Mercurial > repos > mcharles > rapsosnp
diff rapsodyn/mpileupfilterandstat.xml @ 0:442a7c88b886 draft
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author | mcharles |
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date | Wed, 10 Sep 2014 09:18:15 -0400 |
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children | 3f7b0788a1c4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/mpileupfilterandstat.xml Wed Sep 10 09:18:15 2014 -0400 @@ -0,0 +1,59 @@ +<tool id="mpileupfilterandstat" name="mpileupfilterandstat" version="0.08"> +<description>Filter mpileup file entry</description> +<command interpreter="perl"> + #if $stat.do_stat=="YES" + 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 +-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 +-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 +-stat_freq_min $stat.stat_freq_min -stat_freq_max $stat.stat_freq_max -stat_freq_step $stat.stat_freq_step +-stat_dist_min $stat.stat_dist_min -stat_dist_max $stat.stat_dist_max -stat_dist_step $stat.stat_dist_step > $output_file + #else + 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 + #end if + +</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_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"/> +<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_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_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" /> + </when> + <when value="NO"> + + </when> +</conditional> + + + +</inputs> +<outputs> + <data name="output_file" format="pileup" label="${tool.name} MPILEUP on ${on_string}"/> + <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> +</outputs> + +<help> + + + +</help> +</tool>