# HG changeset patch
# User tiagoantao
# Date 1454590226 18000
# Node ID 1a5ebb16aaea014685ce281f855ac443a04680ae
# Parent  f4b429a3494ae59c7733ddadf143f5ac6d6d5147
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty

diff -r f4b429a3494a -r 1a5ebb16aaea STACKS_clone_filter.py
--- a/STACKS_clone_filter.py	Wed Feb 03 10:58:13 2016 -0500
+++ b/STACKS_clone_filter.py	Thu Feb 04 07:50:26 2016 -0500
@@ -1,9 +1,11 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 
-import shutil
+import argparse
+import glob
+import os
 import subprocess
-import argparse
+import shutil
 
 
 def __main__():
@@ -20,10 +22,6 @@
     os.mkdir('job_outputs')
     os.chdir('job_outputs')
 
-    # STACKS_archive
-    # check if zipped files are into the tab
-    extract_compress_files(options.P, os.getcwd())
-
     # create the populations command input line
     cmd_line=['clone_filter']
     if options.f is not None:
@@ -36,7 +34,7 @@
     subprocess.call(cmd_line)
 
     # postprocesses
-    clean_files = glob.glob('*.fq')
+    clean_files = glob.glob('*.fq*')
     if options.f is not None:
         shutil.copy(clean_files[0], 'clean.fq')
     else:
diff -r f4b429a3494a -r 1a5ebb16aaea STACKS_clone_filter.xml
--- a/STACKS_clone_filter.xml	Wed Feb 03 10:58:13 2016 -0500
+++ b/STACKS_clone_filter.xml	Thu Feb 04 07:50:26 2016 -0500
@@ -34,6 +34,17 @@
           <param name="rev" type="data" format="fastq" label="Reverse FASTQ" />
       </when>
   </conditional>
+  <param name="oligo_len_1" type="int" label="length of the single-end oligo sequence in data set"/>
+  <param name="oligo_len_2" type="int" label="length of the paired-end oligo sequence in data set"/>
+  <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_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>
 </inputs>
 
 <outputs>