# HG changeset patch
# User tiagoantao
# Date 1454591612 18000
# Node ID a8b87bc0c3ad22b9a0ec098179b55cc6031983d7
# Parent  2059c028c07aa652fbec027ec57242292bdaa38b
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty

diff -r 2059c028c07a -r a8b87bc0c3ad STACKS_clone_filter.py
--- 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)
 
diff -r 2059c028c07a -r a8b87bc0c3ad STACKS_clone_filter.xml
--- a/STACKS_clone_filter.xml	Thu Feb 04 08:00:32 2016 -0500
+++ b/STACKS_clone_filter.xml	Thu Feb 04 08:13:32 2016 -0500
@@ -18,7 +18,7 @@
   -fwd $data_type.fwd
   -rev $data_type.rev
 #end if
-  $oligo_options
+  -opt $oligo_option
 #if $oligo_len_1 > -1:
   --oligo_len_1 $oligo_len_1
 #end if
@@ -44,11 +44,11 @@
   <param name="oligo_len_1" type="integer" label="length of the single-end oligo sequence in data set (-1 == ignore)"/>
   <param name="oligo_len_2" type="integer" label="length of the paired-end oligo sequence in data set (-1 == ignore)"/>
   <param name="oligo_options" type="select" label="Oligo sequence options">
-      <option value="--inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</option>
-      <option value="--null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option>
-      <option value="--index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option>
-      <option value="--inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option>
-      <option value="--index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option>
+      <option value="inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</option>
+      <option value="null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option>
+      <option value="index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option>
+      <option value="inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option>
+      <option value="index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option>
       <option value="inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option>
       <option value="index_inline">random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data)</option>
   </param>