view mpileupfilter/mpileupfilter.xml @ 5:26d2c851d48e draft

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<tool id="mpileupfilter" name="mpileupfilter" version="0.05">
<description>Filter mpileup file entry</description>
<command interpreter="perl">
    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 > $output_file 
</command>
<inputs>
<param name="input_file"  type="data" format="pileup" label="Select a suitable input file from your history"/>
<param name="min_depth" type="integer" value="2" label="Minimum depth at variant position "/>
<param name="max_depth" type="integer" value="100" label="Maximum depth at variant position "/>
<param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/>
<param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/>
<param name="min_distance" type="integer" value="50" label="Minimum physical distance between variant"/>
</inputs>
<outputs>
 <data name="output_file" format="pileup" label="${tool.name} on ${on_string}"/>
</outputs>

<help>



</help>
</tool>