Hi Jayant,

FYI the error still persists.
>
>
Please find the modified tool configuration file, attached here.
Just redirected your tool output to the result file in the below line

<command interpreter="perl">allsnp_modified.pl $input > $output</command>

HTH, Vipin
<tool id="allSNP" name="extracts all SNPs">
  <description>for each sequence in a file</description>
  <command interpreter="perl">allsnp_modified.pl $input > $output</command>
  <inputs>
		<param type="data" format="txt" name="input" label="Source file" />
  </inputs>
  <outputs>
      <data name="output" format="gff3" />
  </outputs>
  <help>
     extracts all SNPs that have undergone mutation. Output is in gff3 format.
  </help>
</tool>
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