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

Uploaded

--- /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>