--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 11 11:51:06 2015 -0400
@@ -0,0 +1,62 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">2014.11.03.0</token>
+    <xml name="stdio">
+        <stdio>
+            <!-- Anything other than zero is an error -->
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+            <!-- In case the return code has not been set propery check stderr too -->
+            <regex match="Error:" />
+            <regex match="Exception:" />
+        </stdio>
+    </xml>
+    <xml name="aln">
+        <param type="boolean" label="output ALN alignment file (-a)" name="aln"
+            truevalue="-a" falsevalue="" />
+    </xml>
+    <xml name="sam">
+        <param type="boolean" label="output SAM alignment file (-s)" name="sam"
+            truevalue="-s" falsevalue="" />
+    </xml>
+
+    <xml name="rndSeed">
+        <param label="specify a fixed, random seed for the simulation"
+            help="Use -1 to request a random seed (-r)" name="rndSeed"
+            type="integer" value="-1" optional="true" />
+    </xml>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btr708</citation>
+        </citations>
+    </xml>
+
+    <xml name="amplicon">
+        <conditional name="amplicon">
+            <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
+            <when value="amplicon_true">
+                <param label="number of reads per amplicon (for 5'end amplicon sequencing)" name="reads_per_amplicon" type="integer" value="0"/>
+            </when>
+            <when value="amplicon_false">
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="amplicon_pair">
+        <conditional name="amplicon">
+            <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
+            <when value="amplicon_true">
+                <param label="number of read pairs per amplicon (for two-end amplicon sequencing)" name="read_pairs_per_amplicon" type="integer" value="0"/>
+            </when>
+            <when value="amplicon_false">
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="frag_len_sd">
+        <param label="the average DNA fragment size"
+            name="fragment_size" type="integer" value="200" minimum="101" />
+        <param label="the standard deviation of the DNA fragment size"
+            name="fragment_sd" type="integer" value="0"/>
+    </xml>
+</macros>