--- a/macro.xml	Thu Sep 22 07:50:58 2022 +0000
+++ b/macro.xml	Tue Nov 12 09:56:19 2024 +0000
@@ -1,43 +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]"/>
+    <token name="@TOOL_VERSION@">0.6.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.02</token>
+    <token name="@THREADS@"><![CDATA[
+      ##compute the number of ADDITIONAL threads to be used by samtools (-@)
+      addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
+  ]]></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="1.19.2">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 argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/>
+                <param 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>
-          <when value="non_filter">
-          </when>
-      </conditional>
-  </xml>
+        </conditional>
+    </xml>
 </macros>