# HG changeset patch
# User tiagoantao
# Date 1454590832 18000
# Node ID 2059c028c07aa652fbec027ec57242292bdaa38b
# Parent  c50b7a3ff5ad7cb29281d6d8228ae7a65fd6949d
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty

diff -r c50b7a3ff5ad -r 2059c028c07a STACKS_clone_filter.xml
--- a/STACKS_clone_filter.xml	Thu Feb 04 07:51:30 2016 -0500
+++ b/STACKS_clone_filter.xml	Thu Feb 04 08:00:32 2016 -0500
@@ -18,6 +18,13 @@
   -fwd $data_type.fwd
   -rev $data_type.rev
 #end if
+  $oligo_options
+#if $oligo_len_1 > -1:
+  --oligo_len_1 $oligo_len_1
+#end if
+#if $oligo_len_2 > -1:
+  --oligo_len_2 $oligo_len_2
+#end if
 </command>
 
 <inputs>
@@ -34,14 +41,14 @@
           <param name="rev" type="data" format="fastq" label="Reverse FASTQ" />
       </when>
   </conditional>
-  <param name="oligo_len_1" type="integer" label="length of the single-end oligo sequence in data set"/>
-  <param name="oligo_len_2" type="integer" label="length of the paired-end oligo sequence in data set"/>
+  <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>