--- a/macros.xml	Wed Aug 08 08:49:26 2018 -0400
+++ b/macros.xml	Fri Aug 10 19:40:07 2018 -0400
@@ -1,9 +1,35 @@
 <macros>
     <token name="@WRAPPER_VERSION@">0.19.3</token>
 
-    <xml name="adapter_sequence1">
-        <param name="adapter_sequence1" argument="--adapter_sequence" type="text" optional="true" label="Adapter sequence for input 1"
-            help="The adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped.">
+    <xml name="adapter_trimming_options">
+        <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False">
+            <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/>
+            <expand macro="adapter_sequence" read_number="1" />
+            <yield />
+        </section>
+        <section name="global_trimming_options" title="Global Trimming Options" expanded="False">
+            <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
+            <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
+        </section>
+    </xml>
+
+    <xml name="global_trimming_options">
+        <section name="global_trimming_options" title="Global trimming options" expanded="False">
+            <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
+            <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
+            <yield/>
+        </section>
+    </xml>
+
+    <xml name="global_trimming_options_paired">
+        <expand macro="global_trimming_options">
+            <param name="trim_front2" argument="-F" type="integer" optional="true" label="Trim front for input 2" help="Trimming how many bases in front for read2. If it's not specified, it will follow read1's settings."/>
+            <param name="trim_tail2" argument="-T" type="integer" optional="true" label="Trim tail for input 2" help="Trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings."/>
+        </expand>
+    </xml>
+
+    <xml name="adapter_sequence" token_read_number="1">
+        <param name="adapter_sequence@READ_NUMBER@" argument="--adapter_sequence@READ_NUMBER@" type="text" optional="true" label="Adapter sequence for input @READ_NUMBER@" help="The adapter for read@READ_NUMBER@. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped.">
             <sanitizer>
                 <valid>
                     <add value="A"/>
@@ -14,9 +40,11 @@
             </sanitizer>
         </param>
     </xml>
-    <xml name="in1">
-        <param name="in1" argument="-i" type="data" format="fastq,fastq.gz" label="Input 1" help="Input FASTQ file #1"/>
+
+    <xml name="in" token_read_number="1" token_argument="-i">
+        <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastq,fastq.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/>
     </xml>
+
     <xml name="poly_g_min_len">
         <param name="poly_g_min_len" argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length"
             help="The minimum length to detect polyG in the read tail. 10 by default."/>