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29
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1 <tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="1.01">
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25
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2 <description>Filter mpileup with blast results</description>
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3 <command interpreter="perl">
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29
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4 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 > $output_variant_file
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25
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5 </command>
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6 <inputs>
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29
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7 <param name="input_variant_file" type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/>
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8 <param name="input_blast_file" type="data" format="tabular" label="Select a suitable input BLAST file (25 or 5 custom column(qseqid,qstart,qend,ssseq,sseq) from your history"/>
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9 <param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/>
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10 <param name="nb_mismatch_max" type="integer" value="3" label="Threshold for mismatch filter"/>
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25
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11 </inputs>
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12 <outputs>
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29
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13 <data name="output_variant_file" format="pileup" label="${tool.name} on ${on_string}"/>
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14 <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
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25
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15 </outputs>
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16
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17 <help>
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18
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19
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20
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21 </help>
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22 </tool>
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