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| --- | ||
| site: freiburg | ||
| tags: [tools] | ||
| title: UseGalaxy.eu Tool Updates for 2023-10-15 | ||
| supporters: | ||
| - denbi | ||
| - elixir | ||
| --- | ||
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| On 2023-10-15, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #411](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#411/) | ||
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| ## Metabolomics | ||
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| - dimet_abundance_plot was updated to [c9040bdb918c](https://toolshed.g2.bx.psu.edu/view/iuc/dimet_abundance_plot/c9040bdb918c) | ||
| - dimet_differential_analysis was updated to [c46d33411495](https://toolshed.g2.bx.psu.edu/view/iuc/dimet_differential_analysis/c46d33411495) | ||
| - dimet_differential_multigroup_analysis was updated to [e88cf5618b40](https://toolshed.g2.bx.psu.edu/view/iuc/dimet_differential_multigroup_analysis/e88cf5618b40) | ||
| - dimet_enrichment_plot was updated to [254408bfc5c0](https://toolshed.g2.bx.psu.edu/view/iuc/dimet_enrichment_plot/254408bfc5c0) | ||
| - dimet_isotopologues_plot was updated to [a3349c105bd0](https://toolshed.g2.bx.psu.edu/view/iuc/dimet_isotopologues_plot/a3349c105bd0) | ||
| - dimet_metabologram was updated to [a7d3e880e74c](https://toolshed.g2.bx.psu.edu/view/iuc/dimet_metabologram/a7d3e880e74c) | ||
| - dimet_pca_analysis was updated to [04d213632103](https://toolshed.g2.bx.psu.edu/view/iuc/dimet_pca_analysis/04d213632103) | ||
| - dimet_pca_plot was updated to [952808ffa842](https://toolshed.g2.bx.psu.edu/view/iuc/dimet_pca_plot/952808ffa842) | ||
| - dimet_timecourse_analysis was updated to [cb8c4ae59da9](https://toolshed.g2.bx.psu.edu/view/iuc/dimet_timecourse_analysis/cb8c4ae59da9) | ||
| - biotransformer was updated to [e5fcba090b10](https://toolshed.g2.bx.psu.edu/view/recetox/biotransformer/e5fcba090b10) | ||
| - matchms_convert was updated to [d4609fbf8ca3](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_convert/d4609fbf8ca3) | ||
| - matchms_filtering was updated to [13de8005adba](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_filtering/13de8005adba) | ||
| - matchms_fingerprint_similarity was updated to [df85b26201d1](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_fingerprint_similarity/df85b26201d1) | ||
| - matchms_formatter was updated to [ae45992f969e](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_formatter/ae45992f969e) | ||
| - matchms_metadata_export was updated to [7504a8f93699](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_export/7504a8f93699) | ||
| - matchms_metadata_match was updated to [b5b360897004](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_match/b5b360897004) | ||
| - matchms_networking was updated to [9982b85ff4e7](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_networking/9982b85ff4e7) | ||
| - matchms_similarity was updated to [872d8040f713](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_similarity/872d8040f713) | ||
| - matchms_spectral_similarity was updated to [3f96c93f8566](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_spectral_similarity/3f96c93f8566) | ||
| - matchms_split was updated to [97be845e45c2](https://toolshed.g2.bx.psu.edu/view/recetox/matchms_split/97be845e45c2) | ||
| - msmetaenhancer was updated to [3e2cb0bc6959](https://toolshed.g2.bx.psu.edu/view/recetox/msmetaenhancer/3e2cb0bc6959) | ||
| - ramclustr was updated to [09cabbc3d12d](https://toolshed.g2.bx.psu.edu/view/recetox/ramclustr/09cabbc3d12d) | ||
| - ramclustr_define_experiment was updated to [7bbdcce50541](https://toolshed.g2.bx.psu.edu/view/recetox/ramclustr_define_experiment/7bbdcce50541) | ||
| - recetox_aplcms_align_features was updated to [2b6bfa234d8b](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_align_features/2b6bfa234d8b) | ||
| - recetox_aplcms_compute_clusters was updated to [550667ce03f1](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_compute_clusters/550667ce03f1) | ||
| - recetox_aplcms_compute_template was updated to [e2dc815e1b2c](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_compute_template/e2dc815e1b2c) | ||
| - recetox_aplcms_correct_time was updated to [d69ec1171d71](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_correct_time/d69ec1171d71) | ||
| - recetox_aplcms_generate_feature_table was updated to [32b66fb6a6a0](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_generate_feature_table/32b66fb6a6a0) | ||
| - recetox_aplcms_merge_known_table was updated to [8ecb609cc265](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_merge_known_table/8ecb609cc265) | ||
| - recetox_aplcms_recover_weaker_signals was updated to [a9bb2ccc53de](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_recover_weaker_signals/a9bb2ccc53de) | ||
| - recetox_aplcms_remove_noise was updated to [12bf74dd09f1](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_remove_noise/12bf74dd09f1) | ||
| - recetox_xmsannotator_advanced was updated to [50ac7359ffe7](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_xmsannotator_advanced/50ac7359ffe7) | ||
| - riassigner was updated to [8c5e65adf694](https://toolshed.g2.bx.psu.edu/view/recetox/riassigner/8c5e65adf694) | ||
| - rmassbank was updated to [c1a9c990d4b0](https://toolshed.g2.bx.psu.edu/view/recetox/rmassbank/c1a9c990d4b0) | ||
| - waveica was updated to [dbbedb14b44c](https://toolshed.g2.bx.psu.edu/view/recetox/waveica/dbbedb14b44c) | ||
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| ## QIIME 2 | ||
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| - qiime2__deblur__denoise_16S was updated to [2572fc0f88f2](https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2) | ||
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| ## Proteomics | ||
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| - msstatstmt was updated to [fd3dc69b78ff](https://toolshed.g2.bx.psu.edu/view/galaxyp/msstatstmt/fd3dc69b78ff) | ||
| - openms_openpepxl was updated to [a2a842b00f9c](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c) | ||
| - openms_percolatoradapter was updated to [0fc9ae55bcfc](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc) | ||
| - openms_percolatoradapter was updated to [e7881a82b56d](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d) | ||
| - openms_xfdr was updated to [81402a5e4173](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173) | ||
| - openms_xfdr was updated to [9a6e3bb0f358](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358) | ||
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| ## Annotation | ||
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| - cpt_annotation_table was updated to [6998c2570145](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_annotation_table/6998c2570145) | ||
| - cpt_gbk_renumber was updated to [8cac332dbc77](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_gbk_renumber/8cac332dbc77) | ||
| - cpt_genome_editor was updated to [78ce8a1a8fd1](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_genome_editor/78ce8a1a8fd1) | ||
| - cpt_gff_extract_seq was updated to [ab40380424c9](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_gff_extract_seq/ab40380424c9) | ||
| - cpt_gff_rebase was updated to [4f4b413056f6](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_gff_rebase/4f4b413056f6) | ||
| - cpt_intersect_adjacent was updated to [7e393668b4b9](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_intersect_adjacent/7e393668b4b9) | ||
| - cpt_intron_detection was updated to [0a98d5259ef0](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_intron_detection/0a98d5259ef0) | ||
| - cpt_lipory was updated to [b79df4966ebb](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_lipory/b79df4966ebb) | ||
| - cpt_phageqc_annotations was updated to [c3140b08d703](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_phageqc_annotations/c3140b08d703) | ||
| - cpt_require_shine was updated to [a6dc48930318](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_require_shine/a6dc48930318) | ||
| - braker3 was updated to [bd103884a09c](https://toolshed.g2.bx.psu.edu/view/genouest/braker3/bd103884a09c) | ||
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| ## Phylogenetics | ||
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| - cpt_related_genomes_nuc was updated to [5a5fe0a6f78d](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_related_genomes_nuc/5a5fe0a6f78d) | ||
| - cpt_related_genomes_prot was updated to [ebcc87a27f9c](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_related_genomes_prot/ebcc87a27f9c) | ||
| - cpt_xmfa_to_table was updated to [06d8e28d0bd7](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_xmfa_to_table/06d8e28d0bd7) | ||
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| ## Convert Formats | ||
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| - cpt_gbk_to_5col was updated to [1bdd481d5c25](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_gbk_to_5col/1bdd481d5c25) | ||
| - cpt_gbk_to_gff was updated to [bb6332a85aa6](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_gbk_to_gff/bb6332a85aa6) | ||
| - cpt_gff_split was updated to [8bd03ba8510a](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_gff_split/8bd03ba8510a) | ||
| - cpt_gff_to_gbk was updated to [35a6c466e270](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_gff_to_gbk/35a6c466e270) | ||
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| ## Graph/Display Data | ||
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| - cpt_linear_genome_plot was updated to [e923c686ead9](https://toolshed.g2.bx.psu.edu/view/cpt/cpt_linear_genome_plot/e923c686ead9) | ||
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| ## Assembly | ||
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| - hifiasm was updated to [60024a528cbd](https://toolshed.g2.bx.psu.edu/view/bgruening/hifiasm/60024a528cbd) | ||
| - hapog was updated to [7d56a813fd24](https://toolshed.g2.bx.psu.edu/view/iuc/hapog/7d56a813fd24) | ||
| - shovill was updated to [ee17a294d3a3](https://toolshed.g2.bx.psu.edu/view/iuc/shovill/ee17a294d3a3) | ||
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| ## Mothur | ||
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| - mothur_unifrac_unweighted was updated to [6a622b34394a](https://toolshed.g2.bx.psu.edu/view/iuc/mothur_unifrac_unweighted/6a622b34394a) | ||
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| ## RNA Analysis | ||
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| - edger was updated to [070900306913](https://toolshed.g2.bx.psu.edu/view/iuc/edger/070900306913) | ||
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| ## None | ||
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| - data_manager_diamond_database_builder was updated to [4a08b7b76b78](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78) | ||
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| ## hca_sc_scanpy_tools | ||
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| - anndata_ops was updated to [2e8022f1923c](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/anndata_ops/2e8022f1923c) | ||
| - scanpy_compute_graph was updated to [f776e3ed3c03](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_compute_graph/f776e3ed3c03) | ||
| - scanpy_filter_cells was updated to [356fa6c27341](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_filter_cells/356fa6c27341) | ||
| - scanpy_filter_genes was updated to [9a36525a8425](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_filter_genes/9a36525a8425) | ||
| - scanpy_find_cluster was updated to [d19920419c78](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_find_cluster/d19920419c78) | ||
| - scanpy_find_markers was updated to [f0f78d29130f](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_find_markers/f0f78d29130f) | ||
| - scanpy_find_variable_genes was updated to [273faaa2bd69](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_find_variable_genes/273faaa2bd69) | ||
| - scanpy_integrate_bbknn was updated to [12fc7e093094](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_integrate_bbknn/12fc7e093094) | ||
| - scanpy_integrate_combat was updated to [c6611adc8f4a](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_integrate_combat/c6611adc8f4a) | ||
| - scanpy_integrate_harmony was updated to [18e01a7c55c6](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_integrate_harmony/18e01a7c55c6) | ||
| - scanpy_integrate_mnn was updated to [e9788746e0f6](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_integrate_mnn/e9788746e0f6) | ||
| - scanpy_multiplet_scrublet was updated to [fadc4fbf8025](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_multiplet_scrublet/fadc4fbf8025) | ||
| - scanpy_normalise_data was updated to [4bbb2179521c](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_normalise_data/4bbb2179521c) | ||
| - scanpy_parameter_iterator was updated to [99301e5feddc](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_parameter_iterator/99301e5feddc) | ||
| - scanpy_plot_embed was updated to [bfb4d298d75f](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_plot_embed/bfb4d298d75f) | ||
| - scanpy_plot_scrublet was updated to [4276a6dea8d1](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_plot_scrublet/4276a6dea8d1) | ||
| - scanpy_plot_trajectory was updated to [9d746af31fe8](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_plot_trajectory/9d746af31fe8) | ||
| - scanpy_read_10x was updated to [af6ecb5adcc1](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_read_10x/af6ecb5adcc1) | ||
| - scanpy_regress_variable was updated to [bd65279c7ddc](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_regress_variable/bd65279c7ddc) | ||
| - scanpy_run_diffmap was updated to [afec1d52b87d](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_diffmap/afec1d52b87d) | ||
| - scanpy_run_dpt was updated to [2f569aa8c920](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_dpt/2f569aa8c920) | ||
| - scanpy_run_fdg was updated to [cef0ddd01875](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_fdg/cef0ddd01875) | ||
| - scanpy_run_paga was updated to [6b7a5d15a89b](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_paga/6b7a5d15a89b) | ||
| - scanpy_run_pca was updated to [f0eecf608220](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_pca/f0eecf608220) | ||
| - scanpy_run_tsne was updated to [64cd33540fee](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_tsne/64cd33540fee) | ||
| - scanpy_run_umap was updated to [9984f48961d0](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_umap/9984f48961d0) | ||
| - scanpy_scale_data was updated to [bf30bd6355da](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_scale_data/bf30bd6355da) | ||
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