annotate macros.xml @ 41:d129c3d0e920 draft default tip

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 8278322cb9db499c593669d2bb8b740024ecf5dc

<macros>
    <xml name="requirements">
        <requirements>
            <container type="docker">quay.io/galaxy/egapx:@TOOL_VERSION@-alpha</container>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">0.4.1</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">23.0</token>
    <xml name="edam_ontology">
        <edam_operations>
            <edam_operation>operation_0362</edam_operation>
        </edam_operations>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{githubegapx,
                    author = {NCBI},
                    year = 2024,
                    title = {Eukaryotic Genome Annotation Pipeline - External (EGAPx)},
                    publisher = {GitHub},
                    journal = {GitHub repository},
                    url = {https://github.com/ncbi/egapx}
                }
            </citation>
        </citations>
    </xml>
    <xml name="creators">
        <creator>
            <person givenName="Ross" familyName="Lazarus" url="https://orcid.org/0000-0003-3939-1961"/>
            <person givenName="Richard" familyName="Burhans" url="https://science.psu.edu/bmb/people/rcb112"/>
        </creator>
    </xml>
    <xml name="test_outputs">
        <output name="complete_genomic_gff" ftype="gff">
            <assert_contents>
                <has_size min="1"/>
            </assert_contents>
        </output>
        <output_collection name="output_files" type="list">
            <element name="annotated_genome" ftype="asn1">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="complete_genomic_gtf" ftype="gtf">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="complete_genomic_fna" ftype="fasta">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="complete_cds" ftype="fasta">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="complete_transcripts" ftype="fasta">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="complete_proteins" ftype="fasta">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="annotation_data" ftype="tabular">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="sra_metadata" ftype="tabular">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="gnomon_accept_ftable_annot" ftype="txt">
                <assert_contents>
                    <has_size min="0"/>
                </assert_contents>
            </element>
            <element name="gnomon_contam_rpt" ftype="tabular">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="gnomon_report" ftype="txt">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="gnomon_quality_report" ftype="tabular">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="busco_report" ftype="txt">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="busco_report_json" ftype="json">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="stats_feature_counts" ftype="xml">
                <assert_contents>
                    <is_valid_xml/>
                </assert_contents>
            </element>
            <element name="stats_feature_stats" ftype="xml">
                <assert_contents>
                    <is_valid_xml/>
                </assert_contents>
            </element>
            <element name="validated_all_unannotated" ftype="xml">
                <assert_contents>
                    <has_size min="0"/>
                </assert_contents>
            </element>
            <element name="validated_genome" ftype="xml">
                <assert_contents>
                    <is_valid_xml/>
                </assert_contents>
            </element>
        </output_collection>
        <output_collection name="nextflow_stats" type="list">
            <element name="nextflow_log" ftype="txt">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="run_report" ftype="html">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="run_timeline" ftype="html">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="run_trace" ftype="tabular">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
            <element name="run_params" ftype="yaml">
                <assert_contents>
                    <has_size min="1"/>
                </assert_contents>
            </element>
        </output_collection>
    </xml>
</macros>