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comparison macros.xml @ 1:f6806931cc1e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit commit df500c27a6ef0ea25e0361feada7df8dedee98f1
author iuc
date Tue, 30 Jul 2024 15:39:59 +0000
parents b46aaf8edaa2
children
comparison
equal deleted inserted replaced
0:b46aaf8edaa2 1:f6806931cc1e
14 <xml name="creators"> 14 <xml name="creators">
15 <creator> 15 <creator>
16 <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" /> 16 <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" />
17 </creator> 17 </creator>
18 </xml> 18 </xml>
19 <xml name="all_versions_result_group">
20 <option value="statistics">Statistics</option>
21 <option value="sequence_data">Sequence data</option>
22 <option value="functional_analysis">Functional analysis</option>
23 </xml>
24 <xml name="v1.0-v3.0_result_group">
25 <option value="taxonomic_analysis">Taxonomic analysis</option>
26 </xml>
27 <xml name="v4.0-v5.0_result_group">
28 <option value="taxonomic_analysis_ssu_rrna">Taxonomic analysis SSU</option>
29 <option value="taxonomic_analysis_lsu_rrna">Taxonomic analysis LSU</option>
30 <option value="non-coding_rnas">Non-coding RNAs</option>
31 </xml>
32 <xml name="v5.0_result_group">
33 <option value="taxonomic_analysis_itsonedb">Taxonomic analysis ITSoneDB</option>
34 <option value="taxonomic_analysis_unite">Taxonomic analysis ITS UNITE</option>
35 <option value="taxonomic_analysis_motu">Taxonomic analysis mOTU</option>
36 <option value="pathways_and_systems">Pathways and systems</option>
37 </xml>
38 <xml name="file_type_statistics">
39 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
40 <option value="taxa_abundance_distribution">Taxa abundance distribution</option>
41 </param>
42 </xml>
43 <xml name="file_type_sequence_data">
44 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
45 <option value="processed_contigs_nucleotide_reads">Processed contigs/nucleotide reads</option>
46 <option value="processed_contigs_reads_with_annotation">Processed contigs/reads with annotation</option>
47 <option value="processed_contigs_reads_without_annotation">Processed contigs/reads without annotation</option>
48 <option value="processed_contigs_reads_with_pcds">Processed contigs/reads with pCDS</option>
49 <option value="predicted_cds">Predicted CDS (aa)</option>
50 <option value="predicted_cds_with_annotation">Predicted CDS with annotation</option>
51 <option value="predicted_cds_without_annotation">Predicted CDS without annotation</option>
52 <option value="predicted_orf">Predicted ORF (nt)</option>
53 <option value="predicted_orf_with_annotation">Predicted ORF with annotation</option>
54 <option value="predicted_orf_without_annotation">Predicted ORF without annotation</option>
55 </param>
56 </xml>
57 <xml name="file_type_functional_analysis">
58 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
59 <option value="complete_go_annotation">Complete GO annotation</option>
60 <option value="go_slim_annotation">GO slim annotation</option>
61 <option value="interpro_summary">InterPro summary</option>
62 <option value="interpro_matches">InterPro matches</option>
63 <option value="kegg_orthologues_annotation">KEGG orthologues annotation</option>
64 <option value="pfam_annotation">Pfam annotation</option>
65 <option value="combined_annotation">Combined (eggNOG, InterPro, antiSMASH) annotation</option>
66 <option value="diamond_annotation">Diamond annotation</option>
67 <option value="eggnog_annotation">eggNOG annotation</option>
68 <option value="eggnog_seed_orthologs">eggNOG seed orthologs</option>
69 </param>
70 </xml>
71 <xml name="file_type_taxonomic_analysis_ssu_rrna">
72 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
73 <option value="reads_contigs_encoding_ssu">Reads/Contigs encoding SSU rRNA</option>
74 <option value="mapseq_ssu_assignments">MAPseq SSU assignments</option>
75 <option value="ssu_otu_tables">SSU OTU tables</option>
76 <option value="ssu_hdf5_biom">SSU HDF5 BIOM files</option>
77 <option value="ssu_json_biom">SSU JSON BIOM files</option>
78 </param>
79 </xml>
80 <xml name="file_type_taxonomic_analysis_lsu_rrna">
81 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
82 <option value="reads_contigs_encoding_lsu">Reads/Contigs encoding LSU rRNA</option>
83 <option value="mapseq_lsu_assignments">MAPseq LSU assignments</option>
84 <option value="lsu_otu_tables">LSU OTU tables</option>
85 <option value="lsu_hdf5_biom">LSU HDF5 BIOM files</option>
86 <option value="lsu_json_biom">LSU JSON BIOM files</option>
87 </param>
88 </xml>
89 <xml name="file_type_non-coding_rnas">
90 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
91 <option value="predicted_non_coding_rnas">Predicted non-coding RNAs</option>
92 </param>
93 </xml>
94 <xml name="file_type_taxonomic_analysis_itsonedb">
95 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
96 <option value="mapseq_itsonedb_assignments">MAPseq ITSoneDB assignments</option>
97 <option value="itsonedb_otu_tables">ITSoneDB OTU tables</option>
98 <option value="itsonedb_hdf5_biom">ITSoneDB HDF5 BIOM files</option>
99 <option value="itsonedb_json_biom">ITSoneDB JSON BIOM files</option>
100 </param>
101 </xml>
102 <xml name="file_type_taxonomic_analysis_unite">
103 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
104 <option value="mapseq_unite_assignments">MAPseq UNITE assignments</option>
105 <option value="unite_otu_tables">UNITE OTU tables</option>
106 <option value="unite_hdf5_biom">UNITE HDF5 BIOM files</option>
107 <option value="unite_json_biom">UNITE JSON BIOM files</option>
108 </param>
109 </xml>
110 <xml name="file_type_taxonomic_analysis_motu">
111 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
112 <option value="motus_taxonomic_profile">mOTUs taxonomic profile</option>
113 </param>
114 </xml>
115 <xml name="file_type_pathways_and_systems">
116 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
117 <option value="antismash_annotation_gff3">antiSMASH annotation (gff3)</option>
118 <option value="antismash_annotation_embl">antiSMASH annotation(embl)</option>
119 <option value="antismash_annotation_genbank">antiSMASH annotation(genbank)</option>
120 <option value="antismash_summary">antiSMASH summary</option>
121 <option value="genome_properties_annotation">Genome properties annotation</option>
122 <option value="kegg_pathway_annotation">KEGG pathway annotation</option>
123 <option value="kegg_pathway_annotation_contig">KEGG pathway annotation (contig)</option>
124 </param>
125 </xml>
126 <xml name="file_type_taxonomic_analysis">
127 <param name="file_type" type="select" label="File type" multiple="true" optional="false">
128 <option value="phylogenetic_tree"></option>
129 <option value="otus_counts_and_taxonomic_assignments_tsv">OTUs, counts and taxonomic assignments (table)</option>
130 <option value="otus_counts_and_taxonomic_assignments_biom1">OTUs, counts and taxonomic assignments (JSON)</option>
131 <option value="otus_counts_and_taxonomic_assignments_biom2">OTUs, counts and taxonomic assignments (HDF5)</option>
132 <option value="reads_encoding_5s_rrna">Reads enconding 5S rRNA</option>
133 <option value="reads_encoding_16s_rrna">Reads enconding 16S rRNA</option>
134 <option value="reads_encoding_23s_rrna">Reads enconding 23S rRNA</option>
135 </param>
136 </xml>
137 <xml name="file_type_taxonomic_analysis_its">
138 </xml>
19 <xml name="citations"> 139 <xml name="citations">
20 <citations> 140 <citations>
21 <citation type="bibtex"> 141 <citation type="bibtex">
22 @misc{emg_toolkit, 142 @misc{emg_toolkit,
23 author = {EBI Metagenomics}, 143 author = {EBI Metagenomics},