--- a/prinseq.xml	Mon May 15 11:03:57 2017 -0400
+++ b/prinseq.xml	Wed Jul 07 09:22:27 2021 +0000
@@ -1,7 +1,10 @@
-<tool id="prinseq" name="PRINSEQ" version="0.20.4">
+<tool id="prinseq" name="PRINSEQ" version="@TOOL_VERSION+galaxy1">
     <description>to process quality of sequences</description>
+    <macros>
+        <token name="@TOOL_VERSION">0.20.4</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.20.4">prinseq</requirement>
+        <requirement type="package" version="@TOOL_VERSION">prinseq</requirement>
     </requirements>
 
     <stdio>
@@ -34,7 +37,7 @@
                 #if $seq_type.input_singles.is_of_type('fastqillumina'):
                     -phred64
                 #end if
-            #else:
+            #elif $seq_type.seq_type_opt == "paired":
                 -fastq '$seq_type.input_mate1'
                 -fastq2 '$seq_type.input_mate2'
                 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:
@@ -44,6 +47,12 @@
                 #if $seq_type.input_mate1.is_of_type('fastqillumina'):
                     -phred64
                 #end if
+            #else 
+                -fastq '$seq_type.input_collection.forward'
+                -fastq2 '$seq_type.input_collection.reverse'
+                #if $seq_type.input_collection.forward.is_of_type('fastqillumina'):
+                    -phred64
+                #end if
             #end if
 
             -out_good "tmp/good_sequences"
@@ -225,6 +234,7 @@
             <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?">
               <option value="single" selected="true">Single-end</option>
               <option value="paired">Paired-end</option>
+              <option value="paired_collection">Paired Collection</option>
             </param>
             <when value="single">
                 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
@@ -233,6 +243,9 @@
                 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
                 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
             </when>
+            <when value="paired_collection">
+                <param name="input_collection" type="data_collection" collection_type="paired" label="FASTQ collection" help="FASTQ data in a paired collection" />
+            </when>
         </conditional>
 
         <conditional name="filter_treatments">
@@ -651,6 +664,18 @@
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
 
+        <collection name="good_sequences_collection" type="paired">
+            <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
+        </collection>
+
+        <collection name="singletons_collection" type="paired">
+            <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
+        </collection>
+
+        <collection name="rejected_sequences_collection" type="paired">
+            <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
+        </collection>
+
         <!--<data format="html" name="html_file" from_work_dir="stats_html.html"
             label="${tool.name} on ${on_string}: Summary" />-->
     </outputs>