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comparison rapsodyn/mpileupfilterandstat.xml @ 0:442a7c88b886 draft

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author mcharles
date Wed, 10 Sep 2014 09:18:15 -0400
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children 3f7b0788a1c4
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-1:000000000000 0:442a7c88b886
1 <tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="0.08">
2 <description>Filter mpileup file entry</description>
3 <command interpreter="perl">
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
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
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
8 -stat_freq_min $stat.stat_freq_min -stat_freq_max $stat.stat_freq_max -stat_freq_step $stat.stat_freq_step
9 -stat_dist_min $stat.stat_dist_min -stat_dist_max $stat.stat_dist_max -stat_dist_step $stat.stat_dist_step > $output_file
10 #else
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
12 #end if
13
14 </command>
15 <inputs>
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 "/>
18 <param name="max_depth" type="integer" value="100" 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%) "/>
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"/>
22 <conditional name="stat">
23 <param name="do_stat" type="select" label="Compute stats ">
24 <option value="NO">NO</option>
25 <option value="YES">YES</option>
26 </param>
27 <when value="YES">
28 <param name="stat_min_depth_min" type="integer" value = "2" label="min_depth - min" />
29 <param name="stat_min_depth_max" type="integer" value = "10" label="min_depth - max" />
30 <param name="stat_min_depth_step" type="integer" value = "2" label="min_depth - step" />
31 <param name="stat_max_depth_min" type="integer" value = "100" label="max_depth - min" />
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" />
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" />
36 <param name="stat_freq_step" type="float" value = "0.1" label="freq - step" />
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" />
39 <param name="stat_dist_step" type="integer" value = "50" label="dist - step" />
40 </when>
41 <when value="NO">
42
43 </when>
44 </conditional>
45
46
47
48 </inputs>
49 <outputs>
50 <data name="output_file" format="pileup" label="${tool.name} MPILEUP on ${on_string}"/>
51 <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
52 </outputs>
53
54 <help>
55
56
57
58 </help>
59 </tool>