Mercurial > repos > mcharles > rapsosnp
comparison rapsodyn/mpileupfilterandstat.xml @ 7:3f7b0788a1c4 draft
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author | mcharles |
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date | Tue, 07 Oct 2014 10:34:34 -0400 |
parents | 442a7c88b886 |
children |
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6:1776b8ddd87e | 7:3f7b0788a1c4 |
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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"> |