--- a/stacks_shortreads.xml	Wed Sep 01 11:23:22 2021 +0000
+++ b/stacks_shortreads.xml	Thu Apr 14 09:25:46 2022 +0000
@@ -1,5 +1,5 @@
 <!-- this is essentially a copy of stacks_procrad minus the unsupported options -->
-<tool id="stacks2_shortreads" name="Stacks2: process shortreads" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
+<tool id="stacks2_shortreads" name="Stacks2: process shortreads" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
 <description>fast cleaning of randomly sheared genomic or transcriptomic data</description>
     <macros>
         <import>macros.xml</import>
@@ -20,7 +20,17 @@
 
 process_shortreads
 
-@PROCESS_IOOPTIONS@
+-p stacks_inputs/
+#if $input_type.input_type_select == "paired"
+    --paired
+#end if
+-i $inputype
+-b '$barcode'
+$input_type.barcode_encoding
+#if str( $outype ) != "auto"
+    -y $outype
+#end if
+-o stacks_outputs
 @PROCESS_FILTER@
 @COMMON_ADVANCED@
 @RESCUE_BARCODE@
@@ -46,26 +56,41 @@
         </section>
         <expand macro="process_filter"/>
         <expand macro="process_output_types"/>
+        <expand macro="in_log"/>
     </inputs>
 
     <outputs>
         <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file" from_work_dir="stacks_outputs/process_shortreads.log">
             <filter>add_log</filter>
         </data>
-        <expand macro="process_outputs"/>
+        <expand macro="process_outputs">
+            <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads">
+                <filter>input_type['input_type_select'] == "single"</filter>
+                <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;name&gt;.+)" dir="stacks_outputs"/>
+            </collection>
+            <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads">
+                <filter>input_type['input_type_select'] == "paired"</filter>
+                <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs"/>
+            </collection>
+        </expand>
     </outputs>
 
     <tests>
         <!-- test single end, default options -->
         <test expect_num_outputs="2">
             <param name="input_type|input_type_select" value="single"/>
-            <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
+            <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/>
             <param name="input_type|barcode_encoding" value="--inline_null"/>
             <param name="barcode" value="procrad/barcodes"/>
             <param name="add_log" value="yes"/>
             <output name="output_log" file="shortreads/process_shortreads.out" lines_diff="4"/>
             <output_collection name="demultiplexed" count="40">
-                <element name="PopA_01" file="shortreads/PopA_01.fq" ftype="fastqsanger"/>
+                <element name="PopA_01">
+                    <assert_contents>
+                        <has_size value="34964" delta="100"/>
+                        <has_text text="@lane1_fakedata9_0 1:N:0:/1"/>
+                    </assert_contents>
+                </element>
             </output_collection>
         </test>
         <!-- test single end, default options -->
@@ -75,8 +100,8 @@
                 <collection type="list:paired">
                     <element name="reads">
                         <collection type="paired">
-                            <element name="forward" value="procrad/R1.fq" ftype="fastqsanger"/>
-                            <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/>
+                            <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/>
+                            <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/>
                         </collection>
                     </element>
                 </collection>