--- a/macros.xml	Sun Feb 25 13:07:29 2018 -0500
+++ b/macros.xml	Mon Apr 16 16:37:49 2018 -0400
@@ -1,5 +1,41 @@
 <?xml version="1.0"?>
 <macros>
+    <macro name="barcode2_conditional" >
+        <conditional name="barcode">
+            <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">
+                <option value="first_read_only">Barcode on first read only</option>
+                <option value="both_reads">Barcode on both reads</option>
+            </param>
+            <when value="first_read_only"/>
+            <when value="both_reads">
+                <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
+                       help="Use this option to specify the format of the UMI/barcode for
+                             the second read pair if required." >
+                </param>
+            </when>
+        </conditional>
+    </macro>
+    <xml name="input_types">
+        <conditional name="input_type">
+            <param name="type" type="select" label="Library type">
+                <option value="single">Single-end</option>
+                <option value="paired">Paired-end</option>
+                <option value="paired_collection">Paired-end Dataset Collection</option>
+            </param>
+            <when value="single">
+                <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
+            </when>
+            <when value="paired">
+                <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
+                <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
+                <expand macro="barcode2_conditional" />
+            </when>
+            <when value="paired_collection">
+                <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Reads in FASTQ format" />
+                <expand macro="barcode2_conditional" />
+            </when>
+        </conditional>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1101/gr.209601.116</citation>
@@ -20,4 +56,33 @@
         </requirements>
     </xml>
     <token name="@VERSION@">0.5.3</token>
+    <token name="@COMMAND_LINK@"><![CDATA[
+        #set $gz = False
+        #if $input_type.type == 'single':
+            #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
+                ln -s '$input_type.input_single' input_single.gz &&
+                #set $gz = True
+            #else
+                ln -s '$input_type.input_single' input_single.txt &&
+            #end if
+        #elif $input_type.type == 'paired':
+            #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
+                ln -s '$input_type.input_read1' input_read1.gz &&
+                ln -s '$input_type.input_read2' input_read2.gz &&
+                #set $gz = True
+            #else
+                ln -s '$input_type.input_read1' input_read1.txt &&
+                ln -s '$input_type.input_read2' input_read2.txt &&
+            #end if
+        #else  ## paired_collection
+            #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
+                ln -s '$input_type.input_readpair.forward' input_read1.gz &&
+                ln -s '$input_type.input_readpair.reverse' input_read2.gz &&
+                #set $gz = True
+            #else
+                ln -s '$input_type.input_readpair.forward' input_read1.txt &&
+                ln -s '$input_type.input_readpair.reverse' input_read2.txt &&
+            #end if
+        #end if
+    ]]></token>
 </macros>