Run arbitrary R scripts in Galaxy

Rbitrary.xml

<tool id="rbitrary" name="Rbitrary">
	<description>Rbitrary</description>
	<command>cat $Rscript | R --slave --args 
            ## Inputs.
            ${first_input}
            #for $input_file in $input_files:
              ${input_file.additional_input}
            #end for
		


                                     </command>
                                     
                                     
	<inputs>
		<param format="txt" name="Rscript" type="data" label="Rscript"/>
		<param format="txt" name="first_input" type="data" label="First input file" help=""/>
        	<repeat name="input_files" title="Additional Input Files">
            		<param format="txt" name="additional_input" type="data" label="Additional input file" help=""/>
        	</repeat>
	</inputs>

	<outputs>
		<data format="txt" name="output" label="${tool.name} on ${on_string}" from_work_dir="output.txt"/>
	</outputs>


	<help>
<!--	Run an arbitrary R script on 1 data file with 1 output.
	TODO: allow for multiple inputs and outputs, arbitrary arguments passed to R.
(multiple inputs might work now?)
	
	
	Add to tool_conf.xml:
 	<section name="Rbitrary" id="rbitrary">
	    <tool file="rbitrary/Rbitrary.xml" />
  	</section>
-->
	
	
	</help>

</tool>