On 2025-07-21, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #523

Machine Learning

• sklearn_data_preprocess was updated to 50b3e080cef0
• sklearn_generalized_linear was updated to b628de0d101f
• sklearn_nn_classifier was updated to 823ecc0bce45

GIS Data Handling

• xarray_select was updated to 225d0d275a24

Imaging

• cp_convert_objects_to_image was updated to d9fa2e6fae97
• json2yolosegment was updated to 7db48c618bbe
• yolo_predict was updated to e708a1191202
• yolo_training was updated to ece3536c5e0e
• omero_filter was updated to 9d04b28b8dc8

QIIME 2

• qiime2__alignment__mafft was updated to 4e9939e79726
• qiime2__alignment__mafft_add was updated to b413f3a44b8d
• qiime2__alignment__mask was updated to 0a150e6ae9fb
• qiime2__composition__add_pseudocount was updated to 8d588aa467a7
• qiime2__composition__ancom was updated to f90977a357ca
• qiime2__composition__ancombc was updated to 1c2fc88c01c9
• qiime2__composition__tabulate was updated to c0c74c592ff7
• qiime2__cutadapt__demux_paired was updated to 61d6f9f0a0d7
• qiime2__cutadapt__demux_single was updated to 6b5ac8e63b57
• qiime2__cutadapt__trim_paired was updated to 190fb8fa90f4
• qiime2__cutadapt__trim_single was updated to f37d4f87c868
• qiime2__dada2__denoise_ccs was updated to 4d29020147f3
• qiime2__dada2__denoise_paired was updated to 53a7856cfafc
• qiime2__dada2__denoise_pyro was updated to b9c202882848
• qiime2__dada2__denoise_single was updated to be83e72c1ee9
• qiime2__deblur__denoise_16S was updated to 2572fc0f88f2
• qiime2__deblur__denoise_16S was updated to b883cbea5623
• qiime2__deblur__denoise_other was updated to 1d13002bae6b
• qiime2__deblur__visualize_stats was updated to b341b5eb9681
• qiime2__demux__emp_paired was updated to fa47b38a4b6c
• qiime2__demux__emp_single was updated to 8b90ed283fe4
• qiime2__demux__filter_samples was updated to e3d4217c9a64
• qiime2__demux__subsample_paired was updated to b358fb10943e
• qiime2__demux__subsample_single was updated to 5f29bf108ba3
• qiime2__demux__summarize was updated to a257c2e6b285
• qiime2__diversity__adonis was updated to 295acb5522c1
• qiime2__diversity__alpha was updated to 4033b503ac37
• qiime2__diversity__alpha_correlation was updated to 9c7324c4468f
• qiime2__diversity__alpha_group_significance was updated to 074a6c57757a
• qiime2__diversity__alpha_phylogenetic was updated to 8454d1802ed2
• qiime2__diversity__alpha_rarefaction was updated to 8f9b4a0f9ae4
• qiime2__diversity__beta was updated to 8d0c353e301b
• qiime2__diversity__beta_correlation was updated to dae7b5f58d78
• qiime2__diversity__beta_group_significance was updated to c09385bff349
• qiime2__diversity__beta_phylogenetic was updated to 2e7aa115e88d
• qiime2__diversity__beta_rarefaction was updated to 725208b2b09e
• qiime2__diversity__bioenv was updated to 897ac0a07708
• qiime2__diversity__core_metrics was updated to 61d885730311
• qiime2__diversity__core_metrics_phylogenetic was updated to 5d6dcbc8ef00
• qiime2__diversity__filter_alpha_diversity was updated to 992ec6b8a13f
• qiime2__diversity__filter_distance_matrix was updated to 0068bb2a39ff
• qiime2__diversity__mantel was updated to 3458413e304e
• qiime2__diversity__pcoa was updated to f13ed71b6bb2
• qiime2__diversity__pcoa_biplot was updated to a262d3792cd2
• qiime2__diversity__procrustes_analysis was updated to 6c53d0e60bea
• qiime2__diversity__tsne was updated to 6200df7461ae
• qiime2__diversity__umap was updated to 04c2ed9885d4
• qiime2__diversity_lib__alpha_passthrough was updated to e1efcd0c6c19
• qiime2__diversity_lib__beta_passthrough was updated to 4f4e558ec21e
• qiime2__diversity_lib__beta_phylogenetic_meta_passthrough was updated to 318dfdd6987d
• qiime2__diversity_lib__beta_phylogenetic_passthrough was updated to 5e5c3b5ab572
• qiime2__diversity_lib__bray_curtis was updated to 0eaad02b5b0b
• qiime2__diversity_lib__faith_pd was updated to 75def7f03560
• qiime2__diversity_lib__jaccard was updated to 1c3478cdc0db
• qiime2__diversity_lib__observed_features was updated to 0af9de398bbf
• qiime2__diversity_lib__pielou_evenness was updated to c31665c5069c
• qiime2__diversity_lib__shannon_entropy was updated to c80939f5905d
• qiime2__diversity_lib__unweighted_unifrac was updated to 1fedcbc547b6
• qiime2__diversity_lib__weighted_unifrac was updated to 515dc861c2f6
• qiime2__emperor__biplot was updated to c5ffd16c2f87
• qiime2__emperor__plot was updated to b97cc73761ee
• qiime2__emperor__procrustes_plot was updated to f1df7a53f802
• qiime2__feature_classifier__blast was updated to c6916688ac64
• qiime2__feature_classifier__classify_consensus_blast was updated to 9bdc8d573d35
• qiime2__feature_classifier__classify_consensus_vsearch was updated to 12b31c42e559
• qiime2__feature_classifier__classify_hybrid_vsearch_sklearn was updated to 86aee04ba532
• qiime2__feature_classifier__classify_sklearn was updated to 9cac0601eb35
• qiime2__feature_classifier__extract_reads was updated to a1358f6b25af
• qiime2__feature_classifier__find_consensus_annotation was updated to 5d61e1a7bfa5
• qiime2__feature_classifier__fit_classifier_naive_bayes was updated to 758db0fc9654
• qiime2__feature_classifier__fit_classifier_sklearn was updated to 137191c7a16f
• qiime2__feature_classifier__vsearch_global was updated to 1a5a5108cb2e
• qiime2__feature_table__core_features was updated to 9f6c877867e4
• qiime2__feature_table__filter_features was updated to a4ee4441998f
• qiime2__feature_table__filter_features_conditionally was updated to 6112f57a7245
• qiime2__feature_table__filter_samples was updated to ab97e8ef4191
• qiime2__feature_table__filter_seqs was updated to aff2903073ce
• qiime2__feature_table__group was updated to 6bca671e8d47
• qiime2__feature_table__heatmap was updated to 56342a7ffc1c
• qiime2__feature_table__merge was updated to ed63719e43f0
• qiime2__feature_table__merge_seqs was updated to 5cc71e4ddd1c
• qiime2__feature_table__merge_taxa was updated to dbae2d2beec5
• qiime2__feature_table__presence_absence was updated to 1195ceaecf1e
• qiime2__feature_table__rarefy was updated to 93661434070c
• qiime2__feature_table__relative_frequency was updated to ddd71de351d9
• qiime2__feature_table__rename_ids was updated to e15626848bdd
• qiime2__feature_table__summarize was updated to 93efdc769465
• qiime2__feature_table__tabulate_seqs was updated to 2df6f241b583
• qiime2__feature_table__transpose was updated to a9f37c5a3b3f
• qiime2__fragment_insertion__classify_otus_experimental was updated to 9bf34397fe0a
• qiime2__fragment_insertion__filter_features was updated to a752ace26ec1
• qiime2__fragment_insertion__sepp was updated to 2e86638386e2
• qiime2__longitudinal__anova was updated to c884dc776645
• qiime2__longitudinal__feature_volatility was updated to 24d37c376657
• qiime2__longitudinal__first_differences was updated to 83b630da280f
• qiime2__longitudinal__first_distances was updated to 9adb9cf55960
• qiime2__longitudinal__linear_mixed_effects was updated to 49b853a572ca
• qiime2__longitudinal__maturity_index was updated to a3a6a13accb4
• qiime2__longitudinal__nmit was updated to c6e586706e38
• qiime2__longitudinal__pairwise_differences was updated to 0dfb83493dcb
• qiime2__longitudinal__pairwise_distances was updated to 0fd8e8542365
• qiime2__longitudinal__plot_feature_volatility was updated to 2d8372066cd4
• qiime2__longitudinal__volatility was updated to 3951cbee8459
• qiime2__metadata__distance_matrix was updated to 60705b97ad22
• qiime2__metadata__shuffle_groups was updated to 43a3fcc65825
• qiime2__metadata__tabulate was updated to 8bf2391cf240
• qiime2__phylogeny__align_to_tree_mafft_fasttree was updated to f1942b6ece7c
• qiime2__phylogeny__align_to_tree_mafft_iqtree was updated to 0991e282a789
• qiime2__phylogeny__align_to_tree_mafft_raxml was updated to 94f6ae67f942
• qiime2__phylogeny__fasttree was updated to be40a789ee10
• qiime2__phylogeny__filter_table was updated to c5b7513c7a85
• qiime2__phylogeny__filter_tree was updated to 42b0db809909
• qiime2__phylogeny__iqtree was updated to 1e329aa80658
• qiime2__phylogeny__iqtree_ultrafast_bootstrap was updated to 62250c2786e5
• qiime2__phylogeny__midpoint_root was updated to f00f9d2b6acb
• qiime2__phylogeny__raxml was updated to 3f3dfbf2818b
• qiime2__phylogeny__raxml_rapid_bootstrap was updated to 1666e7212a8b
• qiime2__phylogeny__robinson_foulds was updated to da82df33868e
• qiime2__quality_control__bowtie2_build was updated to 085611a6a3c7
• qiime2__quality_control__evaluate_composition was updated to 56f480627ce8
• qiime2__quality_control__evaluate_seqs was updated to 419bdbd7375e
• qiime2__quality_control__evaluate_taxonomy was updated to 2562e48bdb2b
• qiime2__quality_control__exclude_seqs was updated to f2f323297c66
• qiime2__quality_control__filter_reads was updated to d3f25b91679b
• qiime2__quality_filter__q_score was updated to 2eb4241ccb54
• qiime2__rescript__get_bv_brc_genome_features was updated to e06438ea7fb0
• qiime2__rescript__get_bv_brc_genomes was updated to b93fff645871
• qiime2__rescript__get_bv_brc_metadata was updated to e55e6564c5cb
• qiime2__sample_classifier__classify_samples was updated to e6df54d762ac
• qiime2__sample_classifier__classify_samples_from_dist was updated to f53151bf76b3
• qiime2__sample_classifier__classify_samples_ncv was updated to 1e5c17a581be
• qiime2__sample_classifier__confusion_matrix was updated to 1cf5e70cd6b5
• qiime2__sample_classifier__fit_classifier was updated to 9027e5be16da
• qiime2__sample_classifier__fit_regressor was updated to 43fcd8fc5cb2
• qiime2__sample_classifier__heatmap was updated to 3868f59bdab8
• qiime2__sample_classifier__metatable was updated to f03200f2248b
• qiime2__sample_classifier__predict_classification was updated to 2ce80ad95d2a
• qiime2__sample_classifier__predict_regression was updated to d9cef47d5932
• qiime2__sample_classifier__regress_samples was updated to 3177500c29ae
• qiime2__sample_classifier__regress_samples_ncv was updated to fbc1810cb832
• qiime2__sample_classifier__scatterplot was updated to 3a8e6a8284df
• qiime2__sample_classifier__split_table was updated to 102320d08d9e
• qiime2__sample_classifier__summarize was updated to 5809c88c4e4a
• qiime2__stats__alpha_group_significance was updated to cd7d5bb23299
• qiime2__stats__collate_stats was updated to 18f68bb3980b
• qiime2__stats__facet_across was updated to 9fc56b3eea68
• qiime2__stats__facet_within was updated to ca0ce4dc03e9
• qiime2__stats__mann_whitney_u_facet was updated to 438970a86b69
• qiime2__stats__plot_rainclouds was updated to f80d84d8ce8b
• qiime2__stats__prep_alpha_distribution was updated to f55d46b78273
• qiime2__stats__wilcoxon_srt was updated to 2b51fb59a605
• qiime2__stats__wilcoxon_srt_facet was updated to 716490dd0182
• qiime2__taxa__barplot was updated to de8d109b6f3d
• qiime2__taxa__collapse was updated to b42bb00943a9
• qiime2__taxa__filter_seqs was updated to 58975ac028d7
• qiime2__taxa__filter_table was updated to a30681a590e1
• qiime2__vizard__boxplot was updated to 751a2433f1cc
• qiime2__vizard__heatmap was updated to 91db037bcfaf
• qiime2__vizard__lineplot was updated to d18e90f69613
• qiime2__vizard__scatterplot_2d was updated to 228e90d03b6c
• qiime2__vsearch__cluster_features_closed_reference was updated to a0016af52cfb
• qiime2__vsearch__cluster_features_de_novo was updated to 93c93d427232
• qiime2__vsearch__cluster_features_open_reference was updated to 24bb88850c9f
• qiime2__vsearch__dereplicate_sequences was updated to a88d64fca73e
• qiime2__vsearch__fastq_stats was updated to 4262dab8e060
• qiime2__vsearch__merge_pairs was updated to 826db2fbad95
• qiime2__vsearch__uchime_denovo was updated to 10cd4c4fdaa7
• qiime2__vsearch__uchime_ref was updated to 7d815e8ec62f
• qiime2_core__tools__export was updated to 61fb1a11e004
• qiime2_core__tools__import was updated to b2c99f2353b6
• qiime2_core__tools__import_fastq was updated to 081cc6ccab92

ChemicalToolBox

• sucos_docking_scoring was updated to 8161c08627bf
• gmx_editconf was updated to 861b2487aaea

BED

• bedtools was updated to fe5b4cb8356c

Motif Tools

• meme_fimo was updated to 613c75eee7bd
• meme_meme was updated to faa378fa0c81
• meme_psp_gen was updated to 8436beac5eed
• meme_streme was updated to 7653ebd919bb

Proteomics

• iedb_netmhcpan was updated to 88e44dab2988
• openms_fuzzydiff was updated to ed9a839cbbda
• openms_metaboliteadductdecharger was updated to ebc51eae71cd

Convert Formats

• graphicsmagick_image_compare was updated to 19cd03398db8
• graphicsmagick_image_montage was updated to ab55af10f1ff
• tooldistillator was updated to c6b5c2975e51
• tooldistillator_summarize was updated to 3d0223265277

Multiple Alignments

• mafft was updated to 0a507f4bd19a

Get Data

• sra_tools was updated to de0f7e0a3896

Astronomy

• astropy_csv2fits was updated to eba50a1f228e
• astropy_fits2bitmap was updated to 44dbbc093fd6
• astropy_fits2csv was updated to f02f62944fa9
• astropy_fitsinfo was updated to 2237c784d6a7
• fits2tiff_astro_tool was updated to 8f94a9d810c2
• source_extractor_astro_tool was updated to f4648bd69d48

Annotation

• augustus was updated to 534814b64234
• augustus_training was updated to 2fdc599f2814
• braker3 was updated to 0be6820e3268
• genenotebook_genenotebook_build was updated to eae124b1e1f1
• funannotate_annotate was updated to 9c15ca7e764e
• funannotate_predict was updated to 3cc3ef448854
• miniprot was updated to 20d725740701
• miniprot was updated to 52bdc302299b
• miniprot_index was updated to e64445f727cd
• ppanggolin_all was updated to 79f2d2f0ca2c
• ppanggolin_msa was updated to 7a09c51a14be

Assembly

• rnaquast was updated to 3967889cda03

FASTA/FASTQ

• bbtools_bbduk was updated to bf0cb5dd02f2
• fastplong was updated to 8d31d5da8662
• seqkit_fx2tab was updated to 654a2f089252
• seqkit_head was updated to 6fb76225bdb1
• seqkit_locate was updated to fe7a1e57a6cf
• seqkit_sort was updated to 01b1d8c7c031
• seqkit_stats was updated to 3d6d1121a427
• seqkit_translate was updated to 0c011189b47e

Genome editing

• amplican was updated to 6f3df153a095

Graph/Display Data

• circos was updated to e6cbe3190642

Metagenomic Analysis

• cat_add_names was updated to 13192095fd5a

Mothur

• mothur_classify_seqs was updated to 5da484e2c7a4
• mothur_make_contigs was updated to 4e9136c2c4c3
• mothur_merge_groups was updated to f170676a1d12

Quality Control

• multiqc was updated to 161f4383df15

RNA Analysis

• trinity_run_de_analysis was updated to bbbb39ad9a7e

Single-cell

• scanpy_cluster_reduce_dimension was updated to 6f2d2c7f77ee
• velocyto_cli was updated to f66590d0d3af

Variant Calling

• vcffilter was updated to 9442e22779ca
• basil was updated to bf1bdb62d882
• bcftools_merge was updated to e03f2f3ac3a9
• vcfanno was updated to c192a2c7ef00

None

• data_manager_diamond_database_builder was updated to 4a08b7b76b78

hca_sc_scanpy_tools

• scanpy_run_fdg was updated to 14866357fbec