--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cummeRbund_macros.xml	Tue Dec 23 15:58:27 2014 -0500
@@ -0,0 +1,47 @@
+<?xml version="1.0"?>
+<macros>
+    <macro name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+            <regex match="Error:" />
+            <regex match="Exception:" />
+        </stdio>
+    </macro>
+    <macro name="replicates_checkbox">
+        <param name="replicates" type="boolean" truevalue="--replicates" falsevalue="" checked="True" label="Replicates?"/>
+    </macro>
+    <macro name="log10_checkbox">
+        <param name="log10" type="boolean" truevalue="--log10" falsevalue="" checked="True" label="Apply log10 transformation on FPKM values?"/>
+    </macro>
+    <macro name="xy_selector">
+        <param name="x" type="select" label="Sample name for x axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
+        <param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
+    </macro>
+    <macro name="genes_selector">
+        <repeat name="genes" title="Genes">
+            <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
+        </repeat>
+    </macro>
+    <macro name="features_selector">
+        <param name="features" type="select" label="Expression levels to plot?">
+            <option value="gene" selected="true">Genes</option>
+            <option value="isoforms">Isoforms</option>
+            <option value="tss">TSS</option>
+            <option value="cds">CDS</option>
+        </param>
+    </macro>
+    <macro name="multiple_genes_conditional">
+        <conditional name="multiple_genes">
+            <param name="multiple_genes_selector" type="select" label="Limit plot to genes">
+                <option value="no" selected="true">Do not limit</option>
+                <option value="yes">Select genes</option>
+            </param>
+            <when value="yes">
+                <expand macro="features_selector" />
+                <expand macro="genes_selector" />
+            </when>
+            <when value="no" />
+        </conditional>
+    </macro>
+</macros>