fubar/brokenandnotdeletablebyowneroradmin: README.txt annotate

annotate README.txt @ 25:8cc3f3c0e539 default tip

Now uses admin_users to check that the user is authorized to run this tool Docs adjusted.

author	Ross Lazarus <ross.lazarus@gmail.com>
date	Wed, 06 Jun 2012 14:16:25 +1000
parents	8289ebc513ab
children

rev	line source
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	1 # WARNING before you start
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	2 # Install on a private Galaxy ONLY
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	3 # Please NEVER on a public or production instance
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	4
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	5 Read on if You use a production Galaxy;
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	6 Your users sometimes take data out of Galaxy, process it with ugly
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	7 little perl/awk/sed/R... scripts and put it back;
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	8 They do this when they can't do some transformation in Galaxy (the 90/10 rule);
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	9 You don't have enough developer resources for wrapping dozens of even relatively simple tools;
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	10 Your institution would be better off if those nasty, feral scripts were all tucked safely in
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	11 a local toolshed.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	12
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	13 The good news If it can be trivially scripted, it can be running safely in your
25 8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	14 local Galaxy via your own local toolshed in a few minutes.
8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	15
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	16 That's what this tool does. You paste a simple script and the tool returns
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	17 a new, real Galaxy tool, ready to be installed from the local toolshed to local servers.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	18 Scripts can be wrapped and online literally within minutes.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	19
25 8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	20 To fully and safely exploit the awesome power of this tool, Galaxy and the ToolShed,
8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	21 you should be a developer installing this tool on a private/personal/scratch local instance where you are an admin_user.
8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	22 Then, if you break it, you get to keep all the pieces
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	23 see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	24
25 8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	25 To make the tool work R, python, perl etc are needed on your path if you want to run scripts using those interpreters.
8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	26 The HTML file code to shrink R's gross pdfs requires Ghostscript and imagemagick must be installed for generating the thumbnails.
8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	27 If not already there (I just added it to datatypes_conf.xml.sample), please add:
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	28 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
25 8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	29 to your local data_types_conf.xml.
8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	30
8cc3f3c0e539 Now uses admin_users to check that the user is authorized to run this tool Ross Lazarus <ross.lazarus@gmail.com> parents: 24 diff changeset	31 Note that ONLY admin_users can run this tool
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	32
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	33 What it does This is a tool factory for simple scripts in python, R or whatever ails ye.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	34 LIMITED to simple scripts that read one input from the history.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	35 Optionally can write one new history dataset,
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	36 and optionally collect any number of outputs into links on an autogenerated HTML page.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	37 Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	38 A generated script gets you a serious leg up to a more complex one.
17 187c8b023595 more doco good ross lazarus ross.lazarus@gmail.com parents: 16 diff changeset	39
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	40 What you do You paste and run your script
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	41 you fix the syntax errors and eventually it runs
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	42 that's pretty good because you can use the redo button
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	43 to rerun it and edit the script as you debug - cool, but
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	44 now the power really kicks in, because
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	45 once the script works on some test data, you can
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	46 generate a toolshed compatible gzip file
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	47 containing your script neatly wrapped and hidden safely inside an ordinary Galaxy script in your
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	48 local toolshed. That means safe and largely automated installation in any production Galaxy configured
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	49 to use your toolshed or the tool
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	50 Automated build for tests still being worked on - should be done soon
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	51
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	52 Generated tool Security Once you install a generated tool, it's just
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	53 another tool - assuming the script is safe. They just run normally and their user cannot do anything unusually insecure
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	54 but please, practice safe toolshed.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	55 Read the fucking code before you install any tool.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	56 Especially this one - it is really scary.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	57
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	58 If you opt for an HTML output, you get all the script outputs arranged
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	59 as a single Html history item - all output files are linked, thumbnails for all the pdfs.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	60 Ugly but really inexpensive.
17 187c8b023595 more doco good ross lazarus ross.lazarus@gmail.com parents: 16 diff changeset	61
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	62 Patches welcome please.
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	63
17 187c8b023595 more doco good ross lazarus ross.lazarus@gmail.com parents: 16 diff changeset	64
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	65 long route to June 2012 product
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	66 derived from an integrated script model
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	67 called rgBaseScriptWrapper.py
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	68 Note to the unwary:
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	69 This tool allows arbitrary scripting on your Galaxy as the Galaxy user
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	70 There is nothing stopping a malicious user doing whatever they choose
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	71 Extremely dangerous!!
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	72 Totally insecure. So, trusted users only
17 187c8b023595 more doco good ross lazarus ross.lazarus@gmail.com parents: 16 diff changeset	73
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	74
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	75
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	76
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	77 copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	78
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	79 all rights reserved
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	80 Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	81
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 18 diff changeset	82 Material for our more enthusiastic readers continues below
2 d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	83
13 7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	84 Motivation Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	85 - even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible.
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	86
13 7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	87 Benefits For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	88 tasks. Once a user has a working R (or python or perl) script that does something Galaxy cannot currently do (eg transpose a
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	89 tabular file) and takes parameters the way Galaxy supplies them (see example below), they:
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	90
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	91 1. Install the tool factory on a personal private instance
2 d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	92
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	93 2. Upload a small test data set
2 d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	94
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	95 3. Paste the script into the 'script' text box and iteratively run the insecure tool on test data until it works right -
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	96 there is absolutely no reason to do this anywhere other than on a personal private instance.
2 d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	97
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	98 4. Once it works right, set the 'Generate toolshed gzip' option and run it again.
2 d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	99
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	100 5. A toolshed style gzip appears ready to upload and install like any other Toolshed entry.
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	101
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	102 6. Upload the new tool to the toolshed
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	103
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	104 7. Ask the local admin to check the new tool to confirm it's not evil and install it in the local production galaxy
2 d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	105
18 943d4f0ee7c1 More better doco ross lazarus ross.lazarus@gmail.com parents: 17 diff changeset	106 Simple examples on the tool form
13 7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	107
16 36df24947ab3 readme changes Ross Lazarus <ross.lazarus@gmail.com> parents: 14 diff changeset	108 A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file,
36df24947ab3 readme changes Ross Lazarus <ross.lazarus@gmail.com> parents: 14 diff changeset	109 does something (transpose in this case) and writes the results to a new tabular file::
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: 6 diff changeset	110
13 7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	111 # transpose a tabular input file and write as a tabular output file
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	112 ourargs = commandArgs(TRUE)
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	113 inf = ourargs[1]
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	114 outf = ourargs[2]
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	115 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	116 outp = t(inp)
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	117 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	118
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	119 A more complex Rscript example takes no input file but generates a random heatmap pdf - you must make sure the option to create an HTML output file is
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	120 turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page::
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	121
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	122 # note this script takes NO input or output because it generates random data
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	123 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	124 bar = as.matrix(foo)
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	125 pdf( "heattest.pdf" )
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	126 heatmap(bar,main='Random Heatmap')
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	127 dev.off()
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	128
14 6f36c696afa5 readme adjustments ross lazarus ross.lazarus@gmail.com parents: 13 diff changeset	129 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
6f36c696afa5 readme adjustments ross lazarus ross.lazarus@gmail.com parents: 13 diff changeset	130 and pasted into the script box. Note that you can already do this in Galaxy by setting up the cut columns tool with the
6f36c696afa5 readme adjustments ross lazarus ross.lazarus@gmail.com parents: 13 diff changeset	131 correct number of columns in reverse order,but this script will work for any number of columns so is completely generic::
5 9c1a1e0e664a and again ross lazarus ross.lazarus@gmail.com parents: 4 diff changeset	132
13 7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	133 # reverse order of columns in a tabular file
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	134 import sys
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	135 inp = sys.argv[1]
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	136 outp = sys.argv[2]
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	137 i = open(inp,'r')
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	138 o = open(outp,'w')
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	139 for row in i:
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	140 rs = row.rstrip().split('\t')
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	141 rs.reverse()
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	142 o.write('\t'.join(rs))
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	143 o.write('\n')
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	144 i.close()
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	145 o.close()
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	146
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	147
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	148 Attribution Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	149
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	150 All rights reserved.
13 7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	151
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	152 Licensed under the LGPL_
4 3755b2365fb0 More edits to readme ross lazarus ross.lazarus@gmail.com parents: 3 diff changeset	153
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	154
13 7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	155 Obligatory screenshot
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	156 http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
7725e4ab27e1 Adding tests - problem to find the script - needs a fixed string somewhere. ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	157

Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate README.txt @ 25:8cc3f3c0e539 default tip