Mercurial > repos > mcharles > rapsosnp
diff 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 |
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--- a/rapsodyn/mpileupfilterandstat.xml Mon Sep 29 03:02:16 2014 -0400 +++ b/rapsodyn/mpileupfilterandstat.xml Tue Oct 07 10:34:34 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="0.08"> +<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="1.00"> <description>Filter mpileup file entry</description> <command interpreter="perl"> #if $stat.do_stat=="YES" @@ -14,26 +14,26 @@ </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="2" label="Minimum depth at variant position "/> -<param name="max_depth" type="integer" value="100" label="Maximum depth at variant position "/> -<param name="min_frequency" type="float" value="1" label="Minimum variant frequency (between 0-1 : 0.5 for 50%) "/> +<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="50" label="Minimum physical distance between variant"/> +<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 = "2" label="min_depth - min" /> - <param name="stat_min_depth_max" type="integer" value = "10" label="min_depth - max" /> - <param name="stat_min_depth_step" type="integer" value = "2" label="min_depth - step" /> - <param name="stat_max_depth_min" type="integer" value = "100" label="max_depth - min" /> + <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 = "0.1" label="freq - step" /> + <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" />