<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>