--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Dec 13 13:02:36 2016 -0500
@@ -0,0 +1,46 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
+            <requirement type="package" version="4.11.1">meme</requirement>
+            <requirement type="package" version="0.5">multigps</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:"/>
+            <exit_code range=":-1"/>
+            <regex match="Error:"/>
+            <regex match="Exception:"/>
+        </stdio>
+    </xml>
+    <xml name="rd_cond">
+        <conditional name="read_distribution_cond">
+            <param name="read_distribution" type="select" label="Use read distribution file for this replicate?" help="Selecting No uses default distribution.">
+                <option value="no" selected="True">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="read_distribution_file" type="data" format="tabular" label="Read distribution file" />
+            </when>
+            <when value="no" />
+        </conditional>
+    </xml>
+    <xml name="frc_param">
+        <param  name="fixed_read_count" type="select" label="Use fixed per-base read count limit for this replicate?" help="Selecting No uses a global per-base limit that is estimated from a Poisson distribution.">
+            <option value="no" selected="True">No</option>
+            <option value="yes">Yes</option>
+        </param>
+    </xml>
+    <xml name="motif_finding_params">
+        <param name="memenmotifs" type="integer" min="0" value="3" label="Number of motifs MEME should find for each condition" />
+        <param name="mememinw" type="integer" min="0" value="6" label="Minimum motif width for MEME" />
+        <param name="mememaxw" type="integer" min="0" value="16" label="Maximum motif width for MEME" />
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1003501</citation>
+        </citations>
+    </xml>
+</macros>