view mpileupfilteronblastxml/mpileupfilteronblastxml.xml @ 5:26d2c851d48e draft

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<tool id="mpileupfilteronblastxml" name="mpileupfilteronblastxml" version="0.03">
<description>Filter mpileup with blast results</description>
<command interpreter="perl">
    mpileupfilteronblastxml.pl -input_variant_file $input_variant_file -input_blastxml_file $input_blastxml_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max > $output_file 
</command>
<inputs>
<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
<param name="input_blastxml_file"  type="data" format="xml" label="Select a suitable input BLASTXML file from your history"/>
<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
</inputs>
<outputs>
 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}"/>
</outputs>

<help>



</help>
</tool>