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author fubar
date Thu, 21 Mar 2013 23:07:10 -0400
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1 <tool id="Transposer" name="Transposer" version="0.01">
2 <description>Transposes</description>
3 <command interpreter="python">
4 Transposer.py --script_path "$runMe" --interpreter "Rscript"
5 --tool_name "Transposer" --input_tab "$input1" --output_tab "$tab_file"
6 </command>
7 <inputs>
8 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/>
9 <param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="Transposer"/>
10
11 </inputs>
12 <outputs>
13 <data format="tabular" name="tab_file" label="${job_name}"/>
14
15 </outputs>
16 <configfiles>
17 <configfile name="runMe">
18 <![CDATA[
19 # transpose a tabular input file and write as a tabular output file
20 ourargs = commandArgs(TRUE)
21 inf = ourargs[1]
22 outf = ourargs[2]
23 inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
24 outp = t(inp)
25 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
26 ]]>
27 </configfile>
28 </configfiles>
29 <tests><test>
30 <param name="input1" value="Transposer_test1_input.xls" ftype="tabular"/>
31 <param name="job_name" value="test1"/>
32 <param name="runMe" value="$runMe"/>
33 <output name="tab_file" file="Transposer_test1_output.xls" ftype="tabular"/>
34 </test></tests>
35 <help>
36 <![CDATA[
37
38 **What it Does**
39
40 Transposes
41 Blah blah
42
43
44 **Script**
45 Pressing execute will run the following code over your input file and generate some outputs in your history::
46
47 # transpose a tabular input file and write as a tabular output file
48 ourargs = commandArgs(TRUE)
49 inf = ourargs[1]
50 outf = ourargs[2]
51 inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
52 outp = t(inp)
53 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
54
55
56
57 **Attribution** This Galaxy tool was created by admin@admin.com at 22/03/2013 03:04:21
58 using the Galaxy Tool Factory.
59 See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
60 Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team.
61 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
62
63
64 ]]>
65
66 </help>
67 </tool>