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comparison fubar-galaxytoolfactory-2e68c2a22b43/rgToolFactory.xml @ 2:b55b59435fb1 draft

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Now with bash working I think. Special case but working..
author fubar
date Mon, 13 Aug 2012 06:27:26 -0400
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1 <tool id="rgTF" name="Tool Factory" version="0.09">
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="sh">sh</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">$dynScript</configfile>
110 <configfile name="helpme">
111 #if $makeMode.make_Tool == "yes":
112 ${makeMode.help_text}
113 #end if
114 </configfile>
115 </configfiles>
116 <help>
117
118 .. class:: warningmark
119
120 **Local Admins ONLY** Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
121
122 **What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
123
124 **Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history.
125
126 **Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
127 a new HTML report linking all the files and images created by the script can be automatically generated.
128
129 **Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file
130 ready to upload to your local toolshed for sharing and installation. Provide a small sample input when you run generate the tool because
131 it will become the input for the generated functional test.
132
133 .. class:: warningmark
134
135 **Note to system administrators** This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
136 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
137
138 .. class:: warningmark
139
140 **Use on public servers** is STRONGLY discouraged for obvious reasons
141
142 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.
143 We recommend that you follow the good code hygiene practices associated with safe toolshed.
144
145 **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
146 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.
147 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.
148 This can be handy for complex scripts creating lots of output.
149
150 **Simple examples**
151
152 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::
153
154 # transpose a tabular input file and write as a tabular output file
155 ourargs = commandArgs(TRUE)
156 inf = ourargs[1]
157 outf = ourargs[2]
158 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
159 outp = t(inp)
160 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
161
162 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
163 given input file type(s) specified when the tool is generated ::
164
165 # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
166 column = 1 # adjust if necessary for some other kind of input
167 ourargs = commandArgs(TRUE)
168 inf = ourargs[1]
169 outf = ourargs[2]
170 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
171 p = inp[,column]
172 q = p.adjust(p,method='BH')
173 outp = cbind(inp,'BH Adjusted p-value'=q)
174 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
175
176
177 A demonstration Rscript example takes no input file but generates some random data based pdf images
178 You must make sure the option to create an HTML output file is
179 turned on for this to work. Images (pdf) are linked via thumbnails and
180 all files have a link on the resulting HTML page::
181
182 # note this script takes NO input or output because it generates random data
183 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
184 bar = as.matrix(foo)
185 pdf( "heattest.pdf" )
186 heatmap(bar,main='Random Heatmap')
187 dev.off()
188 for (i in 1:49) {
189 foo = runif(100)
190 bar = rnorm(100)
191 pdf(paste('yet',i,"anotherplot.pdf",sep='_'))
192 plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)
193 dev.off()
194 }
195
196 A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces
197 for this to work if cut and pasted into the script box)::
198
199 # reverse order of columns in a tabular file
200 import sys
201 inp = sys.argv[1]
202 outp = sys.argv[2]
203 i = open(inp,'r')
204 o = open(outp,'w')
205 for row in i:
206 rs = row.rstrip().split('\t')
207 rs.reverse()
208 o.write('\t'.join(rs))
209 o.write('\n')
210 i.close()
211 o.close()
212
213 A trivial shell script example to show that it works::
214
215 #!/bin/bash
216 INF=$1
217 OUTF=$2
218 cut -c2,4,6,8,10,12 $INF >$OUTF
219
220
221 **Attribution** Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
222
223 All rights reserved.
224
225 Licensed under the LGPL_
226
227 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
228
229 </help>
230
231 </tool>
232
233