<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="1.00">
<description>Filter mpileup file entry</description>
<command interpreter="perl">
  #if $stat.do_stat=="YES"
        mpileupfilterandstat.pl -input_file $input_file -log_file $log_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 -do_stat $stat.do_stat 
-stat_min_depth_min $stat.stat_min_depth_min -stat_min_depth_max $stat.stat_min_depth_max -stat_min_depth_step $stat.stat_min_depth_step 
-stat_max_depth_min $stat.stat_max_depth_min -stat_max_depth_max $stat.stat_max_depth_max -stat_max_depth_step $stat.stat_max_depth_step 
-stat_freq_min $stat.stat_freq_min -stat_freq_max $stat.stat_freq_max -stat_freq_step $stat.stat_freq_step 
-stat_dist_min $stat.stat_dist_min -stat_dist_max $stat.stat_dist_max -stat_dist_step $stat.stat_dist_step > $output_file 
  #else
        mpileupfilterandstat.pl -input_file $input_file -log_file $log_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 -do_stat $stat.do_stat > $output_file 
  #end if

</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="1" label="Minimum depth at variant position "/>
<param name="max_depth" type="integer" value="500" label="Maximum depth at variant position "/>
<param name="min_frequency" type="float" value="0" 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="0" label="Minimum physical distance between variant"/>
<conditional name="stat">
  <param name="do_stat" type="select" label="Compute stats ">
    <option value="NO">NO</option>
    <option value="YES">YES</option>
  </param>
  <when value="YES">
    <param name="stat_min_depth_min" type="integer" value = "4" label="min_depth - min" />
    <param name="stat_min_depth_max" type="integer" value = "20" label="min_depth - max" />
    <param name="stat_min_depth_step" type="integer" value = "4" label="min_depth - step" />
    <param name="stat_max_depth_min" type="integer" value = "200" label="max_depth - min" />
    <param name="stat_max_depth_max" type="integer" value = "200" label="max_depth - max" />
    <param name="stat_max_depth_step" type="integer" value = "100" label="max_depth - step" />
    <param name="stat_freq_min" type="float" value = "0.8" label="freq - min" />
    <param name="stat_freq_max" type="float" value = "1" label="freq - max" />
    <param name="stat_freq_step" type="float" value = "0.2" label="freq - step" />
    <param name="stat_dist_min" type="integer" value = "0" label="dist - min" />
    <param name="stat_dist_max" type="integer" value = "50" label="dist - max" />
    <param name="stat_dist_step" type="integer" value = "50" label="dist - step" />
  </when>
  <when value="NO">
    
  </when>
</conditional> 



</inputs>
<outputs>
 <data name="output_file" format="pileup" label="${tool.name} MPILEUP on ${on_string}"/>
 <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
</outputs>

<help>



</help>
</tool>