--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Mar 02 15:36:38 2026 +0000
@@ -0,0 +1,43 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.1.4</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">cialign</requirement>
+        </requirements>
+    </xml>
+    <xml name="help">
+    <help><![CDATA[
+What this tool does
+===================
+
+CIAlign is designed to clean, interpret, and visualize multiple sequence alignments (MSAs). 
+It helps identify and remove problematic regions such as insertions, poorly aligned ends, and overly gappy sequences. This improves downstream analyses like phylogenetic inference and comparative genomics.
+
+It also offers tools to generate customizable visualizations, allowing users to inspect alignments and cleaning steps through compact and informative plots.
+
+Input
+=====
+
+CIAlign takes standard multiple sequence alignment files in FASTA format. CIAlign takes standard multiple sequence alignment files in FASTA format.
+
+Output
+======
+
+CIAlign produces a cleaned alignment in FASTA format along with optional log files, summary statistics, and visualization plots.
+
+    ]]></help>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.7717/peerj.12983</citation>
+        </citations>
+    </xml>
+    <xml name="creator">
+        <creator>
+            <organization name="Galaxy Europe"/>
+            <person givenName="Ahmad" familyName="Mahagna" url="https://github.com/Smkingsize"/>
+            <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/>
+        </creator>
+    </xml>
+</macros>
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