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view rapsodyn/extractseq.xml @ 6:1776b8ddd87e draft

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author mcharles
date Mon, 29 Sep 2014 03:02:16 -0400
parents 442a7c88b886
children 3f7b0788a1c4
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<tool id="extractseq" name="extractseq" version="0.03">
<description>Extract Sequence around variant position</description>
<command interpreter="perl">
    extractseq.pl -input_variant_file $input_variant_file -input_assembly_file $input_assembly_file -window_length $window_length > $output_file 
</command>
<inputs>
<param name="input_variant_file"  type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
<param name="input_assembly_file"  type="data" format="fasta" label="Select a suitable input ASSEMBLY file from your history"/>
<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
</inputs>
<outputs>
 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}"/>
</outputs>

<help>



</help>
</tool>