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Run arbitrary R scripts in Galaxy
<tool id="rbitrary" name="Rbitrary">
<command>cat $Rscript | R --slave --args
## Inputs.
#for $input_file in $input_files:
#end for
<param format="txt" name="Rscript" type="data" label="Rscript"/>
<param format="txt" name="first_input" type="data" label="First input file" help=""/>
<repeat name="input_files" title="Additional Input Files">
<param format="txt" name="additional_input" type="data" label="Additional input file" help=""/>
<data format="txt" name="output" label="${} on ${on_string}" from_work_dir="output.txt"/>
<!-- 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" />
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