     "&": "&amp;",
+     ">": "&gt;",
+     "<": "&lt;",
+     "$": "\$"
+     }
+def html_escape(text):
+     """Produce entities within text."""
+     return "".join(html_escape_table.get(c,c) for c in text)
+def html_unescape(text):
+     """Revert entities within text."""
+     t = text.replace('&amp;','&').replace('&gt;','>').replace('&lt;','<').replace('\$','$')
+     return t
+def cmd_exists(cmd):
+     return"type " + cmd, shell=True, 
+           stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
+def parse_citations(citations_text):
+    """
+    """
+    citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
+    citation_tuples = []
+    for citation in citations:
+        if citation.startswith("doi"):
+            citation_tuples.append( ("doi", citation[len("doi"):].strip() ) )
+        else:
+            citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
+    return citation_tuples
+def shell_source(script):
+    """need a way to source a Galaxy tool interpreter to point at the right dependency package 
+    This based on the idea in
+    Note that we have to finesse any wierdly quoted newlines in automagic exports using nulls (env -0) as newlines"""
+    pipe = subprocess.Popen("env -i ; . %s ; env -0" % script, stdout=subprocess.PIPE, shell=True)
+    output = pipe.communicate()[0]
+    outl = output.split('\0')
+    outl = [x for x in outl if len(x.split("=")) == 2]
+    newenv = dict((line.split("=", 1) for line in outl))
+    os.environ.update(newenv)
+class ScriptRunner:
+    """class is a wrapper for an arbitrary script
+    note funky templating. this should all be done proper.
+    Problem is, this kludge developed quite naturally and seems to work ok with
+    little overhead...
+    """
+    def __init__(self,opts=None):
+        """
+        cleanup inputs, setup some outputs
+        """
+        self.toolhtmldepinterpskel = """<?xml version="1.0"?>
+        <tool_dependency>
+            <package name="ghostscript" version="9.10">
+                <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
+            </package>
+            <package name="graphicsmagick" version="1.3.18">
+                <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
+            </package>
+             <package name="%(interpreter_name)s" version="%(interpreter_version)s">
+                <repository name="%(interpreter_pack)s" owner="%(interpreter_owner)s" prior_installation_required="True" />
+            </package>
+                <readme>
+                   %(readme)s
+                   This file was autogenerated by the Galaxy Tool Factory 2
+               </readme>
+        </tool_dependency>
+        """
+        self.toolhtmldepskel = """<?xml version="1.0"?>
+        <tool_dependency>
+            <package name="ghostscript" version="9.10">
+                <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
+            </package>
+            <package name="graphicsmagick" version="1.3.18">
+                <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
+            </package>
+                <readme>
+                   %(readme)s
+                   This file was autogenerated by the Galaxy Tool Factory 2
+               </readme>
+        </tool_dependency>
+        """
+        self.emptytoolhtmldepskel = """<?xml version="1.0"?>
+        <tool_dependency>
+                <readme>
+                   %(readme)s
+                This file was autogenerated by the Galaxy Tool Factory 2
+               </readme>
+        </tool_dependency>
+        """
+        self.protorequirements = """<requirements>
+              <requirement type="package" version="9.10">ghostscript</requirement>
+              <requirement type="package" version="1.3.18">graphicsmagick</requirement>
+          </requirements>"""
+        self.protorequirements_interpreter = """<requirements>
+              <requirement type="package" version="9.10">ghostscript</requirement>
+              <requirement type="package" version="1.3.18">graphicsmagick</requirement>
+              <requirement type="package" version="%(interpreter_version)s">%(interpreter_name)s</requirement>
+          </requirements>"""
+        self.newCommand="""
+            %(toolname) --script_path "$runMe" --interpreter "%(interpreter)s" 
+                --tool_name "%(toolname)s"
+                %(command_inputs)s
+                %(command_outputs)s
+            """
+        self.tooltestsTabOnly = """
+            <test>
+            %(test1Inputs)s
+            <param name="job_name" value="test1"/>
+            <param name="runMe" value="$runMe"/>
+            <output name="output1="%(test1Output)s" ftype="tabular"/>
+            %(additionalParams)s
+            </test>
+            """
+        self.tooltestsHTMLOnly = """
+            <test>
+            %(test1Inputs)s
+            <param name="job_name" value="test1"/>
+            <param name="runMe" value="$runMe"/>
+            %(additionalParams)s
+            <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
+            </test>
+            """
+        self.tooltestsBoth = """
+            <test>
+            %(test1Inputs)s
+            <param name="job_name" value="test1"/>
+            <param name="runMe" value="$runMe"/>
+            %(additionalParams)s
+            <output name="output1" file="%(test1Output)s" ftype="tabular" />
+            <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
+            </test>
+            """
+        self.newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
+<command interpreter="python">
+<configfile name="runMe">
+This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
+    %(citations)s
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
+        self.useGM = cmd_exists('gm')
+        self.useIM = cmd_exists('convert')
+        self.useGS = cmd_exists('gs')
+        self.temp_warned = False # we want only one warning if $TMP not set
+        if opts.output_dir: # simplify for the tool tarball
+            os.chdir(opts.output_dir)
+        self.thumbformat = 'png'
+        self.opts = opts
+        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
+        self.toolid = self.toolname
+        self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
+        self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
+        self.xmlfile = '%s.xml' % self.toolname
+        rx = open(self.opts.script_path,'r').readlines()
+        rx = [x.rstrip() for x in rx] # remove pesky dos line endings if needed
+        self.script = '\n'.join(rx)
+        fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
+        tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
+        tscript.write(self.script)
+        tscript.close()
+        self.indentedScript = "  %s" % '\n'.join([' %s' % html_escape(x) for x in rx]) # for restructured text in help
+        self.escapedScript = "%s" % '\n'.join([' %s' % html_escape(x) for x in rx])
+        self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
+        if opts.output_dir: # may not want these complexities 
+            self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
+            art = '%s.%s' % (self.toolname,opts.interpreter)
+            artpath = os.path.join(self.opts.output_dir,art) # need full path
+            artifact = open(artpath,'w') # use self.sfile as script source for Popen
+            artifact.write(self.script)
+            artifact.close()
+ = []
+        self.html = []
+        self.test1Inputs = [] # now a list
+        a =
+        a(opts.interpreter)
+        a(self.sfile)
+        # if multiple inputs - positional or need to distinguish them with cl params
+        if opts.input_tab:
+            tests = []
+            for i,intab in enumerate(opts.input_tab): # if multiple, make tests
+                if intab.find(',') <> -1:
+                    (gpath,uname) = intab.split(',')
+                else:
+                    gpath = uname = intab
+                tests.append(os.path.basename(gpath))
+            self.test1Inputs =  '<param name="input_tab" value="%s" />' % (','.join(tests))
+        else:
+            self.test1Inputs = ''
+        # we always pass path,name pairs in using python optparse append
+        # but the command line has to be different
+        self.infile_paths = ''
+        self.infile_names = ''
+        if self.opts.input_tab:
+            self.infile_paths = ','.join([x.split(',')[0].strip() for x in self.opts.input_tab])
+            self.infile_names = ','.join([x.split(',')[1].strip() for x in self.opts.input_tab])
+        if self.opts.interpreter == 'python':
+            # yes, this is how additional parameters are always passed in python - to the TF itself and to
+            # scripts to avoid having unknown parameter names (yes, they can be parsed but...) on the command line
+            if self.opts.input_tab:
+                a('--INPATHS "%s"' % (self.infile_paths)) 
+                a('--INNAMES "%s"' % (self.infile_names)) 
+            if self.opts.output_tab:
+                a('--OUTPATH "%s"' % self.opts.output_tab) 
+            for p in opts.additional_parameters:
+                p = p.replace('"','')
+                psplit = p.split(',')
+                param = html_unescape(psplit[0])
+                value = html_unescape(psplit[1])
+                a('%s="%s"' % (param,value))
+        if (self.opts.interpreter == 'Rscript'):
+            # pass params on command line as expressions which the script evaluates - see sample
+            if self.opts.input_tab:
+                a('INPATHS="%s"' % self.infile_paths)
+                a('INNAMES="%s"' % self.infile_names)
+            if self.opts.output_tab:
+                a('OUTPATH="%s"' % self.opts.output_tab) 
+            for p in opts.additional_parameters:
+                p = p.replace('"','')
+                psplit = p.split(',')
+                param = html_unescape(psplit[0])
+                value = html_unescape(psplit[1])
+                a('%s=%s' % (param,quote_non_numeric(value)))
+        if (self.opts.interpreter == 'perl'):
+            # pass positional params on command line - perl script needs to discombobulate the path/name lists
+            if self.opts.input_tab:
+                a('%s' % self.infile_paths)
+                a('%s' % self.infile_names)
+            if self.opts.output_tab:
+                a('%s' % self.opts.output_tab)
+            for p in opts.additional_parameters:
+                # followed by any additional name=value parameter pairs
+                p = p.replace('"','')
+                psplit = p.split(',')
+                param = html_unescape(psplit[0])
+                value = html_unescape(psplit[1])
+                a('%s=%s' % (param,quote_non_numeric(value)))
+        if self.opts.interpreter == 'sh' or self.opts.interpreter == 'bash':
+              # more is better - now move all params into environment AND drop on to command line.
+    ,'env')
+              if self.opts.input_tab:
+        ,'INPATHS=%s' % (self.infile_paths))
+        ,'INNAMES=%s' % (self.infile_names))
+              if self.opts.output_tab:
+        ,'OUTPATH=%s' % (self.opts.output_tab))
+                  a('OUTPATH=%s' % (self.opts.output_tab))
+              # sets those environment variables for the script
+              # additional params appear in CL - yes, it's confusing
+              for i,p in enumerate(opts.additional_parameters):
+                  psplit = p.split(',')
+                  param = html_unescape(psplit[0])
+                  value = html_unescape(psplit[1])
+                  a('%s=%s' % (param,quote_non_numeric(value)))
+        ,'%s=%s' % (param,quote_non_numeric(value)))
+        self.interpreter_owner = 'SYSTEM'
+        self.interpreter_pack = 'SYSTEM'
+        self.interpreter_name = 'SYSTEM'
+        self.interpreter_version = 'SYSTEM'
+        self.interpreter_revision = 'SYSTEM'
+        if opts.envshpath <> 'system': # need to parse out details for our tool_dependency
+            try: # fragile - depends on common naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play
+                # this ONLY happens at tool generation by an admin - the generated tool always uses the default of system so path is from local
+                packdetails = opts.envshpath.split(os.path.sep)[-4:-1]  # eg ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
+                self.interpreter_owner = packdetails[0]
+                self.interpreter_pack = packdetails[1]
+                self.interpreter_name = packdetails[1].split('_')[1].upper()
+                self.interpreter_revision = packdetails[2]
+                self.interpreter_version =  '.'.join(packdetails[1].split('_')[2:])
+            except:
+                pass
+        self.outFormats = opts.output_format
+        self.inputFormats = opts.input_formats
+        self.test1Output = '%s_test1_output.xls' % self.toolname
+        self.test1HTML = '%s_test1_output.html' % self.toolname
+    def makeXML(self):
+        """
+        Create a Galaxy xml tool wrapper for the new script as a string to write out
+        fixme - use templating or something less fugly than this example of what we produce
+        <tool id="reverse" name="reverse" version="0.01">
+            <description>a tabular file</description>
+            <command interpreter="python">
+   --script_path "$runMe" --interpreter "python" 
+            --tool_name "reverse" --input_tab "$input1" --output_tab "$output1" 
+            </command>
+            <inputs>
+            <param name="input1"  type="data" format="tabular" label="Select one or more input files from your history"/>
+            <param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
+            </inputs>
+            <outputs>
+            <data format="tabular" name="output1q" label="${job_name}"/>
+            </outputs>
+            <help>
+**What it Does**
+Reverse the columns in a tabular file
+            </help>
+            <configfiles>
+            <configfile name="runMe">
+# 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')
+            </configfile>
+            </configfiles>
+            </tool>
+        """ 
+        # these templates need a dict with the right keys to match the parameters - outputs, help, code...
+        xdict = {}
+        xdict['additionalParams'] = ''
+        xdict['additionalInputs'] = ''
+        if self.opts.additional_parameters:
+            if self.opts.edit_additional_parameters: # add to new tool form with default value set to original value
+                xdict['additionalInputs'] = '\n'.join(['<param name="%s" value="%s" label="%s" help="%s" type="%s"/>' % \
+                (x.split(',')[0],html_escape(x.split(',')[1]),html_escape(x.split(',')[2]),html_escape(x.split(',')[3]), x.split(',')[4]) for x in self.opts.additional_parameters])
+        xdict['additionalParams'] = '\n'.join(['<param name="%s" value="%s" />' % (x.split(',')[0],html_escape(x.split(',')[1])) for x in self.opts.additional_parameters])
+        xdict['interpreter_owner'] = self.interpreter_owner
+        xdict['interpreter_version'] = self.interpreter_version
+        xdict['interpreter_pack'] = self.interpreter_pack
+        xdict['interpreter_name'] = self.interpreter_name
+        xdict['requirements'] = ''
+        if self.opts.include_dependencies == "yes":
+            if self.opts.envshpath <> 'system':
+                xdict['requirements'] = self.protorequirements_interpreter % xdict       
+            else:    
+                xdict['requirements'] = self.protorequirements
+        xdict['tool_version'] = self.opts.tool_version
+        xdict['test1HTML'] = self.test1HTML
+        xdict['test1Output'] = self.test1Output
+        xdict['test1Inputs'] = self.test1Inputs
+        if self.opts.make_HTML and self.opts.output_tab:
+            xdict['tooltests'] = self.tooltestsBoth % xdict
+        elif self.opts.make_HTML:
+            xdict['tooltests'] = self.tooltestsHTMLOnly % xdict
+        else:
+            xdict['tooltests'] = self.tooltestsTabOnly % xdict
+        xdict['script'] = self.escapedScript 
+        # configfile is least painful way to embed script to avoid external dependencies
+        # but requires escaping of <, > and $ to avoid Mako parsing
+        if self.opts.help_text:
+            helptext = open(self.opts.help_text,'r').readlines()
+            helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
+            xdict['help'] = ''.join([x for x in helptext])
+        else:
+            xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
+        coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
+        coda.append('\n')
+        coda.append(self.indentedScript)
+        coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
+        coda.append('See %s for details of that project' % (toolFactoryURL))
+        coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
+        coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
+        xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
+        if self.opts.tool_desc:
+            xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
+        else:
+            xdict['tooldesc'] = ''
+        xdict['command_outputs'] = '' 
+        xdict['outputs'] = '' 
+        if self.opts.input_tab:
+            cins = ['\n',]
+            cins.append('--input_formats %s' % self.opts.input_formats)
+            cins.append('#for intab in $input1:')
+            cins.append('--input_tab "${intab},${}"')
+            cins.append('#end for\n')
+            xdict['command_inputs'] = '\n'.join(cins)
+            xdict['inputs'] = '''<param name="input_tab" multiple="true"  type="data" format="%s" label="Select one or more %s input files from your history"
+                    help="Multiple inputs may be selected assuming the script can deal with them..."/> \n''' % (self.inputFormats,self.inputFormats)
+        else:
+            xdict['command_inputs'] = '' # assume no input - eg a random data generator       
+            xdict['inputs'] = ''
+        if (len(self.opts.additional_parameters) > 0):
+            cins = ['\n',]
+            for params in self.opts.additional_parameters:
+                    psplit = params.split(',') # name,value...
+                    psplit[3] = html_escape(psplit[3])
+                    if self.opts.edit_additional_parameters:
+                        psplit[1] = '$%s' % psplit[0] # replace with form value
+                    else:
+                        psplit[1] = html_escape(psplit[1]) # leave prespecified value
+                    cins.append('--additional_parameters """%s"""' % ','.join(psplit)) 
+            xdict['command_inputs'] = '%s\n%s' % (xdict['command_inputs'],'\n'.join(cins))
+        xdict['inputs'] += '<param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
+        xdict['toolname'] = self.toolname
+        xdict['toolid'] = self.toolid
+        xdict['interpreter'] = self.opts.interpreter
+        xdict['scriptname'] = self.sfile
+        if self.opts.make_HTML:
+            xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
+            xdict['outputs'] +=  ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
+        else:
+            xdict['command_outputs'] += ' --output_dir "./"' 
+        if self.opts.output_tab:
+            xdict['command_outputs'] += ' --output_tab "$output1"'
+            xdict['outputs'] += ' <data format="%s" name="output1" label="${job_name}"/>\n' % self.outFormats
+        xdict['command'] = self.newCommand % xdict
+        if self.opts.citations:
+            citationstext = open(self.opts.citations,'r').read()
+            citation_tuples = parse_citations(citationstext)
+            citations_xml = ""
+            for citation_type, citation_content in citation_tuples:
+                citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content))
+                citations_xml += citation_xml
+            xdict['citations'] = citations_xml
+        else:
+            xdict['citations'] = ""
+        xmls = self.newXML % xdict
+        xf = open(self.xmlfile,'w')
+        xf.write(xmls)
+        xf.write('\n')
+        xf.close()
+        # ready for the tarball
+    def makeTooltar(self):
+        """
+        a tool is a gz tarball with eg
+        /toolname/tool.xml /toolname/ /toolname/test-data/ ...
+        """
+        retval =
+        if retval:
+            print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
+            sys.exit(1)
+        tdir = self.toolname
+        os.mkdir(tdir)
+        self.makeXML()
+        if self.opts.help_text:
+            hlp = open(self.opts.help_text,'r').read()
+        else:
+            hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
+        readme_dict = {'readme':hlp,'interpreter':self.opts.interpreter,'interpreter_version':self.interpreter_version,'interpreter_name':self.interpreter_name,
+        'interpreter_owner':self.interpreter_owner,'interpreter_pack':self.interpreter_pack}
+        if self.opts.include_dependencies == "yes":
+            if self.opts.envshpath == 'system':
+                tooldepcontent = self.toolhtmldepskel % readme_dict
+            else:
+                tooldepcontent = self.toolhtmldepinterpskel % readme_dict
+        else:
+            tooldepcontent = self.emptytoolhtmldepskel  % readme_dict
+        depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
+        depf.write(tooldepcontent)
+        depf.write('\n')
+        depf.close()
+        testdir = os.path.join(tdir,'test-data')
+        os.mkdir(testdir) # make tests directory
+        for i,intab in enumerate(self.opts.input_tab):
+            si = self.opts.input_tab[i]
+            if si.find(',') <> -1:
+                s = si.split(',')[0]
+                si = s
+            dest = os.path.join(testdir,os.path.basename(si))
+            if si <> dest:
+                shutil.copyfile(si,dest)
+        if self.opts.output_tab:
+            shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
+        if self.opts.make_HTML:
+            shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
+        if self.opts.output_dir:
+            shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
+        outpif = '' % self.toolname # new name
+        outpiname = os.path.join(tdir,outpif) # path for the tool tarball
+        pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
+        notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
+        notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
+        notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
+        pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
+        notes += pi
+        outpi = open(outpiname,'w')
+        outpi.write(''.join(notes))
+        outpi.write('\n')
+        outpi.close()
+        stname = os.path.join(tdir,self.sfile)
+        if not os.path.exists(stname):
+            shutil.copyfile(self.sfile, stname)
+        xtname = os.path.join(tdir,self.xmlfile)
+        if not os.path.exists(xtname):
+            shutil.copyfile(self.xmlfile,xtname)
+        tarpath = "%s.tar.gz" % self.toolname
+        tar =, "w:gz")
+        tar.add(tdir,arcname='%s' % self.toolname)
+        tar.close()
+        shutil.copyfile(tarpath,self.opts.new_tool)
+        shutil.rmtree(tdir)
+        ## TODO: replace with optional direct upload to local toolshed?
+        return retval
+    def compressPDF(self,inpdf=None,thumbformat='png'):
+        """need absolute path to pdf
+           note that GS gets confoozled if no $TMP or $TEMP
+           so we set it
+        """
+        assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
+        hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
+        sto = open(hlog,'a')
+        our_env = os.environ.copy()
+        our_tmp = our_env.get('TMP',None)
+        if not our_tmp:
+            our_tmp = our_env.get('TEMP',None)
+        if not (our_tmp and os.path.exists(our_tmp)):
+            newtmp = os.path.join(self.opts.output_dir,'tmp')
+            try:
+                os.mkdir(newtmp)
+            except:
+                sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
+            our_env['TEMP'] = newtmp
+            if not self.temp_warned:
+               sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
+               self.temp_warned = True          
+        outpdf = '%s_compressed' % inpdf
+        cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
+        x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
+        retval1 = x.wait()
+        sto.close()
+        if retval1 == 0:
+            os.unlink(inpdf)
+            shutil.move(outpdf,inpdf)
+            os.unlink(hlog)
+        hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
+        sto = open(hlog,'w')
+        outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
+        if self.useGM:        
+            cl2 = ['gm', 'convert', inpdf, outpng]
+        else: # assume imagemagick
+            cl2 = ['convert', inpdf, outpng]
+        x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
+        retval2 = x.wait()
+        sto.close()
+        if retval2 == 0:
+             os.unlink(hlog)
+        retval = retval1 or retval2
+        return retval
+    def getfSize(self,fpath,outpath):
+        """
+        format a nice file size string
+        """
+        size = ''
+        fp = os.path.join(outpath,fpath)
+        if os.path.isfile(fp):
+            size = '0 B'
+            n = float(os.path.getsize(fp))
+            if n > 2**20:
+                size = '%1.1f MB' % (n/2**20)
+            elif n > 2**10:
+                size = '%1.1f KB' % (n/2**10)
+            elif n > 0:
+                size = '%d B' % (int(n))
+        return size
+    def makeHtml(self):
+        """ Create an HTML file content to list all the artifacts found in the output_dir
+        """
+        galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" ""> 
+        <html xmlns="" xml:lang="en" lang="en"> 
+        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 
+        <meta name="generator" content="Galaxy %s tool output - see" /> 
+        <title></title> 
+        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
+        </head> 
+        <body> 
+        <div class="toolFormBody"> 
+        """ 
+        galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="">Galaxy Tool Factory</a></div><br/>""" 
+        galhtmlpostfix = """</div></body></html>\n"""
+        flist = os.listdir(self.opts.output_dir)
+        flist = [x for x in flist if x <> 'Rplots.pdf']
+        flist.sort()
+        html = []
+        html.append(galhtmlprefix % progname)
+        html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
+        fhtml = []
+        if len(flist) > 0:
+            logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
+            logfiles.sort()
+            logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
+            logfiles.append(os.path.abspath(self.tlog)) # make it the last one
+            pdflist = []
+            npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
+            for rownum,fname in enumerate(flist):
+                dname,e = os.path.splitext(fname)
+                sfsize = self.getfSize(fname,self.opts.output_dir)
+                if e.lower() == '.pdf' : # compress and make a thumbnail
+                    thumb = '%s.%s' % (dname,self.thumbformat)
+                    pdff = os.path.join(self.opts.output_dir,fname)
+                    retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
+                    if retval == 0:
+                        pdflist.append((fname,thumb))
+                    else:
+                        pdflist.append((fname,fname))
+                if (rownum+1) % 2 == 0:
+                    fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
+                else:
+                    fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
+            for logfname in logfiles: # expect at least tlog - if more
+                if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
+                    sectionname = 'All tool run'
+                    if (len(logfiles) > 1):
+                        sectionname = 'Other'
+                    ourpdfs = pdflist
+                else:
+                    realname = os.path.basename(logfname)
+                    sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
+                    ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
+                    pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
+                nacross = 1
+                npdf = len(ourpdfs)
+                if npdf > 0:
+                    nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
+                    if int(nacross)**2 != npdf:
+                        nacross += 1
+                    nacross = int(nacross)
+                    width = min(400,int(1200/nacross))
+                    html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
+                    html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
+                    ntogo = nacross # counter for table row padding with empty cells
+                    html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
+                    for i,paths in enumerate(ourpdfs): 
+                        fname,thumb = paths
+                        s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" 
+                           alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
+                        if ((i+1) % nacross == 0):
+                            s += '</tr>\n'
+                            ntogo = 0
+                            if i < (npdf - 1): # more to come
+                               s += '<tr>'
+                               ntogo = nacross
+                        else:
+                            ntogo -= 1
+                        html.append(s)
+                    if html[-1].strip().endswith('</tr>'):
+                        html.append('</table></div>\n')
+                    else:
+                        if ntogo > 0: # pad
+                           html.append('<td>&nbsp;</td>'*ntogo)
+                        html.append('</tr></table></div>\n')
+                logt = open(logfname,'r').readlines()
+                logtext = [x for x in logt if x.strip() > '']
+                html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
+                if len(logtext) > 1:
+                    html.append('\n<pre>\n')
+                    html += logtext
+                    html.append('\n</pre>\n')
+                else:
+                    html.append('%s is empty<br/>' % logfname)
+        if len(fhtml) > 0:
+           fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
+           fhtml.append('</table></div><br/>')
+           html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
+           html += fhtml # add all non-pdf files to the end of the display
+        else:
+            html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
+        html.append(galhtmlpostfix)
+        htmlf = file(self.opts.output_html,'w')
+        htmlf.write('\n'.join(html))
+        htmlf.write('\n')
+        htmlf.close()
+        self.html = html
+    def run(self):
+        """
+        Some devteam tools have this defensive stderr read so I'm keeping with the faith
+        Feel free to update. 
+        """
+        if self.opts.envshpath <> 'system':
+            shell_source(self.opts.envshpath)
+            # this only happens at tool generation - the generated tool relies on the dependencies all being set up
+            # at toolshed installation by sourcing local 
+        if self.opts.output_dir:
+            ste = open(self.elog,'wb')
+            sto = open(self.tlog,'wb')
+            s = ' '.join(
+            sto.write('## Executing Toolfactory generated command line = %s\n' % s)
+            sto.flush()
+            p = subprocess.Popen(,shell=False,stdout=sto,stderr=ste,cwd=self.opts.output_dir)
+            retval = p.wait()
+            sto.close()
+            ste.close()
+            tmp_stderr = open( self.elog, 'rb' )
+            err = ''
+            buffsize = 1048576
+            try:
+                while True:
+                    err += buffsize )
+                    if not err or len( stderr ) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+            tmp_stderr.close()
+        else:
+            p = subprocess.Popen(,shell=False)
+            retval = p.wait()
+        if self.opts.output_dir:
+            if retval <> 0 and err: # problem
+                print >> sys.stderr,err
+        if self.opts.make_HTML:
+            self.makeHtml()
+        return retval
+def main():
+    u = """
+    This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
+    <command interpreter="python"> --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
+    </command>
+    """
+    op = optparse.OptionParser()
+    a = op.add_option
+    a('--script_path',default=None)
+    a('--tool_name',default=None)
+    a('--interpreter',default=None)
+    a('--output_dir',default='./')
+    a('--output_html',default=None)
+    a('--input_tab',default=[], action="append") # these are "galaxypath,metadataname" pairs
+    a("--input_formats",default="tabular")
+    a('--output_tab',default=None)
+    a('--output_format',default='tabular')
+    a('--user_email',default='Unknown')
+    a('--bad_user',default=None)
+    a('--make_Tool',default=None)
+    a('--make_HTML',default=None)
+    a('--help_text',default=None)
+    a('--tool_desc',default=None)
+    a('--new_tool',default=None)
+    a('--tool_version',default=None)
+    a('--include_dependencies',default="yes")   
+    a('--citations',default=None)
+    a('--additional_parameters', dest='additional_parameters', action='append', default=[])
+    a('--edit_additional_parameters', action="store_true", default=False)
+    a('--envshpath',default="system")   
+    opts, args = op.parse_args()
+    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)
+    assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
+    assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
+    assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
+    if opts.output_dir:
+        try:
+            os.makedirs(opts.output_dir)
+        except:
+            pass
+    opts.input_tab = [x.replace('"','').replace("'",'') for x in opts.input_tab]
+    for i,x in enumerate(opts.additional_parameters): # remove quotes we need to deal with spaces in CL params
+        opts.additional_parameters[i] = opts.additional_parameters[i].replace('"','')
+    r = ScriptRunner(opts)
+    if opts.make_Tool:
+        retcode = r.makeTooltar()
+    else:
+        retcode =
+    os.unlink(r.sfile)
+    if retcode:
+        sys.exit(retcode) # indicate failure to job runner
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgToolFactory2.xml	Mon Feb 02 20:57:40 2015 -0500
@@ -0,0 +1,442 @@
+<tool id="rgTF2" name="Tool Factory Two" version="1.17">
+  <description>Scripts into tools</description>
+   <requirements>
+      <requirement type="package" version="9.10">ghostscript</requirement>
+      <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+  </requirements>
+  <code file=""/>
+  <command interpreter="python">
+#if ( $__user_email__ not in $__admin_users__ ):
+ --bad_user $__user_email__
+ --script_path "$runme" --interpreter "$interp.interpreter" 
+     --tool_name "$tool_name"  --user_email "$__user_email__" --citations "$citeme"
+     --envshpath "$interp.envpath"
+    #if $make_TAB.value=="yes":
+          --output_tab "$output1"
+          --output_format "$output_format"
+    #end if
+    #if $makeMode.make_Tool=="yes":
+      --make_Tool "$makeMode.make_Tool"
+      --tool_desc "$makeMode.tool_desc"
+      --tool_version "$makeMode.tool_version"
+      --new_tool "$new_tool"
+      --help_text "$helpme"
+      #if $make_HTML.value=="yes":
+          #if $makeMode.include_deps.value=="yes":
+             --include_dependencies "yes"
+          #end if
+      #end if
+    #end if
+    #if $additional_parameters != 'None':
+      #if $edit_params.value == "yes":
+         --edit_additional_parameters
+      #end if
+      #for i in $additional_parameters:
+        --additional_parameters "$i.param_name,$i.param_value,$i.param_label,$i.param_help,$i.param_type"
+      #end for
+    #end if
+    #if $make_HTML.value=="yes":
+      --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
+    #else:
+       --output_dir "."
+    #end if
+    #if len($input_tab) != 0:
+        --input_formats "$input_formats"
+        #for $intab in $input_tab:
+            #if $intab.ext != 'data':
+              --input_tab "${intab},${}"
+            #end if
+        #end for
+    #end if
+#end if 
+  </command>
+  <inputs>
+    <param name="input_tab"  type="data"  label="Select one or more input file(s) from your history" optional="true" size="120" multiple="true"
+       help="Use the multiple input widget (above/right of input box) for multiple inputs - your script MUST be ready to parse the command line right - see samples below"/>
+    <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
+      help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
+       <options from_parameter="">
+        <column name="value" index="0"/>
+       </options>
+    </param>
+    <param name="tool_name" type="text" value="My dynamic script"   label="New tool ID and title for outputs" size="60"
+         help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
+        <sanitizer invalid_char="">
+            <valid initial="string.letters,string.digits">
+                <add value="_"/>
+            </valid>
+        </sanitizer>
+    </param>
+    <conditional name="makeMode">
+        <param name="make_Tool" type="select" label="Generate new tool as  a tar.gz file ready to upload to a toolshed repository" 
+          help="Generate a toolshed archive - upload to a toolshed from where it can be auto-installed via the Galaxy admin functions" 
+          size="60">
+        <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
+        <option value="" selected="true">No. Just run the script please</option>
+        </param>
+        <when value = "yes">
+            <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
+            help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
+            <param name="tool_desc" label="Tool Description" type="text" value="" size="40" 
+             help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
+            <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" 
+             size="8x120" value="**What it Does**" 
+             help="Supply the brief user documentation to appear on the new tool form as reStructured text -" >           
+                <sanitizer>
+                    <valid initial="string.printable">
+                    </valid>
+                    <mapping initial="none"/>
+                </sanitizer>
+            </param>
+            <repeat name="citations" title="Citation">
+                <conditional name="citation_type">
+                    <param name="type" type="select" label="Citation Type">
+                        <option value="doi">DOI</option>
+                        <option value="bibtex">BibTeX</option>
+                    </param>
+                    <when value="doi">
+                        <param name="doi" label="DOI" type="text" value="" 
+                        help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." />
+                    </when>
+                    <when value="bibtex">
+                        <param name="bibtex" label="BibTex" type="text" area="true" size="8x120"
+                            help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
+                            <sanitizer>
+                                <valid initial="string.printable">
+                                </valid>
+                                <mapping initial="none"/>
+                            </sanitizer>
+                        </param>
+                    </when>
+                </conditional>
+            </repeat>
+            <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
+            help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
+                <option value="">Rely on system ghostscript and graphicsmagick rather than include these as dependencies</option>
+                <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option>
+            </param>
+        </when>
+        <when value = "">
+        </when>
+    </conditional> 
+    <param name="make_HTML" type="select" label="Create an HTML report with links to every output file your script writes to the current directory" size="60"
+         help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
+        <option value="yes">Yes, arrange and link all output files written by my script to the current directory as an HTML page</option>
+        <option value="" selected="true">No, no HTML output file thanks</option>
+    </param>
+    <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an HTML file specified above" 
+         help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
+        <option value="yes" selected="true">My script writes to a new history output</option>
+        <option value="">I do not want a new history output file</option>
+    </param>
+    <param name="output_format" type="select" multiple="false" label="Select the datatype that your tool/script emits as output"
+      help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
+     <options from_parameter="">
+        <column name="value" index="0"/>
+     </options>
+    </param>
+    <conditional name="interp">
+    <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
+        <option value="Rscript" selected="true">Rscript</option>
+        <option value="python">python</option>
+        <option value="perl">perl</option>
+        <option value="bash">bash</option>
+        <option value="sh">sh</option>
+    </param>
+    <when value="Rscript">
+        <param name="envpath"  type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_r_')"
+        help = "Select the R interpreter to use when running this code - should show all installed tool shed package_r_..." /> 
+    </when>
+    <when value="python">
+        <param name="envpath"  type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_python_')"
+        help = "Select the python dependency to use when running this code - should show all installed tool shed package_python_..." /> 
+    </when>
+    <when value="perl">
+        <param name="envpath"  type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_perl_')"
+        help = "Select the Perl interpreter to use when running this code - should show all installed tool shed package_perl_..." /> 
+    </when>
+    </conditional>
+    <param name="edit_params" type="select" label="Add all additional parameters to the generated tool form so they are user editable?" 
+         help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
+        <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option>
+        <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option>
+    </param>
+    <repeat name="additional_parameters" title="Pass additional parameters to the script"
+         help="See examples below to see how these can be parsed by scripts in the various languages">
+      <param name="param_name" type="text" value="parameter_name" label="Choose the name for this parameter" size="60">
+        <sanitizer invalid_char="">
+          <valid initial="string.letters,string.digits"/>
+          <mapping initial="none"/> 
+        </sanitizer>
+      </param>
+      <param name="param_type" type="select" label="Select the type for this parameter">
+        <option value="text" selected="true">text</option>
+        <option value="integer">integer</option>
+        <option value="float">float</option>
+        <option value="file">file</option>
+        <option value="library_data">library_data</option>
+      </param>
+      <param name="param_value" type="text" value="parameter_value" label="Enter this parameter's default value" size="60"
+        help="Note that commas and double quotes cannot be used in this text field - please work around this technical limitation" >
+        <sanitizer invalid_char="">
+          <valid initial="string.printable"> <remove value=','/> <remove value='"'/> </valid>
+          <mapping initial="none"/>
+        </sanitizer>
+      </param>
+      <param name="param_label" type="text" value="parameter_label" label="Enter this parameter's label for the form" size="60" 
+         help="Note that commas and double quotes cannot be used in this text field - please creatively work around this technical limitation" >
+        <sanitizer invalid_char="">
+          <valid initial="string.printable"> <remove value=','/> <remove value='"'/> </valid>
+          <mapping initial="none"/>
+        </sanitizer>
+      </param>
+      <param name="param_help" type="text" value="parameter_help" label="Help for this parameter"
+         help="Note that commas and double quotes cannot be used in this text field - please work around this technical limitation" size="60">
+        <sanitizer invalid_char="">
+          <valid initial="string.printable"> <remove value=','/> <remove value='"'/> </valid>
+          <mapping initial="none"/>
+        </sanitizer>
+      </param>
+    </repeat> 
+    <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="20x120"  
+      help="Script must deal with three command line parameters: please cut and paste from examples below for the appropriate scripting language">
+      <sanitizer>
+         <valid initial="string.printable">
+         </valid>
+         <mapping initial="none"/>
+      </sanitizer>
+     </param>
+  </inputs>
+  <outputs>
+    <data name="output1" label="${tool_name}.${output_format}" format="tabular" metadata_source="input_tab">
+        <filter>make_TAB=="yes"</filter>
+        <actions>
+          <action type="format">
+                <option type="from_param" name="output_format" />
+          </action>
+        </actions>
+    </data>
+    <data format="html" name="html_file" label="${tool_name}.html">
+        <filter>make_HTML == "yes"</filter>
+    </data>
+    <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
+        <filter>makeMode['make_Tool'] == "yes"</filter>
+    </data>
+  </outputs>
+<configfile name="runme">$dynScript</configfile>
+<configfile name="helpme">
+#if $makeMode.make_Tool == "yes":
+#end if
+<configfile name="citeme">
+#if $makeMode.make_Tool == "yes":
+#for $citation in $makeMode.citations:
+#if $citation.citation_type.type == "bibtex":
+#end if
+#end for
+#end if
+    <param name='input_tab' value='tf2_test_in.xls' ftype='tabular' />
+    <param name='tool_name' value='tf2_test' />
+    <param name='make_Tool' value='yes' />
+    <param name='tool_version' value='0.01' />
+    <param name="tool_desc" value='testing_tf2' />
+    <param name="help_text" value='help text goes here' />
+    <param name='include_deps' value='yes' />
+    <param name="make_HTML" value="yes" />
+    <param name="make_TAB" value="yes" />
+    <param name="output_format" value="tabular" />
+    <param name="input_formats" value="tabular" />
+    <param name="interpreter" value='python' />
+    <param name="envpath" value='system' />
+    <param name="runme" value=""/>
+    <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/>
+    <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/>
+    <output name='new_tool' file="tf2_test.toolshed.gz" compare="sim_size" delta="600" />
+.. class:: warningmark
+**Details and attribution** 
+(see GTF_)
+**Local Admins ONLY** 
+Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
+**If you find a bug** 
+Please raise an issue at the bitbucket repository GTFI_
+**What it does** 
+This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy passing
+any number of input files and their metadata names to the script for use in (eg) summaries or reports.
+This allows quick generation of tools capable of taking some arbitrary number of user selected inputs
+for the "reduce" step of a map-reduce HPC model.
+**Input options** 
+This version allows multiple input file selected from the history - their paths and metadata names
+are provided to your script - see the examples below for each scripting language. Python uses argparse.
+Rscript uses some code to create all the command line variables. Parameters are injected into the bash/sh
+execution environment so they magically "appear" as $ prefixed variables and will also be found on the
+command line as parameters to be parsed if that's your preference.
+Note that additional parameters are NOT presented to the user of the generated tool but are frozen with the script.
+If there's demand, it would not be too hard to add them to the generated script...
+**Output options** 
+Optional script outputs include one single new history tabular file and for scripts that create multiple file reports
+or analyses, an Html page linking every file and image created by the script can be automatically generated.
+**Tool Generation option** 
+Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a Tool Shed (gzip) repository file
+ready to upload to your local toolshed for sharing and installation.
+Provide a small sample input when you run generate the tool because it will become the input for the generated functional test.
+.. class:: warningmark
+**Note to system administrators** 
+This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
+Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
+.. class:: warningmark
+**Use on public servers**  is STRONGLY discouraged for obvious reasons
+The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation.
+We recommend that you follow the good code hygiene practices associated with safe toolshed.
+**Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not select one, and the path to the optional
+output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below.
+Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output.
+This can be handy for complex scripts creating lots of output.
+**Multiple 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
+ # 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()
+ # tool factory Rscript parser suggested by Forester
+ #
+ # 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())
+ # 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 "CL=$@" >> "$OUTPATH"
+ open(my $fh, '>', $OUTPATH) or die "Could not open file '$OUTPATH' $!";
+ close $fh;
+Paper_ :
+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
+Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
+All rights reserved.
+Licensed under the LGPL_
+.. _LGPL:
+.. _GTF:
+.. _GTFI:
+.. _Paper:;keytype=ref
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tf2_test.html	Mon Feb 02 20:57:40 2015 -0500
@@ -0,0 +1,25 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" ""> 
+        <html xmlns="" xml:lang="en" lang="en"> 
+        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 
+        <meta name="generator" content="Galaxy tool output - see" /> 
+        <title></title> 
+        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
+        </head> 
+        <body> 
+        <div class="toolFormBody"> 
+<div class="infomessage">Galaxy Tool "tf2_test" run at 29/01/2015 11:24:54</div><br/>
+<div class="toolFormTitle">tf2 log output</div>
+tf2_test_error.log is empty<br/>
+<div class="toolFormTitle">Other log output</div>
+/tmp/tmpdRM3H0/job_working_directory/000/2/dataset_3_files/tf2_test_runner.log is empty<br/>
+<div class="toolFormTitle">All output files available for downloading</div>
+<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
+<tr><td><a href="tf2_test.python">tf2_test.python</a></td><td>0 B</td></tr>
+<tr class="odd_row"><td><a href="tf2_test_error.log">tf2_test_error.log</a></td><td>0 B</td></tr>
+<tr><td><a href="tf2_test_runner.log">tf2_test_runner.log</a></td><td>226 B</td></tr>
Binary file test-data/tf2_test.toolshed.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tf2_test_in.xls	Mon Feb 02 20:57:40 2015 -0500
@@ -0,0 +1,3 @@
+col1	col2	col3
+r11	r12	r13
+r21	r22	r23
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/	Mon Feb 02 20:57:40 2015 -0500
@@ -0,0 +1,25 @@
+### bog standard argparse for 3 possible comma separated lists
+## followed by some silly reverse each row code provided as an example
+## you're supposed to replace it with your great code..
+import sys
+import argparse
+import copy
+argp.add_argument('otherargs', nargs=argparse.REMAINDER)
+args = argp.parse_args()
+fout = open(args.OUTPATH,'w')
+sins = open(args.INPATHS.split(',')[0]).readlines()
+for i,sin in enumerate(sins):
+    row = sin.strip().split('\t')
+    rrow = copy.copy(row)
+    lrow = len(row)
+    if (lrow > 1):
+        for j in range(lrow):
+            rrow[j] = row[lrow-j-1]
+        fout.write('\t'.join(rrow))
+        fout.write('\n')
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Feb 02 20:57:40 2015 -0500
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+    <package name="ghostscript" version="9.10">
+        <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" toolshed="" />
+    </package>
+    <package name="graphicsmagick" version="1.3.20">
+        <repository changeset_revision="d87c457bbbc2" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="" />
+    </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
+       </readme>