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7
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1 <tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="1.00">
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0
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2 <description>Filter mpileup file entry</description>
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3 <command interpreter="perl">
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4 #if $stat.do_stat=="YES"
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5 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
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6 -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
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7 -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
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8 -stat_freq_min $stat.stat_freq_min -stat_freq_max $stat.stat_freq_max -stat_freq_step $stat.stat_freq_step
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9 -stat_dist_min $stat.stat_dist_min -stat_dist_max $stat.stat_dist_max -stat_dist_step $stat.stat_dist_step > $output_file
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10 #else
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11 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
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12 #end if
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13
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14 </command>
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15 <inputs>
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16 <param name="input_file" type="data" format="pileup" label="Select a suitable input file from your history"/>
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7
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17 <param name="min_depth" type="integer" value="1" label="Minimum depth at variant position "/>
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18 <param name="max_depth" type="integer" value="500" label="Maximum depth at variant position "/>
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19 <param name="min_frequency" type="float" value="0" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/>
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0
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20 <param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/>
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21 <param name="min_distance" type="integer" value="0" label="Minimum physical distance between variant"/>
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0
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22 <conditional name="stat">
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23 <param name="do_stat" type="select" label="Compute stats ">
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24 <option value="NO">NO</option>
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25 <option value="YES">YES</option>
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26 </param>
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27 <when value="YES">
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28 <param name="stat_min_depth_min" type="integer" value = "4" label="min_depth - min" />
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29 <param name="stat_min_depth_max" type="integer" value = "20" label="min_depth - max" />
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30 <param name="stat_min_depth_step" type="integer" value = "4" label="min_depth - step" />
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31 <param name="stat_max_depth_min" type="integer" value = "200" label="max_depth - min" />
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0
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32 <param name="stat_max_depth_max" type="integer" value = "200" label="max_depth - max" />
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33 <param name="stat_max_depth_step" type="integer" value = "100" label="max_depth - step" />
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34 <param name="stat_freq_min" type="float" value = "0.8" label="freq - min" />
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35 <param name="stat_freq_max" type="float" value = "1" label="freq - max" />
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36 <param name="stat_freq_step" type="float" value = "0.2" label="freq - step" />
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37 <param name="stat_dist_min" type="integer" value = "0" label="dist - min" />
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38 <param name="stat_dist_max" type="integer" value = "50" label="dist - max" />
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39 <param name="stat_dist_step" type="integer" value = "50" label="dist - step" />
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40 </when>
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41 <when value="NO">
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42
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43 </when>
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44 </conditional>
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45
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46
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47
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48 </inputs>
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49 <outputs>
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50 <data name="output_file" format="pileup" label="${tool.name} MPILEUP on ${on_string}"/>
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51 <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
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52 </outputs>
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53
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54 <help>
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55
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56
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57
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58 </help>
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59 </tool>
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