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comparison rapsodyn/mpileupfilterandstat.xml @ 7:3f7b0788a1c4 draft

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author mcharles
date Tue, 07 Oct 2014 10:34:34 -0400
parents 442a7c88b886
children
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6:1776b8ddd87e 7:3f7b0788a1c4
1 <tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="0.08"> 1 <tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="1.00">
2 <description>Filter mpileup file entry</description> 2 <description>Filter mpileup file entry</description>
3 <command interpreter="perl"> 3 <command interpreter="perl">
4 #if $stat.do_stat=="YES" 4 #if $stat.do_stat=="YES"
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 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
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 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
12 #end if 12 #end if
13 13
14 </command> 14 </command>
15 <inputs> 15 <inputs>
16 <param name="input_file" type="data" format="pileup" label="Select a suitable input file from your history"/> 16 <param name="input_file" type="data" format="pileup" label="Select a suitable input file from your history"/>
17 <param name="min_depth" type="integer" value="2" label="Minimum depth at variant position "/> 17 <param name="min_depth" type="integer" value="1" label="Minimum depth at variant position "/>
18 <param name="max_depth" type="integer" value="100" label="Maximum depth at variant position "/> 18 <param name="max_depth" type="integer" value="500" label="Maximum depth at variant position "/>
19 <param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/> 19 <param name="min_frequency" type="float" value="0" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/>
20 <param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/> 20 <param name="min_forward_and_reverse" type="integer" value="0" label="Minimum variant coverage by forward and reverse reads"/>
21 <param name="min_distance" type="integer" value="50" label="Minimum physical distance between variant"/> 21 <param name="min_distance" type="integer" value="0" label="Minimum physical distance between variant"/>
22 <conditional name="stat"> 22 <conditional name="stat">
23 <param name="do_stat" type="select" label="Compute stats "> 23 <param name="do_stat" type="select" label="Compute stats ">
24 <option value="NO">NO</option> 24 <option value="NO">NO</option>
25 <option value="YES">YES</option> 25 <option value="YES">YES</option>
26 </param> 26 </param>
27 <when value="YES"> 27 <when value="YES">
28 <param name="stat_min_depth_min" type="integer" value = "2" label="min_depth - min" /> 28 <param name="stat_min_depth_min" type="integer" value = "4" label="min_depth - min" />
29 <param name="stat_min_depth_max" type="integer" value = "10" label="min_depth - max" /> 29 <param name="stat_min_depth_max" type="integer" value = "20" label="min_depth - max" />
30 <param name="stat_min_depth_step" type="integer" value = "2" label="min_depth - step" /> 30 <param name="stat_min_depth_step" type="integer" value = "4" label="min_depth - step" />
31 <param name="stat_max_depth_min" type="integer" value = "100" label="max_depth - min" /> 31 <param name="stat_max_depth_min" type="integer" value = "200" label="max_depth - min" />
32 <param name="stat_max_depth_max" type="integer" value = "200" label="max_depth - max" /> 32 <param name="stat_max_depth_max" type="integer" value = "200" label="max_depth - max" />
33 <param name="stat_max_depth_step" type="integer" value = "100" label="max_depth - step" /> 33 <param name="stat_max_depth_step" type="integer" value = "100" label="max_depth - step" />
34 <param name="stat_freq_min" type="float" value = "0.8" label="freq - min" /> 34 <param name="stat_freq_min" type="float" value = "0.8" label="freq - min" />
35 <param name="stat_freq_max" type="float" value = "1" label="freq - max" /> 35 <param name="stat_freq_max" type="float" value = "1" label="freq - max" />
36 <param name="stat_freq_step" type="float" value = "0.1" label="freq - step" /> 36 <param name="stat_freq_step" type="float" value = "0.2" label="freq - step" />
37 <param name="stat_dist_min" type="integer" value = "0" label="dist - min" /> 37 <param name="stat_dist_min" type="integer" value = "0" label="dist - min" />
38 <param name="stat_dist_max" type="integer" value = "50" label="dist - max" /> 38 <param name="stat_dist_max" type="integer" value = "50" label="dist - max" />
39 <param name="stat_dist_step" type="integer" value = "50" label="dist - step" /> 39 <param name="stat_dist_step" type="integer" value = "50" label="dist - step" />
40 </when> 40 </when>
41 <when value="NO"> 41 <when value="NO">