# HG changeset patch
# User iuc
# Date 1495407281 14400
# Node ID 95e37a28704be564743564c461db640844d082f0
# Parent  db683c98e4555aacaa5816c755d8f0306528224d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439

diff -r db683c98e455 -r 95e37a28704b macros.xml
--- a/macros.xml	Thu Apr 27 04:17:14 2017 -0400
+++ b/macros.xml	Sun May 21 18:54:41 2017 -0400
@@ -391,4 +391,19 @@
             </when>
         </conditional>
     </xml>
+
+    <xml name="barcode_encoding_single">
+        <option value="--inline_null" selected="True">Barcode is inline with sequence</option>
+        <option value="--index_null">Barcode is provided in FASTQ header</option>
+    </xml>
+
+    <xml name="barcode_encoding_pair">
+        <option value="--inline_null" selected="True">Barcode is inline with sequence</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>
+    </xml>
 </macros>
diff -r db683c98e455 -r 95e37a28704b test-data/clonefilter/R1_0001.1.fq.gz
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diff -r db683c98e455 -r 95e37a28704b test-data/clonefilter/R2_0001.2.fq.gz
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diff -r db683c98e455 -r 95e37a28704b test-data/clonefilter/Removed1_0001.1.1.fq.gz
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diff -r db683c98e455 -r 95e37a28704b test-data/clonefilter/Removed1_0001.1.1.fq.single.gz
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diff -r db683c98e455 -r 95e37a28704b test-data/clonefilter/Removed2_0001.2.2.fq.gz
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