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5
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1 <tool id="mpileupfilter" name="mpileupfilter" version="0.05">
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2 <description>Filter mpileup file entry</description>
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3 <command interpreter="perl">
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4 mpileupfilter.pl -input_file $input_file -min_depth $min_depth -min_frequency $min_frequency -min_distance $min_distance -min_forward_and_reverse $min_forward_and_reverse -max_depth $max_depth > $output_file
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5 </command>
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6 <inputs>
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7 <param name="input_file" type="data" format="pileup" label="Select a suitable input file from your history"/>
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8 <param name="min_depth" type="integer" value="2" label="Minimum depth at variant position "/>
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9 <param name="max_depth" type="integer" value="100" label="Maximum depth at variant position "/>
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10 <param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/>
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11 <param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/>
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12 <param name="min_distance" type="integer" value="50" label="Minimum physical distance between variant"/>
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13 </inputs>
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14 <outputs>
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15 <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
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16 </outputs>
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17
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18 <help>
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19
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20
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21
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22 </help>
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23 </tool>
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