<tool id="vgp_chromosome_assignment" name="VGP Chromosome Assignment" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Assign chromosome names to scaffolds</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ## Create output directory
        mkdir -p output_dir &&

        ## Run chromosome_assignment
        chromosome_assignment
            -a '$agp'
            -f '$fasta'
            -o output_dir

    ]]></command>
    <inputs>
        <param name="agp" type="data" format="tabular" label="Haplotype AGP file"
            help="Input haplotype AGP file without haplotig duplications." />
        <param name="fasta" type="data" format="fasta" label="Sorted FASTA file"
            help="Input sorted FASTA file." />
    </inputs>
    <outputs>
        <data name="inter_chr" format="tabular" from_work_dir="output_dir/inter_chr.tsv"
            label="${tool.name} on ${on_string}: Chromosome Mapping Table"/>
        <data name="chr_level_fasta" format="fasta" from_work_dir="output_dir/hap.chr_level.fa"
            label="${tool.name} on ${on_string}: Chromosome-level FASTA"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="agp" value="test_hap1_unlocs_no_hapdups.agp" ftype="tabular"/>
            <param name="fasta" value="test_hap1_sorted.fa" ftype="fasta"/>
            <output name="inter_chr" file="expected_hap1_inter_chr.tsv" ftype="tabular"/>
            <output name="chr_level_fasta" file="expected_hap1_chr_level.fa" ftype="fasta"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

chromosome_assignment substitutes scaffold identifiers with chromosome assignments, generating chromosome-level
sequences and mapping tables.

The tool processes AGP metadata to:

1. Identify sex chromosomes (X, Y, W, Z) and regular chromosomes
2. Filter autosomal scaffolds and assign sequential ``SUPER_`` identifiers
3. Rename sex-linked scaffolds with ``SUPER_X/Y/W/Z`` prefixes
4. Handle unlocalized contigs by replacing parent scaffold names with chromosomal assignments
5. Generate documentation mapping original names to new names

**Inputs**

- **Haplotype AGP file**: Tab-delimited AGP file with chromosome assignment metadata (typically hap.unlocs.no_hapdups.agp from split_agp)
- **Sorted FASTA file**: Sorted sequence file containing scaffolds/contigs (typically sorted using gfastats)

**Outputs**

- **Chromosome Mapping Table (inter_chr.tsv)**: Tab-separated file documenting all scaffold-to-chromosome name transformations
- **Chromosome-level FASTA**: FASTA file with sequences renamed to chromosome-level assignments

**Workflow Context**

This tool is typically run twice in the VGP curation pipeline, once for each haplotype:

1. Run on Haplotype 1: Use Hap1 AGP and Hap1 sorted FASTA
2. Run on Haplotype 2: Use Hap2 AGP and Hap2 sorted FASTA

**Input Preparation**

Before running this tool:

1. Run split_agp to split haplotypes and correct AGP files
2. Use gfastats to sort each haplotype with its corresponding AGP file:
   - gfastats hap1.fa -a hap1_unlocs_no_hapdups.agp -o hap1.sorted.fa
   - gfastats hap2.fa -a hap2_unlocs_no_hapdups.agp -o hap2.sorted.fa

**Next Steps**

After running chromosome_assignment on both haplotypes:

1. Run MashMap to align the two chromosome-level haplotypes
2. Use sak_generation with the two inter_chr.tsv files and MashMap output to generate SAK instructions

.. class:: infomark

**More Information**

This tool is part of the VGP ProcessCuration pipeline for preparing curated genome assemblies for submission.

<expand macro="help_common"/>
    ]]></help>
    <expand macro="citations"/>
</tool>