Have you tried adding another output definition? Two changes below, first another output element, second changing output.id to output_id ('.' has special meaning). On Feb 17, 2010, at 9:56 AM, vill wrote:
<tool id="GAPSS_igf_2_WIG" name="GAPSS - IGF to WIG"> <description></description> <command interpreter="perl">galaxy-wrapper_GAPSS_igf2wig.v2.pl $input $SeperateStrands $CutOff $output $output_id</command> <inputs> <param name="input" type="data" label="IGF File input" /> <param name="SeperateStrands" type="select" help="on seperate strands" label="0 or 1"> <option value="0">0</option> <option value="1">1</option> </param> <param name="CutOff" type="select" help="Select Cutoff" label="Cutoff size" > <option value="1">1</option> <option value="0">0</option> </param>
</inputs>
<outputs> <data name="output" format="interval" /> <data name="output_id" format="txt" />
</outputs>