<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">vgp-processcuration</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.0</token>
    <token name="@PROFILE@">21.09</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
            <edam_topic>topic_3797</edam_topic> <!-- Genome assembly -->
        </edam_topics>
    </xml>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">vgp-processcuration</xref>
        </xrefs>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
@misc{vgl_curation,
    author = {VGL-Hub},
    title = {VGL Curation - ProcessCuration toolkit for genome assembly submission},
    year = {2025},
    url = {https://github.com/vgl-hub/vgl-curation},
}
            </citation>
        </citations>
    </xml>
    <xml name="help_common">
        <![CDATA[
**About ProcessCuration**

ProcessCuration is a Python-based toolkit designed to process manually curated genome assemblies for submission.
It reconciles AGP files (A Golden Path) created in PretextView with genome assembly FASTAs, preparing them for
database submission through renaming, reorienting, and sorting operations.

The toolkit is part of the VGP (Vertebrate Genomes Project) curation pipeline and works in conjunction with
tools like gfastats and MashMap.

**Input Naming Convention**

Scaffolds must follow the naming pattern before curation:
- Haplotype 1: H1.scaffold_X
- Haplotype 2: H2.scaffold_X

**More Information**

- GitHub repository: https://github.com/vgl-hub/vgl-curation
- VGP Genome Assembly Pipeline: https://vertebrategenomesproject.org/
        ]]>
    </xml>
</macros>