--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macro.xml	Thu Sep 22 07:51:48 2022 +0000
@@ -0,0 +1,43 @@
+
+<macros>
+  <token name="@TOOL_VERSION@">0.5.0</token>
+  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@PROFILE@">21.05</token>
+  <token name="@THREADS@">\${GALAXY_SLOTS:-7}</token>
+  <xml name="version_command">
+     <version_command><![CDATA[polypolish -V]]></version_command>
+  </xml>
+  <xml name="xrefs">
+    <xrefs>
+      <xref type='bio.tools'>Polypolish</xref>
+    </xrefs>
+  </xml>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
+      <requirement type="package" version="1.13">samtools</requirement>
+    </requirements>
+  </xml>
+  <xml name="citations">
+      <citations>
+          <citation type="doi">10.1371/journal.pcbi.1009802</citation>
+      </citations>
+  </xml>
+  <!-- Filter option of polypolish -->
+  <xml name="filter_option">
+      <conditional name="insert_filter">
+          <param name="filter_select" type="select" label="Filter by insert size ? [recommanded]"
+                 help="Exclude some alignments based on their insert size. It reduce the number of excessive alignments,
+                 particularly near the edges of repeat sequences">
+              <option value="filter" selected="true">Filter by insert size</option>
+              <option value="non_filter"> No filtering step</option>
+          </param>
+          <when value="filter">
+              <param name="low" argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/>
+              <param name="high" argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/>
+          </when>
+          <when value="non_filter">
+          </when>
+      </conditional>
+  </xml>
+</macros>