--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Transposer/Transposer.xml	Thu Mar 21 23:07:10 2013 -0400
@@ -0,0 +1,67 @@
+<tool id="Transposer" name="Transposer" version="0.01">
+<description>Transposes</description>
+<command interpreter="python">
+            Transposer.py --script_path "$runMe" --interpreter "Rscript" 
+            --tool_name "Transposer" --input_tab "$input1"   --output_tab "$tab_file" 
+            </command>
+<inputs>
+<param name="input1"  type="data" format="tabular" label="Select a suitable input file from your history"/> 
+<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="Transposer"/> 
+
+</inputs>
+<outputs>
+ <data format="tabular" name="tab_file" label="${job_name}"/>
+
+</outputs>
+<configfiles>
+<configfile name="runMe">
+<![CDATA[   
+# transpose a tabular input file and write as a tabular output file
+ourargs = commandArgs(TRUE)
+inf = ourargs[1]
+outf = ourargs[2]
+inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
+outp = t(inp)
+write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
+]]>
+</configfile>
+</configfiles>
+<tests><test>
+        <param name="input1" value="Transposer_test1_input.xls" ftype="tabular"/>
+        <param name="job_name" value="test1"/>
+        <param name="runMe" value="$runMe"/>
+        <output name="tab_file" file="Transposer_test1_output.xls" ftype="tabular"/>
+        </test></tests>
+<help>
+<![CDATA[   
+
+**What it Does**
+
+Transposes
+Blah blah
+
+
+**Script**
+Pressing execute will run the following code over your input file and generate some outputs in your history::
+
+ # transpose a tabular input file and write as a tabular output file
+ ourargs = commandArgs(TRUE)
+ inf = ourargs[1]
+ outf = ourargs[2]
+ inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
+ outp = t(inp)
+ write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
+
+
+
+**Attribution** This Galaxy tool was created by admin@admin.com at 22/03/2013 03:04:21
+using the Galaxy Tool Factory.
+See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
+Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. 
+Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
+
+
+]]>
+
+</help>
+</tool>