<tool id="liftoff" name="Liftoff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Lift gene annotations between genome assemblies</description>
    <macros>
        <token name="@TOOL_VERSION@">1.6.3</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">24.2</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">liftoff</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">liftoff</requirement>
    </requirements>
    <version_command>liftoff --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
set -euo pipefail &&
ln -s '$target_fasta' target.fa &&
ln -s '$reference_fasta' reference.fa &&
ln -s '$annotation' annotation.gff &&

liftoff 
    -g annotation.gff 
    -o mapped.gff3 
    -u unmapped_features.txt 
    -dir liftoff_intermediate 
    -p \${GALAXY_SLOTS:-1} 
    -a $min_feature_coverage 
    -s $min_identity 
    -d $distance_factor 
    -flank $flank_fraction 
#if $feature_types and str($feature_types).strip()
    -f "${feature_types}" 
#end if
#if str($exclude_partial).strip()
    $exclude_partial 
#end if
#if str($infer_genes).strip()
    $infer_genes 
#end if
#if str($infer_transcripts).strip()
    $infer_transcripts 
#end if
#if $chrom_map and str($chrom_map).strip().lower() != 'none'
    -chroms "$chrom_map" 
#end if
#if $unplaced_sequences and str($unplaced_sequences).strip().lower() != 'none'
    -unplaced "$unplaced_sequences" 
#end if
#if str($copy_detection.find_copies) == "true"
    -copies 
    -sc $copy_detection.copy_min_identity 
    -overlap $copy_detection.copy_max_overlap 
    -mismatch $copy_detection.copy_mismatch_penalty 
    -gap_open $copy_detection.copy_gap_open_penalty 
    -gap_extend $copy_detection.copy_gap_extend_penalty
#end if
    target.fa reference.fa
]]></command>
    <inputs>
        <param name="target_fasta" type="data" format="fasta" label="Target genome FASTA" help="Genome assembly to lift annotations onto."/>
        <param name="reference_fasta" type="data" format="fasta" label="Reference genome FASTA" help="Genome assembly that already has annotations."/>
        <param name="annotation" type="data" format="gff3,gtf" label="Annotation file (GFF3/GTF)" help="Reference annotation to lift over."/>

        <section name="alignment" title="Alignment and mapping parameters" expanded="false">
            <param argument="-a" name="min_feature_coverage" type="float" value="0.5" min="0" max="1" label="Minimum feature coverage"/>
            <param argument="-s" name="min_identity" type="float" value="0.5" min="0" max="1" label="Minimum exon/CDS identity"/>
            <param argument="-d" name="distance_factor" type="float" value="2.0" min="0" label="Distance scaling factor (-d)"/>
            <param argument="-flank" name="flank_fraction" type="float" value="0.0" min="0" max="1" label="Flanking sequence fraction"/>
            <param argument="-f" name="feature_types" type="text" optional="true" label="Feature types to lift" help="Comma-separated list (default: infer from annotation)."/>
            <param argument="-exclude_partial" type="boolean" truevalue="-exclude_partial" falsevalue="" label="Send partial mappings to unmapped output" checked="false"/>
        </section>

        <section name="annotation_structure" title="Annotation structure helpers" expanded="false">
            <param argument="-infer_genes" type="boolean" truevalue="-infer_genes" falsevalue="" label="Infer genes if annotation lacks gene records" checked="false"/>
            <param argument="-infer_transcripts" type="boolean" truevalue="-infer_transcripts" falsevalue="" label="Infer transcripts if annotation lacks them" checked="false"/>
        </section>

        <section name="chromosome_mapping" title="Chromosome and copy handling" expanded="false">
            <param argument="-chroms" name="chrom_map" type="data" format="txt" optional="true" label="Chromosome mapping file" help="Text file listing corresponding chromosome names between reference and target."/>
            <param argument="-unplaced" name="unplaced_sequences" type="data" format="txt" optional="true" label="Unplaced sequence list" help="List of sequence names to map after chromosome mapping completes."/>
            <conditional name="copy_detection">
                <param argument="-copies" name="find_copies" type="select" label="Search for extra copies in target">
                    <option value="false" selected="true">No</option>
                    <option value="true">Yes</option>
                </param>
                <when value="false"/>
                <when value="true">
                    <param argument="-sc" name="copy_min_identity" type="float" value="1.0" min="0" max="1" label="Minimum exon identity for copies"/>
                    <param argument="-overlap" name="copy_max_overlap" type="float" value="0.1" min="0" max="1" label="Maximum overlap fraction"/>
                    <param argument="-mismatch" name="copy_mismatch_penalty" type="integer" value="2" min="0" label="Mismatch penalty"/>
                    <param argument="-gap_open" name="copy_gap_open_penalty" type="integer" value="2" min="0" label="Gap open penalty"/>
                    <param argument="-gap_extend" name="copy_gap_extend_penalty" type="integer" value="1" min="0" label="Gap extend penalty"/>
                </when>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data name="liftoff_gff" format="gff3" from_work_dir="mapped.gff3" label="Liftoff lifted annotations on ${on_string}"/>
        <data name="unmapped" format="txt" from_work_dir="unmapped_features.txt" label="Liftoff unmapped features on ${on_string}"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="target_fasta" value="target.fa" ftype="fasta"/>
            <param name="reference_fasta" value="reference.fa" ftype="fasta"/>
            <param name="annotation" value="annotation.gff3" ftype="gff3"/>
            <output name="liftoff_gff">
                <assert_contents>
                    <has_text text="tgt1"/>
                    <has_text text="ID=gene1"/>
                    <has_n_lines n="7"/>
                </assert_contents>
            </output>
            <output name="unmapped">
                <assert_contents>
                    <has_n_lines n="0"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**Liftoff** maps gene annotations (GFF or GTF) from a reference genome to a target genome by aligning the gene sequences with **minimap2** and reconstructing transcripts/exons that maximize identity while preserving structure.

-----

### Inputs

1. **Target genome FASTA** – assembly that should receive annotations.
2. **Reference genome FASTA** – assembly that already has annotations.
3. **Annotation file** – GFF3 or GTF containing the gene models to lift over.

Optional sections expose core Liftoff parameters (coverage, identity, minimap2 flags) as well as helpers for inferring missing gene/transcript features, providing chromosome mapping files, and searching for additional gene copies.

### Outputs

- **Lifted annotations** (`gff3`) – annotation projected onto the target genome.
- **Unmapped features** (`txt`) – records that Liftoff could not confidently place (and, optionally, partial mappings if requested).

### References

- Shumate & Salzberg (2021) *Bioinformatics* 37(12):1639–1643. DOI: 10.1093/bioinformatics/btaa1016
- Liftoff source: https://github.com/agshumate/Liftoff
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btaa1016</citation>
    </citations>
</tool>