# HG changeset patch
# User iuc
# Date 1495407137 14400
# Node ID 57910d476be938dc74a1c69b1ab897876d5a4dca
# Parent  bec1f08cdfcca813e0eafbfc8cf2c5bc55a511a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439

diff -r bec1f08cdfcc -r 57910d476be9 macros.xml
--- a/macros.xml	Thu Apr 27 04:19:34 2017 -0400
+++ b/macros.xml	Sun May 21 18:52:17 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 bec1f08cdfcc -r 57910d476be9 stacks_procrad.xml
--- a/stacks_procrad.xml	Thu Apr 27 04:19:34 2017 -0400
+++ b/stacks_procrad.xml	Sun May 21 18:52:17 2017 -0400
@@ -90,8 +90,7 @@
                 <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" />
 
                 <param name="barcode_encoding" type="select" label="Barcode location">
-                    <option value="--inline_null" selected="True">Barcode is inline with sequence</option>
-                    <option value="--index_null">Barcode is provided in FASTQ header</option>
+                    <expand macro="barcode_encoding_single" />
                 </param>
             </when>
             <when value="paired">
@@ -99,12 +98,7 @@
                 <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" />
 
                 <param name="barcode_encoding" type="select" label="Barcode location">
-                    <option value="--inline_null" selected="True">Barcode is inline with sequence, only on the single-end read (read 1)</option>
-                    <option value="--index_null">Barcode is provided in FASTQ header, only on the single-end read (read 1)</option>
-                    <option value="--inline_inline">Barcode is inline with sequence, on both single and paired-end read (read 1 and 2)</option>
-                    <option value="--index_index">Barcode is provided in FASTQ header, on both single and paired-end read (read 1 and 2)</option>
-                    <option value="--inline_index">Barcode is inline with sequence on single-end read (read 1), and in FASTQ header for paired-end read (read 2)</option>
-                    <option value="--index_inline">Barcode is provided in FASTQ header on single-end read (read 1), and is inline with sequence on paired-end read (read 2)</option>
+                    <expand macro="barcode_encoding_pair" />
                 </param>
             </when>
         </conditional>
diff -r bec1f08cdfcc -r 57910d476be9 test-data/clonefilter/R1_0001.1.fq.gz
Binary file test-data/clonefilter/R1_0001.1.fq.gz has changed
diff -r bec1f08cdfcc -r 57910d476be9 test-data/clonefilter/R2_0001.2.fq.gz
Binary file test-data/clonefilter/R2_0001.2.fq.gz has changed
diff -r bec1f08cdfcc -r 57910d476be9 test-data/clonefilter/Removed1_0001.1.1.fq.gz
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diff -r bec1f08cdfcc -r 57910d476be9 test-data/clonefilter/Removed1_0001.1.1.fq.single.gz
Binary file test-data/clonefilter/Removed1_0001.1.1.fq.single.gz has changed
diff -r bec1f08cdfcc -r 57910d476be9 test-data/clonefilter/Removed2_0001.2.2.fq.gz
Binary file test-data/clonefilter/Removed2_0001.2.2.fq.gz has changed