diff macros.xml @ 1:f6806931cc1e draft default tip

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

--- a/macros.xml	Tue Jul 16 09:23:42 2024 +0000
+++ b/macros.xml	Tue Jul 30 15:39:59 2024 +0000
@@ -16,6 +16,126 @@
             <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">