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1 <tool id="extractseq" name="extractseq" version="0.03">
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2 <description>Extract Sequence around variant position</description>
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3 <command interpreter="perl">
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4 extractseq.pl -input_variant_file $input_variant_file -input_assembly_file $input_assembly_file -window_length $window_length > $output_file
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5 </command>
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6 <inputs>
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7 <param name="input_variant_file" type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
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8 <param name="input_assembly_file" type="data" format="fasta" label="Select a suitable input ASSEMBLY file from your history"/>
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9 <param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
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10 </inputs>
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11 <outputs>
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12 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}"/>
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13 </outputs>
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14
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15 <help>
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16
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17
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18
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19 </help>
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20 </tool>
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