--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 20 11:07:47 2013 -0400
@@ -0,0 +1,30 @@
+<macros>
+  <macro name="threshold">
+    <conditional name="threshold">
+      <param type="select" name="type" label="Specify Threshold">
+        <option value="none">None (just use deafults></option>
+        <option value="simple">With Simple Options</option>
+        <option value="advanced">With Advanced Options</option>
+      </param>
+      <when value="none">
+      </when>
+      <when value="simple">
+        <expand macro="simple_options" />
+      </when>
+      <when value="advanced">
+        <expand macro="simple_options" />
+        <param type="boolean" truevalue="" falsevalue="--ignore_charge_1" label="Use Charge +1" name="ignore_charge_1" checked="true" />
+        <param type="boolean" truevalue="" falsevalue="--ignore_charge_2" label="Use Charge +2" name="ignore_charge_2" checked="true" />
+        <param type="boolean" truevalue="" falsevalue="--ignore_charge_3" label="Use Charge +3" name="ignore_charge_3" checked="true" />
+        <param type="boolean" truevalue="" falsevalue="--ignore_charge_4" label="Use Charge +4 and Higher" name="ignore_charge_4" checked="true" />
+        <param name="minimum_ntt" label="Minimum Number of Enzymatic Termini (NTT)" type="integer" help="" value="0" />
+        <param name="minimum_peptide_length" label="Minimum Peptide Length" type="integer" help="" value="0" />
+      </when>
+    </conditional>
+  </macro>
+  <macro name="simple_options">
+    <param name="protein_probability" label="Protein Probability" type="float" help="" value="0.99" />
+    <param name="minimum_peptide_count" label="Minimum Peptide Count" type="integer" help="" value="2" />
+    <param name="peptide_probability" label="Peptide Probability" type="float" help="" value="0.95" />
+  </macro>
+</macros>
\ No newline at end of file