--- a/stacks_procrad.xml	Fri Jan 04 03:36:24 2019 -0500
+++ b/stacks_procrad.xml	Wed Feb 27 09:59:35 2019 -0500
@@ -1,16 +1,17 @@
-<tool id="stacks2_procrad" name="Stacks2: process radtags" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
-<description>the Stacks demultiplexing script</description>
+<tool id="stacks2_procrad" name="Stacks2: process radtags" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
+    <description>the Stacks demultiplexing script</description>
     <macros>
         <import>macros.xml</import>
         <import>macros_process.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <expand macro="stdio"/>
     <expand macro="version_cmd"/>
-    <command><![CDATA[
-@CLEAN_EXT@
+    <command detect_errors="aggressive"><![CDATA[
+@FASTQ_INPUT_FUNCTIONS@
 mkdir stacks_inputs stacks_outputs &&
-@FASTQ_INPUT_PREPROC@
+
+#set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
+$link_command
 
 process_radtags
 
@@ -36,15 +37,14 @@
 
 ## Output options
 ## --merge not implemented in Galaxy
-
-&& mv stacks_outputs/process_radtags.stacks_inputs.log $output_log
-
+#if $output_log
+    && mv stacks_outputs/process_radtags.stacks_inputs.log $output_log
+#end if
 @PROCESS_FASTQ_POSTPROC@
     ]]></command>
 
     <inputs>
-        <expand macro="process_inputs"/>
-
+        <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/>
         <conditional name="options_enzyme">
             <param name="options_enzyme_selector" type="select" label="Number of enzymes">
                 <option value="1">One</option>
@@ -66,26 +66,26 @@
         </conditional>
 
         <section name="options_advanced" title="advanced options" expanded="False">
-	    <expand macro="common_advanced"/>
-            <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads" />
-            <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="disable checking if the RAD site is intact" />
-	    <expand macro="rescue_barcode"/>
-	    <expand macro="process_adapter"/>
+            <expand macro="common_advanced"/>
+            <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads" />
+            <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact" />
+            <expand macro="rescue_barcode"/>
+            <expand macro="process_adapter"/>
         </section>
 
-	<expand macro="process_filter"/>
-	<expand macro="process_output_types"/>
+        <expand macro="process_filter"/>
+        <expand macro="process_output_types"/>
         <expand macro="in_log"/>
     </inputs>
 
     <outputs>
         <expand macro="out_log"/>
-	<expand macro="process_outputs"/>
+        <expand macro="process_outputs"/>
     </outputs>
     <tests>
         <!-- single single ended input, no filtering (hence no capturing) + log -->
         <test>
-            <param name="input_type|options_type_selector" value="single"/>
+            <param name="input_type|input_type_select" value="single"/>
             <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
             <param name="input_type|barcode_encoding" value="--inline_null"/>
             <param name="barcode" value="procrad/barcodes"/>
@@ -100,7 +100,7 @@
         <!-- multiple (zipped) single end input (misusing R2 as add single end read file),
              discarding by quality and capturing them -->
         <test>
-            <param name="input_type|options_type_selector" value="single"/>
+            <param name="input_type|input_type_select" value="single"/>
             <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/>
             <param name="input_type|barcode_encoding" value="--inline_null"/>
             <param name="barcode" value="procrad/barcodes"/>
@@ -131,7 +131,7 @@
         </test>
         <!-- paired input, no quality but length filter, gzfasta output -->
         <test>
-            <param name="input_type|options_type_selector" value="paired"/>
+            <param name="input_type|input_type_select" value="paired"/>
             <param name="input_type|fqinputs">
                 <collection type="list:paired">
                     <element name="reads">
@@ -175,7 +175,7 @@
         </test>
         <!-- paired input (gzipped) + advanced options + two enzymes, fasta output -->
         <test>
-            <param name="input_type|options_type_selector" value="paired"/>
+            <param name="input_type|input_type_select" value="paired"/>
             <param name="input_type|fqinputs">
                 <collection type="list:paired">
                     <element name="reads">
@@ -250,7 +250,7 @@
 
 Input files:
 
-- A set of one or more FASTQ files (either selected manually, a data set list, or a paired data set list)
+- A set of one or more FASTQ files (either selected manually, a dataset list, or a paired dataset list)
 
 - Barcode File