Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate rgToolFactory.xml @ 23:6146509c9c2d

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
mostly working again
author ross lazarus ross.lazarus@gmail.com
date Tue, 05 Jun 2012 23:25:35 +1000
parents c23e53f768ed
children 8289ebc513ab
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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">
19
a87a262220a4 Adding proof of concept for optional output formats.
ross lazarus ross.lazarus@gmail.com
parents: 15
diff changeset
4 #if ( $__user_email__ not in ['yourID@email','ross.lazarus@gmail.com'] ):
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"/>
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
29 <param name="tool_name" type="text" value="My dynamic script" size="80" label="Title for job outputs" help="Supply a meaningful name here to remind you what the outputs contain">
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry:
ross lazarus ross.lazarus@gmail.com
parents: 11
diff changeset
30 <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
31 <valid initial="string.letters,string.digits">
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry:
ross lazarus ross.lazarus@gmail.com
parents: 11
diff changeset
32 <mapping initial="none"/>
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 </valid>
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 </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
35 </param>
22
c23e53f768ed Think I finally got the output selection stuff working..
ross lazarus ross.lazarus@gmail.com
parents: 19
diff changeset
36 <conditional name="makeMode">
8
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
37 <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
38 <option value="yes">Yes</option>
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
39 <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
40 </param>
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
41 <when value = "yes">
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
42 <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
43 <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
44 <sanitizer>
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
45 <valid initial="string.printable">
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
46 </valid>
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
47 <mapping initial="none"/>
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
48 </sanitizer>
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
49 </param>
22
c23e53f768ed Think I finally got the output selection stuff working..
ross lazarus ross.lazarus@gmail.com
parents: 19
diff changeset
50 </when>
c23e53f768ed Think I finally got the output selection stuff working..
ross lazarus ross.lazarus@gmail.com
parents: 19
diff changeset
51 <when value = "">
c23e53f768ed Think I finally got the output selection stuff working..
ross lazarus ross.lazarus@gmail.com
parents: 19
diff changeset
52
8
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
53 </when>
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
54 </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
55 <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
56 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
57 <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
58 <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
59 </param>
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
c23e53f768ed Think I finally got the output selection stuff working..
ross lazarus ross.lazarus@gmail.com
parents: 19
diff changeset
62 <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
63 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
64 <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
65 <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
66 </param>
c23e53f768ed Think I finally got the output selection stuff working..
ross lazarus ross.lazarus@gmail.com
parents: 19
diff changeset
67 <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
68 <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
69 <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
70 <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
71 <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
72 </param>
7
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
73 <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
74 <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
75 <option value="python">python</option>
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
76 <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
77 </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
78 <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
79 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
80 <sanitizer>
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
81 <valid initial="string.printable">
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
82 </valid>
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
83 <mapping initial="none"/>
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
84 </sanitizer>
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
85 </param>
7
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
86 </inputs>
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
87 <outputs>
22
c23e53f768ed Think I finally got the output selection stuff working..
ross lazarus ross.lazarus@gmail.com
parents: 19
diff changeset
88 <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
89 <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
90 <change_format>
22
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="interval" format="interval" />
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="gz" format="gz" />
c23e53f768ed Think I finally got the output selection stuff working..
ross lazarus ross.lazarus@gmail.com
parents: 19
diff changeset
93 <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
94 </change_format>
7
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
95 </data>
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
96 <data format="html" name="html_file" label="${tool_name}.html">
12
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry:
ross lazarus ross.lazarus@gmail.com
parents: 11
diff changeset
97 <filter>make_HTML == "yes"</filter>
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry:
ross lazarus ross.lazarus@gmail.com
parents: 11
diff changeset
98 </data>
23
6146509c9c2d mostly working again
ross lazarus ross.lazarus@gmail.com
parents: 22
diff changeset
99 <data format="toolshed.gz" name="new_tool" label="${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
100 <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
101 </data>
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
102 </outputs>
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
103 <configfiles>
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
104 <configfile name="runme">
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
105 ${dynScript}
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
106 </configfile>
9
e09c76551bed Can run without input or output or either..
ross lazarus ross.lazarus@gmail.com
parents: 8
diff changeset
107
e09c76551bed Can run without input or output or either..
ross lazarus ross.lazarus@gmail.com
parents: 8
diff changeset
108 <configfile name="helpme">
22
c23e53f768ed Think I finally got the output selection stuff working..
ross lazarus ross.lazarus@gmail.com
parents: 19
diff changeset
109 #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
110 ${makeMode.help_text}
9
e09c76551bed Can run without input or output or either..
ross lazarus ross.lazarus@gmail.com
parents: 8
diff changeset
111 #end if
8
220885b2d7ee End to end test works. Add tests next
ross lazarus ross.lazarus@gmail.com
parents: 7
diff changeset
112 </configfile>
7
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
113 </configfiles>
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
114 <help>
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
115 **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
116
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry:
ross lazarus ross.lazarus@gmail.com
parents: 11
diff changeset
117 **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
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 **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
120 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
121
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry:
ross lazarus ross.lazarus@gmail.com
parents: 11
diff changeset
122 **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
123 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
124
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 **Permission to to use this tool** must be explicitly granted by an administrator adding approved Galaxy user IDs to the local tool XML list of permitted users. *It will not run otherwise*
10
71f2ac0eee95 Updated tarball with some test material - still need code generated...
ross lazarus ross.lazarus@gmail.com
parents: 9
diff changeset
126
71f2ac0eee95 Updated tarball with some test material - still need code generated...
ross lazarus ross.lazarus@gmail.com
parents: 9
diff changeset
127 .. class:: warningmark
71f2ac0eee95 Updated tarball with some test material - still need code generated...
ross lazarus ross.lazarus@gmail.com
parents: 9
diff changeset
128
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
129 **Note to system administrators** This tool offers *NO* built in protection against malicious scripts and should only be installed on private/personnal Galaxy instances.
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry:
ross lazarus ross.lazarus@gmail.com
parents: 11
diff changeset
130 Under no circumstances should you allow any user to use this tool unless you really, really trust them with the power to do what they want as the Galaxy user.
7
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
131
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
132 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.
7
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
133
10
71f2ac0eee95 Updated tarball with some test material - still need code generated...
ross lazarus ross.lazarus@gmail.com
parents: 9
diff changeset
134 .. class:: warningmark
71f2ac0eee95 Updated tarball with some test material - still need code generated...
ross lazarus ross.lazarus@gmail.com
parents: 9
diff changeset
135
71f2ac0eee95 Updated tarball with some test material - still need code generated...
ross lazarus ross.lazarus@gmail.com
parents: 9
diff changeset
136 **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
137
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
138 **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
139 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
140 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
141 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
142
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
143 **Simple examples**
7
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
144
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
145 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
146
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
147 # 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
148 ourargs = commandArgs(TRUE)
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
149 inf = ourargs[1]
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
150 outf = ourargs[2]
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
151 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
152 outp = t(inp)
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
153 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
154
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
155 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
156 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
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 # 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
159 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
160 bar = as.matrix(foo)
e09c76551bed Can run without input or output or either..
ross lazarus ross.lazarus@gmail.com
parents: 8
diff changeset
161 pdf( "heattest.pdf" )
e09c76551bed Can run without input or output or either..
ross lazarus ross.lazarus@gmail.com
parents: 8
diff changeset
162 heatmap(bar,main='Random Heatmap')
e09c76551bed Can run without input or output or either..
ross lazarus ross.lazarus@gmail.com
parents: 8
diff changeset
163 dev.off()
e09c76551bed Can run without input or output or either..
ross lazarus ross.lazarus@gmail.com
parents: 8
diff changeset
164
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
165 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
166
d12728e33c3d Changed to deliver a gz file - requires a new datatypes_conf.xml entry:
ross lazarus ross.lazarus@gmail.com
parents: 11
diff changeset
167 # 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
168 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
169 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
170 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
171 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
172 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
173 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
174 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
175 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
176 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
177 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
178 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
179 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
180
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
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 **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
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 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
185
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 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
187
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 .. _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
189
7
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
190 </help>
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
191
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
192 </tool>
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
193
7221619caefa Updated name and added crude gzip generator for toolshed
ross lazarus ross.lazarus@gmail.com
parents:
diff changeset
194