|
7
|
1 <tool id="cdf" name="CDF">
|
|
|
2 <description>plot of multiple numeric columns</description>
|
|
|
3 <command>cat $script_file | R --vanilla --slave > $out_log </command>
|
|
|
4 <inputs>
|
|
|
5 <param name="title" type="text" value="CDF plot" size="30" label="Plot title"/>
|
|
|
6 <param name="xlabel" type="text" value="value" size="30" label="xlabel"/>
|
|
|
7 <param name="log" label="log2 transform the data" type="boolean" truevalue="log" falsevalue="none" checked="False"/>
|
|
|
8 <param name="zero" label="remove zero" type="boolean" truevalue="zero" falsevalue="none" checked="False"/>
|
|
|
9 <param name="legendloc" type="select" label="legend location on CDF plot" >
|
|
|
10 <option value="bottomright" selected="true">bottomright</option>
|
|
|
11 <option value="bottomleft">bottomleft</option>
|
|
|
12 <option value="bottom">bottom</option>
|
|
|
13 <option value="left">left</option>
|
|
|
14 <option value="topleft">topleft</option>
|
|
|
15 <option value="top">top</option>
|
|
|
16 <option value="topright">topright</option>
|
|
|
17 <option value="right">right</option>
|
|
|
18 <option value="center">center</option>
|
|
|
19 </param>
|
|
|
20 <repeat name="series" title="sample">
|
|
|
21 <param name="label" type="text" value="" size="30" label="data label"/>
|
|
|
22 <param name="input" type="data" format="tabular" label="dataset"/>
|
|
|
23 <param name="column" type="integer" value="2" label="column number (-1 for last column)"/>
|
|
|
24 </repeat>
|
|
|
25
|
|
|
26 </inputs>
|
|
|
27
|
|
|
28 <configfiles>
|
|
|
29 <configfile name="script_file">
|
|
|
30 ## Setup R error handling to go to stderr
|
|
|
31 options(warn=-1)
|
|
|
32 source("/Users/xuebing/galaxy-dist/tools/mytools/cdf.r")
|
|
|
33 uselog = as.character("${log}")
|
|
|
34 zero = as.character("${zero}")
|
|
|
35 title = as.character("${title}")
|
|
|
36 xlabel = as.character("${xlabel}")
|
|
|
37 if (uselog=='log'){
|
|
|
38 xlabel = paste('log2',xlabel)
|
|
|
39 }
|
|
|
40
|
|
|
41 labels = character(0)
|
|
|
42 x = list()
|
|
|
43 #for $i, $s in enumerate( $series )
|
|
|
44 labels = c(labels,"${s.label.value}")
|
|
|
45 x0 = read.table( "${s.input.file_name}" ,sep='\t')
|
|
|
46 col = ${s.column.value}
|
|
|
47 if (col == -1) {col = ncol(x0)}
|
|
|
48 x0 = x0[,col]
|
|
|
49 if (zero == 'zero'){
|
|
|
50 x0 = x0[x0 != 0]
|
|
|
51 }
|
|
|
52 if (uselog=='log'){
|
|
|
53 x0=log2(1+x0)
|
|
|
54 }
|
|
|
55 print("${s.label.value}")
|
|
|
56 summary(x0)
|
|
|
57 x[[$i+1]] = x0
|
|
|
58 #end for
|
|
|
59 pdf("${out_file}")
|
|
|
60 mycdf(x,title,labels,"${legendloc}",xlabel,'')
|
|
|
61 dev.off()
|
|
|
62 </configfile>
|
|
|
63 </configfiles>
|
|
|
64
|
|
|
65 <outputs>
|
|
|
66 <data format="txt" name="out_log" label="${tool.name} on ${on_string}: (log)" />
|
|
|
67 <data format="pdf" name="out_file" label="${tool.name} on ${on_string}: (plot)" />
|
|
|
68 </outputs>
|
|
|
69
|
|
|
70 <help>
|
|
|
71
|
|
|
72 .. class:: infomark
|
|
|
73
|
|
|
74 This tool generate barplot and CDF plot comparing multiple numeric columns in different files.
|
|
|
75
|
|
|
76
|
|
|
77 </help>
|
|
|
78 </tool>
|
