annotate macros.xml @ 1:b613e5dd5e83 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit commit df500c27a6ef0ea25e0361feada7df8dedee98f1

<macros>
    <token name="@TOOL_VERSION@">0.10.4</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">mg-toolkit</requirement>
        </requirements>
    </xml>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">mg-toolkit</xref>
        </xrefs>
    </xml>
    <xml name="creators">
        <creator>
            <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" />
        </creator>
    </xml>
    <xml name="all_versions_result_group">
        <option value="statistics">Statistics</option>
        <option value="sequence_data">Sequence data</option>
        <option value="functional_analysis">Functional analysis</option>
    </xml>
    <xml name="v1.0-v3.0_result_group">
        <option value="taxonomic_analysis">Taxonomic analysis</option>
    </xml>
    <xml name="v4.0-v5.0_result_group">
        <option value="taxonomic_analysis_ssu_rrna">Taxonomic analysis SSU</option>
        <option value="taxonomic_analysis_lsu_rrna">Taxonomic analysis LSU</option>
        <option value="non-coding_rnas">Non-coding RNAs</option>
    </xml>
    <xml name="v5.0_result_group">
        <option value="taxonomic_analysis_itsonedb">Taxonomic analysis ITSoneDB</option>
        <option value="taxonomic_analysis_unite">Taxonomic analysis ITS UNITE</option>
        <option value="taxonomic_analysis_motu">Taxonomic analysis mOTU</option>
        <option value="pathways_and_systems">Pathways and systems</option>
    </xml>
    <xml name="file_type_statistics">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="taxa_abundance_distribution">Taxa abundance distribution</option>
        </param>
    </xml>
    <xml name="file_type_sequence_data">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="processed_contigs_nucleotide_reads">Processed contigs/nucleotide reads</option>
            <option value="processed_contigs_reads_with_annotation">Processed contigs/reads with annotation</option>
            <option value="processed_contigs_reads_without_annotation">Processed contigs/reads without annotation</option>
            <option value="processed_contigs_reads_with_pcds">Processed contigs/reads with pCDS</option>
            <option value="predicted_cds">Predicted CDS (aa)</option>
            <option value="predicted_cds_with_annotation">Predicted CDS with annotation</option>
            <option value="predicted_cds_without_annotation">Predicted CDS without annotation</option>
            <option value="predicted_orf">Predicted ORF (nt)</option>
            <option value="predicted_orf_with_annotation">Predicted ORF with annotation</option>
            <option value="predicted_orf_without_annotation">Predicted ORF without annotation</option>
        </param>
    </xml>
    <xml name="file_type_functional_analysis">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="complete_go_annotation">Complete GO annotation</option>
            <option value="go_slim_annotation">GO slim annotation</option>
            <option value="interpro_summary">InterPro summary</option>
            <option value="interpro_matches">InterPro matches</option>
            <option value="kegg_orthologues_annotation">KEGG orthologues annotation</option>
            <option value="pfam_annotation">Pfam annotation</option>
            <option value="combined_annotation">Combined (eggNOG, InterPro, antiSMASH) annotation</option>
            <option value="diamond_annotation">Diamond annotation</option>
            <option value="eggnog_annotation">eggNOG annotation</option>
            <option value="eggnog_seed_orthologs">eggNOG seed orthologs</option>
        </param>
    </xml>
    <xml name="file_type_taxonomic_analysis_ssu_rrna">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="reads_contigs_encoding_ssu">Reads/Contigs encoding SSU rRNA</option>
            <option value="mapseq_ssu_assignments">MAPseq SSU assignments</option>
            <option value="ssu_otu_tables">SSU OTU tables</option>
            <option value="ssu_hdf5_biom">SSU HDF5 BIOM files</option>
            <option value="ssu_json_biom">SSU JSON BIOM files</option>
        </param>
    </xml>
    <xml name="file_type_taxonomic_analysis_lsu_rrna">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="reads_contigs_encoding_lsu">Reads/Contigs encoding LSU rRNA</option>
            <option value="mapseq_lsu_assignments">MAPseq LSU assignments</option>
            <option value="lsu_otu_tables">LSU OTU tables</option>
            <option value="lsu_hdf5_biom">LSU HDF5 BIOM files</option>
            <option value="lsu_json_biom">LSU JSON BIOM files</option>
        </param>
    </xml>
    <xml name="file_type_non-coding_rnas">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="predicted_non_coding_rnas">Predicted non-coding RNAs</option>
        </param>
    </xml>
    <xml name="file_type_taxonomic_analysis_itsonedb">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="mapseq_itsonedb_assignments">MAPseq ITSoneDB assignments</option>
            <option value="itsonedb_otu_tables">ITSoneDB OTU tables</option>
            <option value="itsonedb_hdf5_biom">ITSoneDB HDF5 BIOM files</option>
            <option value="itsonedb_json_biom">ITSoneDB JSON BIOM files</option>
        </param>
    </xml>
    <xml name="file_type_taxonomic_analysis_unite">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="mapseq_unite_assignments">MAPseq UNITE assignments</option>
            <option value="unite_otu_tables">UNITE OTU tables</option>
            <option value="unite_hdf5_biom">UNITE HDF5 BIOM files</option>
            <option value="unite_json_biom">UNITE JSON BIOM files</option>
        </param>
    </xml>
    <xml name="file_type_taxonomic_analysis_motu">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="motus_taxonomic_profile">mOTUs taxonomic profile</option>
        </param>
    </xml>
    <xml name="file_type_pathways_and_systems">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="antismash_annotation_gff3">antiSMASH annotation (gff3)</option>
            <option value="antismash_annotation_embl">antiSMASH annotation(embl)</option>
            <option value="antismash_annotation_genbank">antiSMASH annotation(genbank)</option>
            <option value="antismash_summary">antiSMASH summary</option>
            <option value="genome_properties_annotation">Genome properties annotation</option>
            <option value="kegg_pathway_annotation">KEGG pathway annotation</option>
            <option value="kegg_pathway_annotation_contig">KEGG pathway annotation (contig)</option>
        </param>
    </xml>
    <xml name="file_type_taxonomic_analysis">
        <param name="file_type" type="select" label="File type" multiple="true" optional="false">
            <option value="phylogenetic_tree"></option>
            <option value="otus_counts_and_taxonomic_assignments_tsv">OTUs, counts and taxonomic assignments (table)</option>
            <option value="otus_counts_and_taxonomic_assignments_biom1">OTUs, counts and taxonomic assignments (JSON)</option>
            <option value="otus_counts_and_taxonomic_assignments_biom2">OTUs, counts and taxonomic assignments (HDF5)</option>
            <option value="reads_encoding_5s_rrna">Reads enconding 5S rRNA</option>
            <option value="reads_encoding_16s_rrna">Reads enconding 16S rRNA</option>
            <option value="reads_encoding_23s_rrna">Reads enconding 23S rRNA</option>
        </param>
    </xml>
    <xml name="file_type_taxonomic_analysis_its">
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{emg_toolkit,
                    author = {EBI Metagenomics},
                    title = {EMG Toolkit},
                    year = {2024},
                    howpublished = {\url{https://github.com/EBI-metagenomics/emg-toolkit}},
                    note = {Accessed: 2024-07-11}
                }
            </citation>
        </citations>
    </xml>
</macros>