fubar/brokenandnotdeletablebyowneroradmin: rgToolFactory.xml annotate

annotate rgToolFactory.xml @ 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
11 a0a5d0757e39 Minor tool help changes and fixes to tests - still no code ross lazarus ross.lazarus@gmail.com parents: 10 diff changeset	1 <tool id="rgTF" name="Tool Factory" version="0.05">
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	2 <description>Makes scripts into tools</description>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	3 <command interpreter="python">
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	4 #if ( $__user_email__ not in $__admin_users__ ):
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	5 rgToolFactory.py --bad_user $__user_email__
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	6 #else:
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	8 --tool_name "$tool_name"
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	9 #if $make_TAB.value=="yes":
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	10 --output_tab "$tab_file"
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	11 #end if
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	12 #if $makeMode.make_Tool=="yes":
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	13 --make_Tool "$makeMode.make_Tool"
23 6146509c9c2d mostly working again ross lazarus ross.lazarus@gmail.com parents: 22 diff changeset	14 --help_text "$helpme"
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	15 --tool_desc "tool_desc"
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	16 --new_tool "$new_tool"
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	17 #end if
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	18 #if $make_HTML.value=="yes":
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	19 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	20 #end if
10 71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	21 #if $input1 != 'None':
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	22 --input_tab "$input1"
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	23 #end if
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	24 #end if
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	25 </command>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	26 <inputs>
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	27 <param name="input1" type="data" label="Select an input file from your history" optional="true"
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	28 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
24 8289ebc513ab More tweaks to docs and installation notes Ross Lazarus <ross.lazarus@gmail.com> parents: 23 diff changeset	29 <param name="tool_name" type="text" value="My dynamic script" size="80" label="Title for job outputs and new tool ID"
8289ebc513ab More tweaks to docs and installation notes Ross Lazarus <ross.lazarus@gmail.com> parents: 23 diff changeset	30 help="This will become the toolshed repository name so please choose thoughtfully">
8289ebc513ab More tweaks to docs and installation notes Ross Lazarus <ross.lazarus@gmail.com> parents: 23 diff changeset	31 <sanitizer invalid_char="">
8289ebc513ab More tweaks to docs and installation notes Ross Lazarus <ross.lazarus@gmail.com> parents: 23 diff changeset	32 <valid initial="string.letters,string.digits"/>
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	33 </sanitizer>
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	34 </param>
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	35 <conditional name="makeMode">
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	36 <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!">
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	37 <option value="yes">Yes</option>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	38 <option value="" selected="true">Not yet, it's still broken</option>
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	39 </param>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	40 <when value = "yes">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	41 <param name="tool_desc" type="text" width="120" value="" help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	42 <param name="help_text" type="text" area="true" size="8x80" width="120" value="What it Does" help="Supply the brief user documentation to appear on the new tool form as reStructured text" >
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	43 <sanitizer>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	44 <valid initial="string.printable">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	45 </valid>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	46 <mapping initial="none"/>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	47 </sanitizer>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	48 </param>
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	49 </when>
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	50 <when value = "">
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	51
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	52 </when>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	53 </conditional>
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	54 <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images"
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	55 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	56 <option value="yes" selected="true">Yes</option>
a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	57 <option value="">No</option>
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	58 </param>
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	59
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	60
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	61 <param name="make_TAB" type="select" label="Create a new (default tabular) history output"
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	62 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	63 <option value="yes" selected="true">Make a new history output file</option>
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	64 <option value="">No new history output file. Will use an HTML file</option>
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	65 </param>
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	66 <param name="out_format" type="select" label="Galaxy datatype for your tool's output file" help="You may need to edit the xml to extend this list">
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	67 <option value="tabular" selected="true">Tabular</option>
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	68 <option value="interval">Interval</option>
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	69 <option value="gz">gz</option>
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	70 <option value="text">text</option>
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	71 </param>
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	72 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	73 <option value="Rscript" selected="true">Rscript</option>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	74 <option value="python">python</option>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	75 <option value="perl (ugh)">perl</option>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	76 </param>
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	77 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x80" width="80"
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	78 help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None').">
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	79 <sanitizer>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	80 <valid initial="string.printable">
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	81 </valid>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	82 <mapping initial="none"/>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	83 </sanitizer>
220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	84 </param>
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	85 </inputs>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	86 <outputs>
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	87 <data format="tabular" name="tab_file" label="${tool_name}.${out_format}">
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	88 <filter>make_TAB=="yes"</filter>
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	89 <change_format>
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	90 <when input="out_format" value="interval" format="interval" />
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	91 <when input="out_format" value="gz" format="gz" />
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	92 <when input="out_format" value="text" format="text" />
19 a87a262220a4 Adding proof of concept for optional output formats. ross lazarus ross.lazarus@gmail.com parents: 15 diff changeset	93 </change_format>
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	94 </data>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	95 <data format="html" name="html_file" label="${tool_name}.html">
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	96 <filter>make_HTML == "yes"</filter>
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	97 </data>
23 6146509c9c2d mostly working again ross lazarus ross.lazarus@gmail.com parents: 22 diff changeset	98 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	99 <filter>makeMode['make_Tool'] == "yes"</filter>
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	100 </data>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	101 </outputs>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	102 <configfiles>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	103 <configfile name="runme">
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	104 ${dynScript}
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	105 </configfile>
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	106
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	107 <configfile name="helpme">
22 c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	108 #if $makeMode.make_Tool == "yes":
c23e53f768ed Think I finally got the output selection stuff working.. ross lazarus ross.lazarus@gmail.com parents: 19 diff changeset	109 ${makeMode.help_text}
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	110 #end if
8 220885b2d7ee End to end test works. Add tests next ross lazarus ross.lazarus@gmail.com parents: 7 diff changeset	111 </configfile>
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	112 </configfiles>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	113 <help>
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	114
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	115 .. class:: warningmark
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	116
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	117 Local Admins ONLY Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
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	118
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	119 What it does This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	120
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	121 Input options This version is limited to simple transformation or reporting requiring only a single input file selected from the history.
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	122
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	123 Output options Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	124 a new HTML report linking all the files and images created by the script can be automatically generated.
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	125
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	126 Tool Generation option Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	127 ready to upload to your local toolshed for sharing and installation.
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	128
10 71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	129 .. class:: warningmark
71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	130
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	131 Note to system administrators This tool offers NO built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
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	132 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	133
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	134 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.
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	135 We recommend that you follow the good code hygiene practices associated with safe toolshed.
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	136
10 71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	137 .. class:: warningmark
71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	138
71f2ac0eee95 Updated tarball with some test material - still need code generated... ross lazarus ross.lazarus@gmail.com parents: 9 diff changeset	139 Use on public servers is STRONGLY discouraged for obvious reasons
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	140
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	141 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
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	142 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.
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	143 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.
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	144 This can be handy for complex scripts creating lots of output.
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	145
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	146 Simple examples
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	147
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	148 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::
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	149
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	150 # transpose a tabular input file and write as a tabular output file
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	151 ourargs = commandArgs(TRUE)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	152 inf = ourargs[1]
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	153 outf = ourargs[2]
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	154 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	155 outp = t(inp)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	156 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	157
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	158 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
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	159 turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page::
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	160
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	161 # note this script takes NO input or output because it generates random data
9 e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	162 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	163 bar = as.matrix(foo)
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	164 pdf( "heattest.pdf" )
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	165 heatmap(bar,main='Random Heatmap')
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	166 dev.off()
e09c76551bed Can run without input or output or either.. ross lazarus ross.lazarus@gmail.com parents: 8 diff changeset	167
12 d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	168 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)::
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	169
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	170 # reverse order of columns in a tabular file
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	171 import sys
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	172 inp = sys.argv[1]
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	173 outp = sys.argv[2]
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	174 i = open(inp,'r')
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	175 o = open(outp,'w')
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	176 for row in i:
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	177 rs = row.rstrip().split('\t')
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	178 rs.reverse()
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	179 o.write('\t'.join(rs))
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	180 o.write('\n')
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	181 i.close()
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	182 o.close()
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	183
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	184
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	185 Attribution Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	186
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	187 All rights reserved.
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	188
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	189 Licensed under the LGPL_
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	190
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	191 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry: ross lazarus ross.lazarus@gmail.com parents: 11 diff changeset	192
7 7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	193 </help>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	194
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	195 </tool>
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	196
7221619caefa Updated name and added crude gzip generator for toolshed ross lazarus ross.lazarus@gmail.com parents: diff changeset	197

Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate rgToolFactory.xml @ 25:8cc3f3c0e539 default tip