diff STACKS_clone_filter.py @ 8:a8b87bc0c3ad draft

planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty

--- a/STACKS_clone_filter.py	Thu Feb 04 08:00:32 2016 -0500
+++ b/STACKS_clone_filter.py	Thu Feb 04 08:13:32 2016 -0500
@@ -10,10 +10,19 @@
 
 def __main__():
     parser = argparse.ArgumentParser()
+
+    #files (single or pair)
     parser.add_argument('-f', type=str)
     parser.add_argument('-fwd', type=str)
     parser.add_argument('-rev', type=str)
 
+    #oligos
+    parser.add_argument('-oligo_len_1', type=int)
+    parser.add_argument('-oligo_len_2', type=int)
+
+    #options (allways there)
+    parser.add_argument('-opt', type=str)
+
     #parser.add_argument('-k', action='store_true')
 
     options = parser.parse_args()
@@ -30,6 +39,12 @@
         cmd_line.extend(['-1', options.fwd])
         cmd_line.extend(['-2', options.rev])
 
+    if options.oligo_len_1 > -1:
+        cmd_line.extend(['--oligo_len_1', options.oligo_len_1])
+    if options.oligo_len_2 > -1:
+        cmd_line.extend(['--oligo_len_2', options.oligo_len_2])
+    cmd_line.append('--' + options.oligo_len_2)
+
     print "[CMD]:"+' '.join(cmd_line)
     subprocess.call(cmd_line)