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view rapsodyn/ParseBlastForUniqueMatch.xml @ 0:442a7c88b886 draft

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author mcharles
date Wed, 10 Sep 2014 09:18:15 -0400
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<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="0.01">
<description>Filter mpileup with blast results</description>
<command interpreter="perl">
    ParseBlastForUniqueMatch.pl $input_variant_file $input_blast_file $window_length $nb_mismatch_max > $output_file 
</command>
<inputs>
<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
<param name="input_blast_file"  type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/>
<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
</inputs>
<outputs>
 <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
</outputs>

<help>



</help>
</tool>