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comparison fubar-galaxytoolfactory-cfcf6c9df5b7/rgToolFactory.xml @ 1:87613ace5113 draft

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author fubar
date Sat, 11 Aug 2012 02:41:28 -0400
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1 <tool id="rgTF" name="Tool Factory" version="0.08">
2 <description>Makes scripts into tools</description>
3 <command interpreter="python">
4 #if ( $__user_email__ not in $__admin_users__ ):
5 rgToolFactory.py --bad_user $__user_email__
6 #else:
7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
8 --tool_name "$tool_name" --user_email "$__user_email__"
9 #if $make_TAB.value=="yes":
10 --output_tab "$tab_file"
11 #end if
12 #if $makeMode.make_Tool=="yes":
13 --make_Tool "$makeMode.make_Tool"
14 --tool_desc "$makeMode.tool_desc"
15 --tool_version "$makeMode.tool_version"
16 --new_tool "$new_tool"
17 --help_text "$helpme"
18 #end if
19 #if $make_HTML.value=="yes":
20 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
21 #end if
22 #if $input1 != 'None':
23 --input_tab "$input1"
24 #end if
25 #end if
26 </command>
27 <inputs>
28 <param name="input1" type="data" label="Select an input file from your history" optional="true" size="120"
29 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
30 <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60"
31 help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
32 <sanitizer invalid_char="">
33 <valid initial="string.letters,string.digits"/>
34 </sanitizer>
35 </param>
36 <conditional name="makeMode">
37 <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!" size="60">
38 <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
39 <option value="" selected="true">No. Just run the script please</option>
40 </param>
41 <when value = "yes">
42 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
43 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
44 <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
45 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
46 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
47 size="8x120" value="**What it Does**"
48 help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
49 <sanitizer>
50 <valid initial="string.printable">
51 </valid>
52 <mapping initial="none"/>
53 </sanitizer>
54 </param>
55 </when>
56 <when value = "">
57 </when>
58 </conditional>
59 <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
60 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
61 <option value="yes">Yes, arrange all outputs in an HTML output</option>
62 <option value="" selected="true">No, no HTML output file thanks</option>
63 </param>
64
65
66 <param name="make_TAB" type="select" label="Create a new (default tabular) history output"
67 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
68 <option value="yes" selected="true">My script writes to a new history output</option>
69 <option value="">I only want an HTML output file</option>
70 </param>
71 <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">
72 <option value="tabular" selected="true">Tabular</option>
73 <option value="interval">Interval</option>
74 <option value="gz">gz</option>
75 <option value="text">text</option>
76 </param>
77 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
78 <option value="Rscript" selected="true">Rscript</option>
79 <option value="python">python</option>
80 <option value="perl">perl</option>
81 <option value="bash">bash</option>
82 </param>
83 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120"
84 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').">
85 <sanitizer>
86 <valid initial="string.printable">
87 </valid>
88 <mapping initial="none"/>
89 </sanitizer>
90 </param>
91 </inputs>
92 <outputs>
93 <data format="tabular" name="tab_file" label="${tool_name}.${out_format}">
94 <filter>make_TAB=="yes"</filter>
95 <change_format>
96 <when input="out_format" value="interval" format="interval" />
97 <when input="out_format" value="gz" format="gz" />
98 <when input="out_format" value="text" format="text" />
99 </change_format>
100 </data>
101 <data format="html" name="html_file" label="${tool_name}.html">
102 <filter>make_HTML == "yes"</filter>
103 </data>
104 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
105 <filter>makeMode['make_Tool'] == "yes"</filter>
106 </data>
107 </outputs>
108 <configfiles>
109 <configfile name="runme">
110 $dynScript
111 </configfile>
112
113 <configfile name="helpme">
114 #if $makeMode.make_Tool == "yes":
115 ${makeMode.help_text}
116 #end if
117 </configfile>
118 </configfiles>
119 <help>
120
121 .. class:: warningmark
122
123 **Local Admins ONLY** Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
124
125 **What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
126
127 **Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history.
128
129 **Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
130 a new HTML report linking all the files and images created by the script can be automatically generated.
131
132 **Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file
133 ready to upload to your local toolshed for sharing and installation. Provide a small sample input when you run generate the tool because
134 it will become the input for the generated functional test.
135
136 .. class:: warningmark
137
138 **Note to system administrators** This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
139 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
140
141 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.
142 We recommend that you follow the good code hygiene practices associated with safe toolshed.
143
144 .. class:: warningmark
145
146 **Use on public servers** is STRONGLY discouraged for obvious reasons
147
148 **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
149 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.
150 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.
151 This can be handy for complex scripts creating lots of output.
152
153 **Simple examples**
154
155 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::
156
157 # transpose a tabular input file and write as a tabular output file
158 ourargs = commandArgs(TRUE)
159 inf = ourargs[1]
160 outf = ourargs[2]
161 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
162 outp = t(inp)
163 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
164
165 Calculate a multiple test adjusted p value from a column of p values - for this script to be useful, it needs the right column for the input to be specified in the code for the
166 given input file type(s) specified when the tool is generated ::
167
168 # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
169 column = 1 # adjust if necessary for some other kind of input
170 ourargs = commandArgs(TRUE)
171 inf = ourargs[1]
172 outf = ourargs[2]
173 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
174 p = inp[,column]
175 q = p.adjust(p,method='BH')
176 outp = cbind(inp,'BH Adjusted p-value'=q)
177 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
178
179
180 A demonstration Rscript example takes no input file but generates some random data based pdf images
181 You must make sure the option to create an HTML output file is
182 turned on for this to work. Images (pdf) are linked via thumbnails and
183 all files have a link on the resulting HTML page::
184
185 # note this script takes NO input or output because it generates random data
186 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
187 bar = as.matrix(foo)
188 pdf( "heattest.pdf" )
189 heatmap(bar,main='Random Heatmap')
190 dev.off()
191 for (i in 1:49) {
192 foo = runif(100)
193 bar = rnorm(100)
194 pdf(paste('yet',i,"anotherplot.pdf",sep='_'))
195 plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)
196 dev.off()
197 }
198
199 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)::
200
201 # reverse order of columns in a tabular file
202 import sys
203 inp = sys.argv[1]
204 outp = sys.argv[2]
205 i = open(inp,'r')
206 o = open(outp,'w')
207 for row in i:
208 rs = row.rstrip().split('\t')
209 rs.reverse()
210 o.write('\t'.join(rs))
211 o.write('\n')
212 i.close()
213 o.close()
214
215
216 **Attribution** Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
217
218 All rights reserved.
219
220 Licensed under the LGPL_
221
222 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
223
224 </help>
225
226 </tool>
227
228