--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Apr 25 13:50:59 2019 -0400
@@ -0,0 +1,51 @@
+<macros>
+    <token name="@VERSION@">1.0.0</token>
+    <token name="@GVERSION@">1.0.0-0</token>
+    <xml name="requirements">
+        <requirements>
+          <requirement type="package" version="@VERSION@">metaquantome</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="db">
+      <param argument="db_tar" type="data" label="Database Archive File"/>
+    </xml>
+    <xml name="ONTOLOGY_ARGS">
+      <conditional name="ontology_args">
+        <param name="ontology" type="select" label="Ontology">
+          <option value="go">Gene Ontology (GO terms)</option>
+          <option value="ec">Enzyme Commission (EC) numbers</option>
+          <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
+        </param>
+        <when value="go">
+          <param argument="--slim_down" type="boolean" label="Use slim GO"/>
+        </when>
+        <when value="ec">
+          <!-- do nothing -->
+        </when>
+        <when value="cog">
+          <!-- do nothing -->
+        </when>
+      </conditional>
+    </xml>
+    <token name="@COMMON_PARAMS@"><![CDATA[
+            --samps '$samps'
+            --mode '$mode_args.mode'
+            #if $mode_args.mode == 'f'
+                --ontology='$mode_args.ontology_args.ontology'
+            #end if
+            #if $mode_args.mode == 'ft'
+                --ontology='$mode_args.ontology_args.ontology'
+            #end if
+    ]]>
+    </token>
+    <xml name="SAMPS">
+      <param name="samps" type="data" format="tabular" label="Samples file"
+        help="must be created by 'metaQuantome: create samples file'"/>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <yield />
+        </citations>
+    </xml>
+</macros>