On 2024-09-16, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #475

Ecoregionalization

• ecoregion_brt_analysis was updated to 2129484beb61
• ecoregion_geonearestneighbor was updated to 36637718c51d

Metabolomics

• mfassignr_histnoise was updated to 12b63108d645
• mfassignr_isofiltr was updated to e7ef7718505d
• mfassignr_kmdnoise was updated to 39a642fc9638
• mfassignr_mfassign was updated to d5745e78fcfe
• mfassignr_mfassigncho was updated to b96a462d9c3f
• mfassignr_recal was updated to a3113a7c1767
• mfassignr_recallist was updated to ddb9d330ecc0
• mfassignr_snplot was updated to 434fa3233e96

QIIME 2

• qiime2__alignment__mafft was updated to c4a4ba3c7a9c
• qiime2__alignment__mafft_add was updated to 51e7e9d2c302
• qiime2__alignment__mask was updated to 1d37aa0aed4f
• qiime2__composition__add_pseudocount was updated to cd98e4bb92ee
• qiime2__composition__ancom was updated to f072d901c63c
• qiime2__composition__ancombc was updated to 4b71e36cc3d2
• qiime2__composition__tabulate was updated to 45a7de813cd5
• qiime2__cutadapt__demux_paired was updated to 9b5a775806be
• qiime2__cutadapt__demux_single was updated to fcb0c9bd84a3
• qiime2__cutadapt__trim_paired was updated to b2b61aecb444
• qiime2__cutadapt__trim_single was updated to 9a9d639bd2ec
• qiime2__dada2__denoise_ccs was updated to a22807aaff34
• qiime2__dada2__denoise_paired was updated to d2bf79e0bd52
• qiime2__dada2__denoise_pyro was updated to 16c1fce384ab
• qiime2__dada2__denoise_single was updated to a2112f424054
• qiime2__deblur__denoise_16S was updated to 2572fc0f88f2
• qiime2__deblur__denoise_16S was updated to b883cbea5623
• qiime2__deblur__denoise_other was updated to 27ba31d2202b
• qiime2__deblur__visualize_stats was updated to e02092a0b2db
• qiime2__demux__emp_paired was updated to a9ce731fab29
• qiime2__demux__emp_single was updated to 19e2495b60e8
• qiime2__demux__filter_samples was updated to b507d1f2196c
• qiime2__demux__subsample_paired was updated to 7b44ee1e60ea
• qiime2__demux__subsample_single was updated to 26139ebc17ea
• qiime2__demux__summarize was updated to acb0f8837379
• qiime2__diversity__adonis was updated to 472a46b5d416
• qiime2__diversity__alpha was updated to 5c2c4ceabe7e
• qiime2__diversity__alpha_correlation was updated to 339546317bfa
• qiime2__diversity__alpha_group_significance was updated to eae22172c84e
• qiime2__diversity__alpha_phylogenetic was updated to 6af85aa9f62d
• qiime2__diversity__alpha_rarefaction was updated to a19425489a68
• qiime2__diversity__beta was updated to 7ed55f1323ee
• qiime2__diversity__beta_correlation was updated to 26b99164f629
• qiime2__diversity__beta_group_significance was updated to 35c850ccce45
• qiime2__diversity__beta_phylogenetic was updated to 83d06804b15c
• qiime2__diversity__beta_rarefaction was updated to 08aa9fb4ffc8
• qiime2__diversity__bioenv was updated to 1e4f0944ae33
• qiime2__diversity__core_metrics was updated to 2b7bcbf8bdf3
• qiime2__diversity__core_metrics_phylogenetic was updated to d14296c8a1b8
• qiime2__diversity__filter_distance_matrix was updated to c6cab84f4198
• qiime2__diversity__mantel was updated to 9a97bf1e0e05
• qiime2__diversity__pcoa was updated to 250e13179e54
• qiime2__diversity__pcoa_biplot was updated to 30a01d00df77
• qiime2__diversity__procrustes_analysis was updated to 888d37bd0b9b
• qiime2__diversity__tsne was updated to f5dde68b544d
• qiime2__diversity__umap was updated to 955fd41ac481
• qiime2__diversity_lib__alpha_passthrough was updated to 444cd66d6101
• qiime2__diversity_lib__beta_passthrough was updated to da6fdc7618c7
• qiime2__diversity_lib__beta_phylogenetic_meta_passthrough was updated to 4de686329a37
• qiime2__diversity_lib__beta_phylogenetic_passthrough was updated to 2be808ff0cd2
• qiime2__diversity_lib__bray_curtis was updated to 4111b5b17fd4
• qiime2__diversity_lib__faith_pd was updated to c5a92b4cb5db
• qiime2__diversity_lib__jaccard was updated to a80fde700012
• qiime2__diversity_lib__observed_features was updated to a08147f79fe9
• qiime2__diversity_lib__pielou_evenness was updated to a10d8f198b93
• qiime2__diversity_lib__shannon_entropy was updated to 7f8e31cd33ed
• qiime2__diversity_lib__unweighted_unifrac was updated to 7de32a239176
• qiime2__diversity_lib__weighted_unifrac was updated to eafeb0b89ece
• qiime2__emperor__biplot was updated to 6830d5e1f0db
• qiime2__emperor__plot was updated to 41cb62f3cb7b
• qiime2__emperor__procrustes_plot was updated to 4a9f1bf4499e
• qiime2__feature_classifier__blast was updated to 6f881a1c40be
• qiime2__feature_classifier__classify_consensus_blast was updated to 1ca4b5d6ea40
• qiime2__feature_classifier__classify_consensus_vsearch was updated to 1006c36b2b57
• qiime2__feature_classifier__classify_hybrid_vsearch_sklearn was updated to 9162ded52c6a
• qiime2__feature_classifier__classify_sklearn was updated to d6632af373ab
• qiime2__feature_classifier__extract_reads was updated to 4ad70e7b2dba
• qiime2__feature_classifier__find_consensus_annotation was updated to 333ce5304712
• qiime2__feature_classifier__fit_classifier_naive_bayes was updated to a6c8858199f5
• qiime2__feature_classifier__fit_classifier_sklearn was updated to fe5fc2afd727
• qiime2__feature_classifier__vsearch_global was updated to 84d83752cc49
• qiime2__feature_table__core_features was updated to 5bd93c10087b
• qiime2__feature_table__filter_features was updated to d6536f0c370c
• qiime2__feature_table__filter_features_conditionally was updated to 6c8f74d8df6d
• qiime2__feature_table__filter_samples was updated to 40647f5aa13b
• qiime2__feature_table__filter_seqs was updated to 3d5a194fbdcb
• qiime2__feature_table__group was updated to d8d9cde18805
• qiime2__feature_table__heatmap was updated to 75a470897973
• qiime2__feature_table__merge was updated to 02074619b5e8
• qiime2__feature_table__merge_seqs was updated to 656b878d4049
• qiime2__feature_table__merge_taxa was updated to c7299241e3a7
• qiime2__feature_table__presence_absence was updated to 02f7e34192b1
• qiime2__feature_table__rarefy was updated to 76f44ad77e0c
• qiime2__feature_table__relative_frequency was updated to b775f27fe8db
• qiime2__feature_table__rename_ids was updated to f73f0cda6560
• qiime2__feature_table__summarize was updated to 517cc51856dd
• qiime2__feature_table__tabulate_seqs was updated to 9fe85eec5420
• qiime2__feature_table__transpose was updated to acadff77dd50
• qiime2__fragment_insertion__classify_otus_experimental was updated to 2821f5e19fe7
• qiime2__fragment_insertion__filter_features was updated to fef2604b8a87
• qiime2__fragment_insertion__sepp was updated to 157b7ea4cd38
• qiime2__longitudinal__anova was updated to b281d1caa69c
• qiime2__longitudinal__feature_volatility was updated to e1f34a303e1c
• qiime2__longitudinal__first_differences was updated to c6a55025afec
• qiime2__longitudinal__first_distances was updated to 2acedcd22341
• qiime2__longitudinal__linear_mixed_effects was updated to d67d2a61549b
• qiime2__longitudinal__maturity_index was updated to ae21a4eac775
• qiime2__longitudinal__nmit was updated to d17232fb5897
• qiime2__longitudinal__pairwise_differences was updated to d93df4dd5168
• qiime2__longitudinal__pairwise_distances was updated to 2dba2c15b48e
• qiime2__longitudinal__plot_feature_volatility was updated to 6fd0dec3112c
• qiime2__longitudinal__volatility was updated to 7c4629181605
• qiime2__metadata__distance_matrix was updated to 3ff91b9bf4bb
• qiime2__metadata__shuffle_groups was updated to e5920de13a94
• qiime2__metadata__tabulate was updated to f53749d24081
• qiime2__phylogeny__align_to_tree_mafft_fasttree was updated to 39b5b030033a
• qiime2__phylogeny__align_to_tree_mafft_iqtree was updated to 3258ec546d07
• qiime2__phylogeny__align_to_tree_mafft_raxml was updated to f094149c5203
• qiime2__phylogeny__fasttree was updated to 91061b2e9766
• qiime2__phylogeny__filter_table was updated to 167ee24ffe2f
• qiime2__phylogeny__filter_tree was updated to 6106d14aabd1
• qiime2__phylogeny__iqtree was updated to 6d01299f597a
• qiime2__phylogeny__iqtree_ultrafast_bootstrap was updated to d29e3e6a10fd
• qiime2__phylogeny__midpoint_root was updated to ad4c87cd901a
• qiime2__phylogeny__raxml was updated to a874d4dfbac6
• qiime2__phylogeny__raxml_rapid_bootstrap was updated to eb6c15cd603b
• qiime2__phylogeny__robinson_foulds was updated to a43f0d5cfd3f
• qiime2__quality_control__bowtie2_build was updated to 7291a764b254
• qiime2__quality_control__evaluate_composition was updated to 4f9bd4924e66
• qiime2__quality_control__evaluate_seqs was updated to 53f089ad7161
• qiime2__quality_control__evaluate_taxonomy was updated to de2941482b65
• qiime2__quality_control__exclude_seqs was updated to 051ac848cd6b
• qiime2__quality_control__filter_reads was updated to 4a4e207de234
• qiime2__quality_filter__q_score was updated to 363bb431c355
• qiime2__sample_classifier__classify_samples was updated to 84156d6e1291
• qiime2__sample_classifier__classify_samples_from_dist was updated to 2dad5e35f34c
• qiime2__sample_classifier__classify_samples_ncv was updated to f00cbad41c55
• qiime2__sample_classifier__confusion_matrix was updated to 0307995b05a4
• qiime2__sample_classifier__fit_classifier was updated to 745c0bca48dd
• qiime2__sample_classifier__fit_regressor was updated to c2c6554fda49
• qiime2__sample_classifier__heatmap was updated to 8fa6957e6cb0
• qiime2__sample_classifier__metatable was updated to ac49a2a49935
• qiime2__sample_classifier__predict_classification was updated to 4b8696ef6dbe
• qiime2__sample_classifier__predict_regression was updated to 6e134166916b
• qiime2__sample_classifier__regress_samples was updated to f28bc42125b6
• qiime2__sample_classifier__regress_samples_ncv was updated to 629fe9f7d95a
• qiime2__sample_classifier__scatterplot was updated to fcd6d3d308b7
• qiime2__sample_classifier__split_table was updated to d325f1c254c5
• qiime2__sample_classifier__summarize was updated to 10191f1db325
• qiime2__taxa__barplot was updated to d9d69991f2b2
• qiime2__taxa__collapse was updated to f17ae5fa0c60
• qiime2__taxa__filter_seqs was updated to 22f155638105
• qiime2__taxa__filter_table was updated to a8972ecf15c1
• qiime2__vsearch__cluster_features_closed_reference was updated to f1a4c7d2e5a7
• qiime2__vsearch__cluster_features_de_novo was updated to 3377d6ce369c
• qiime2__vsearch__cluster_features_open_reference was updated to 3dbcb981c4c9
• qiime2__vsearch__dereplicate_sequences was updated to 9c9e6b7d7286
• qiime2__vsearch__fastq_stats was updated to 6acd7854064f
• qiime2__vsearch__merge_pairs was updated to 4756c43a7181
• qiime2__vsearch__uchime_denovo was updated to 40ea1722fbab
• qiime2__vsearch__uchime_ref was updated to f13c03b34e2d
• qiime2_core__tools__export was updated to 37e37518cad1
• qiime2_core__tools__import was updated to f9e68fa06585

Proteomics

• fragpipe was updated to da9ebef968bd
• openms_openpepxl was updated to 40cc19c0dbd6
• openms_openpepxl was updated to a2a842b00f9c
• openms_openpepxl was updated to fc36cfd19834
• openms_percolatoradapter was updated to 0fc9ae55bcfc
• openms_percolatoradapter was updated to e7881a82b56d
• openms_xfdr was updated to 81402a5e4173
• openms_xfdr was updated to 9a6e3bb0f358

Machine Learning

• chatgpt_openai_api was updated to 7770a4bd42e2

Metagenomic Analysis

• motus was updated to d20f3b9a59a2
• coverm_contig was updated to 688a777e1b19
• gtdbtk_classify_wf was updated to 65d52c693b8e

Annotation

• braker3 was updated to c42bf6424ba4
• microsatbed was updated to 5f8efb080f49

None

• data_manager_build_kraken2_database was updated to ed1518ce2237
• data_manager_diamond_database_builder was updated to 4a08b7b76b78
• data_manager_gtdbtk_database_installer was updated to 10232d2b5062
• data_manager_metaphlan_database_downloader was updated to d8dc037e3c13
• data_manager_omamer was updated to e1502e4f8725

FASTA/FASTQ

• falco was updated to babbcf02d35c

Mothur

• mothur_pairwise_seqs was updated to 39c7213ca279

Phylogenetics

• hyphy_prime was updated to 4072360120e4

RNA Analysis

• seurat_clustering was updated to 94f1b9c7286f
• seurat_create was updated to d0c26c9430f2
• seurat_data was updated to 50c5abeb08ba
• seurat_integrate was updated to 4341b8ff2a46
• seurat_plot was updated to 2622dd85416f
• seurat_preprocessing was updated to c3170652bd98
• seurat_reduce_dimension was updated to e49429e8d6dd
• graphprot_predict_profile was updated to 20429f4c1b95
• graphprot_predict_profile was updated to ddcf35a868b8
• ribotaper was updated to 579b3be2559f

SAM/BAM

• samtools_sort was updated to a577ea614bed

Single-cell

• anndata_export was updated to cfaf5a405371
• anndata_import was updated to d330b3082107
• anndata_inspect was updated to 0bf7fddf90c7
• anndata_manipulate was updated to 7e8c677a7b71
• modify_loom was updated to 0f1aaff9b22d
• scanpy_cluster_reduce_dimension was updated to 178242b82297
• scanpy_filter was updated to 713a0c65b1fe
• scanpy_filter was updated to 8b9610ab366a
• scanpy_inspect was updated to 18262103fa61
• scanpy_normalize was updated to 5dada6f76047
• scanpy_plot was updated to 2dfb2227a16c
• scanpy_remove_confounders was updated to b70219da4a96

Peak Calling

• peakachu was updated to 940b1d632f4d