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view rapsodyn/ParseBlastForUniqueMatch.xml @ 7:3f7b0788a1c4 draft

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author mcharles
date Tue, 07 Oct 2014 10:34:34 -0400
parents 442a7c88b886
children 0a6c1cfe4dc8
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<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="1.01">
<description>Filter mpileup with blast results</description>
<command interpreter="perl">
    ParseBlastForUniqueMatch.pl -input_variant_file $input_variant_file -input_blast_file $input_blast_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max -log_file $log_file > $output_variant_file 
</command>
<inputs>
	<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
	<param name="input_blast_file"  type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/>
	<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
	<param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
</inputs>
<outputs>
	<data name="output_variant_file" format="pileup" label="${tool.name} on ${on_string}"/>
	<data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
</outputs>

<help>



</help>
</tool>