Mercurial > repos > fubar > toolfactory

comparison rgToolFactory.xml @ 9:e4e097a41064 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Wed, 19 Mar 2014 21:42:08 -0400
parents 78c04d9fe621
children 59bce2efadfe
comparison
equal deleted inserted replaced
8:78c04d9fe621 9:e4e097a41064
1 <tool id="rgTF" name="Tool Factory" version="0.10"> 1 <tool id="rgTF" name="Tool Factory" version="1.10">
2 <description>Makes scripts into tools</description> 2 <description>Makes scripts into tools</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="9.10">ghostscript</requirement> 4 <requirement type="package" version="9.10">ghostscript</requirement>
5 <requirement type="package" version="1.3.18">graphicsmagick</requirement> 5 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
6 </requirements> 6 </requirements>
60 <when value = ""> 60 <when value = "">
61 </when> 61 </when>
62 </conditional> 62 </conditional>
63 <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" 63 <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"
64 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output"> 64 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
65 <option value="yes">Yes, arrange all outputs in an HTML output</option> 65 <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
66 <option value="" selected="true">No, no HTML output file thanks</option> 66 <option value="" selected="true">No, no HTML output file thanks</option>
67 </param> 67 </param>
68 68 <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an HTML file specified above"
69
70 <param name="make_TAB" type="select" label="Create a new (default tabular) history output"
71 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes"> 69 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
72 <option value="yes" selected="true">My script writes to a new history output</option> 70 <option value="yes" selected="true">My script writes to a new history output</option>
73 <option value="">I only want an HTML output file</option> 71 <option value="">I do not want a new history output file</option>
74 </param> 72 </param>
75 <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"> 73 <param name="out_format" type="select" label="Galaxy datatype for your tool's output file if any" help="You may need to edit the xml to extend this list">
76 <option value="tabular" selected="true">Tabular</option> 74 <option value="tabular" selected="true">Tabular</option>
77 <option value="interval">Interval</option> 75 <option value="interval">Interval</option>
78 <option value="gz">gz</option> 76 <option value="gz">gz</option>
79 <option value="text">text</option> 77 <option value="text">text</option>
80 </param> 78 </param>
195 193
196 # note this script takes NO input or output because it generates random data 194 # note this script takes NO input or output because it generates random data
197 for (i in 1:10) { 195 for (i in 1:10) {
198 foo = runif(100) 196 foo = runif(100)
199 bar = rnorm(100) 197 bar = rnorm(100)
198 bar = foo + 0.2*bar
200 pdf(paste('yet',i,"anotherplot.pdf",sep='_')) 199 pdf(paste('yet',i,"anotherplot.pdf",sep='_'))
201 plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6) 200 plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)
202 dev.off() 201 dev.off()
203 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) 202 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
204 bar = as.matrix(foo) 203 bar = as.matrix(foo)