--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 14 03:09:32 2018 -0400
@@ -0,0 +1,39 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.6.6">trinity</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@WRAPPER_VERSION@">2.6.6</token>
+
+    <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
+        #if $pool.inputs.strand.is_strand_specific:
+            --SS_lib_type $pool.inputs.strand.library_type
+        #end if
+
+        $pool.inputs.jaccard_clip
+    </token>
+
+    <xml name="input_paired_strand_jaccard">
+        <conditional name="strand">
+            <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+            <when value="false" />
+            <when value="true">
+                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
+                    <option value="FR">Forward-Reverse</option>
+                    <option value="RF">Reverse-Forward</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="jaccard_clip" argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/>
+    </xml>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1038/nbt.1883</citation>
+        </citations>
+    </xml>
+</macros>