<tool id="vgp_split_agp" name="VGP Split AGP" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Correct AGP files and split haplotypes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        split_agp
            -f '$fasta'
            -a '$agp'
            -o './'
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta,fasta.gz" label="Assembly FASTA file"
            help="Input assembly FASTA file containing both haplotypes." />
        <param name="agp" type="data" format="tabular" label="Curated AGP file"
            help="Input curated AGP file created in PretextView with haplotype markers (Hap_1/H1 and Hap_2/H2)." />
    </inputs>
    <outputs>
        <data name="corrected_agp" format="tabular" from_work_dir="corrected.agp"
            label="${tool.name} on ${on_string}: Corrected AGP"/>

        <!-- Haplotype 1 outputs -->
        <data name="hap1_agp" format="tabular" from_work_dir="Hap_1/hap1.agp" label="${tool.name} on ${on_string}: Hap1 AGP"/>
        <data name="hap1_unlocs_no_hapdups" format="tabular" from_work_dir="Hap_1/hap.unlocs.no_hapdups.agp" label="${tool.name} on ${on_string}: Hap1 Unlocs without haplotig AGP"/>
        <data name="hap1_haplotigs" format="tabular" from_work_dir="Hap_1/haplotigs.agp" label="${tool.name} on ${on_string}: Hap1 Haplotigs AGP"/>

        <!-- Haplotype 2 outputs -->
        <data name="hap2_agp" format="tabular" from_work_dir="Hap_2/hap2.agp" label="${tool.name} on ${on_string}: Hap2 AGP"/>
        <data name="hap2_unlocs_no_hapdups" format="tabular" from_work_dir="Hap_2/hap.unlocs.no_hapdups.agp" label="${tool.name} on ${on_string}: Hap2 Unlocs without haplotigs AGP"/>
        <data name="hap2_haplotigs" format="tabular" from_work_dir="Hap_2/haplotigs.agp" label="${tool.name} on ${on_string}: Hap2 Haplotigs AGP"/>
    </outputs>
    <tests>
        <test expect_num_outputs="7">
            <param name="fasta" value="test_input.fasta.gz" ftype="fasta.gz"/>
            <param name="agp" value="test_input.agp" ftype="tabular"/>
            <output name="corrected_agp" file="expected_corrected.agp" ftype="tabular"/>
            <output name="hap1_agp" file="expected_hap1.agp" ftype="tabular"/>
            <output name="hap1_unlocs_no_hapdups" file="expected_hap1_unlocs_no_hapdups.agp" ftype="tabular"/>
            <output name="hap1_haplotigs" file="expected_hap1_haplotigs.agp" ftype="tabular"/>
            <output name="hap2_agp" file="expected_hap2.agp" ftype="tabular"/>
            <output name="hap2_unlocs_no_hapdups" file="expected_hap2_unlocs_no_hapdups.agp" ftype="tabular"/>
            <output name="hap2_haplotigs" file="expected_hap2_haplotigs.agp" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

split_agp corrects AGP files for sequence length discrepancies, splits haplotypes into separate files,
assigns unlocalized sequences, and removes haplotig duplications.

This tool performs three sequential operations:

1. **AGPcorrect**: Validates sequence lengths from FASTA against AGP coordinates, adjusting start/end positions
2. **hap_split**: Segregates lines containing haplotype markers into separate directories (Hap_1 and Hap_2)
3. **unloc**: Processes metadata tags, renames unloc scaffolds with sequential numbering, removes haplotigs

**Inputs**

- **Assembly FASTA file**: FASTA file containing both haplotypes (may be gzip-compressed)
- **Curated AGP file**: Tab-delimited AGP file with haplotype markers (Hap_1/H1 or Hap_2/H2)

**Outputs**

- **Corrected AGP**: Length-validated AGP file with corrected coordinates
- **Hap1 AGP**: Haplotype 1 AGP file
- **Hap1 Unlocs No Hapdups**: Haplotype 1 AGP with unlocalized sequences assigned and haplotigs removed
- **Hap1 Haplotigs**: Removed duplicate haplotigs from Haplotype 1
- **Hap2 AGP**: Haplotype 2 AGP file
- **Hap2 Unlocs No Hapdups**: Haplotype 2 AGP with unlocalized sequences assigned and haplotigs removed
- **Hap2 Haplotigs**: Removed duplicate haplotigs from Haplotype 2

**Input Naming Requirements**

⚠️ **Important**: Scaffolds in the input FASTA must follow this naming convention:
- Haplotype 1: H1.scaffold_X
- Haplotype 2: H2.scaffold_X

This naming pattern is required before manual curation in PretextView.

**Next Steps**

After running split_agp, use the gfastats tool to sort each haplotype:

1. Sort Haplotype 1: gfastats with Hap1 Unlocs No Hapdups AGP
2. Sort Haplotype 2: gfastats with Hap2 Unlocs No Hapdups AGP

Then proceed to the chromosome_assignment tool to assign chromosome-level names.

.. 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>