On 2024-09-29, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #477

Species abundance

• pampa_presabs was updated to 07b081730994

Data and Metadata Management

• eal_table_template was updated to 672e25c2c8c8
• eal_templates was updated to 5faa25ba905e
• eal_templates was updated to debfa8a223c0
• eml2eal was updated to 0fa9d8240dc3
• eml2eal was updated to 3d14d6a4ef7c
• eml2eal was updated to c1d2c0922362
• eml_validate was updated to ad96b20423cf
• entities_template was updated to 299db57196ac
• entities_template was updated to 8de58d879d6e
• geo_cov_template was updated to 4f5816b57c13
• geo_cov_template was updated to ea302cc18332
• makeeml was updated to 34dcb86a9351
• makeeml was updated to 49f38336f28f
• raster_template was updated to 06e29cdc08bf
• raster_template was updated to 36150f04b524
• raster_template was updated to b34c5a70b706
• taxo_cov_template was updated to 2af7401f13e0
• taxo_cov_template was updated to 4f2d8a7c97fa
• taxo_cov_template was updated to 9507334a3303
• vector_template was updated to 330f15f2ad3f
• vector_template was updated to 40eb35199537

SAM/BAM

• bam_to_sam was updated to f57df915aa10

Metabolomics

• hmdb_ms_search was updated to 505956db90c5
• xcms_summary was updated to 27e7da5f6848
• matchms_add_key was updated to 8fb8ac6c37b0
• matchms_remove_key was updated to dd1b4515c5cd
• matchms_spectral_similarity was updated to beae81d5a475
• matchms_subsetting was updated to 9231f7bee46d
• recetox_aplcms_compute_clusters was updated to 550667ce03f1
• use_theoretical_mz_annotations was updated to b3d41b1fcb18

QIIME 2

• qiime2__deblur__denoise_16S was updated to 2572fc0f88f2
• qiime2__deblur__denoise_16S was updated to b883cbea5623

ChemicalToolBox

• chembl was updated to 6f8458d1cf46
• enumerate_charges was updated to 0f3e5c69251e
• openbabel_structure_distance_finder was updated to 2c5c7da26e08
• openbabel_structure_distance_finder was updated to 49242402887b
• rdock_rbcavity was updated to 2f218be61685
• rdock_rbdock was updated to 309fd04bcfd2
• rdock_rbdock was updated to a428230b38f6
• sucos_docking_scoring was updated to a3c1e2eea7d3
• sucos_max_score was updated to 55ac04db36aa

Convert Formats

• bam_to_scidx was updated to b737f6d83f48
• crossmap_gff was updated to e80720e27001
• ucsc_axtchain was updated to 05afdd33dac7
• ucsc_maftoaxt was updated to a6540beef35f
• ucsc_twobittofa was updated to 3c6f9e8a4c17
• ucsc_wigtobigwig was updated to 98704d357ede

Graph/Display Data

• jbrowse2 was updated to af482048ca1a
• jbrowse2 was updated to c017111e976a
• export2graphlan was updated to b16989c1e3a7
• ggplot2_pca was updated to 1b9406a1a769
• ggplot2_violin was updated to 637cf21db396
• jbrowse was updated to 69c5e9c0add0

RNA Analysis

• salmon was updated to 6b0ba6de1424
• arriba was updated to 45c2ec061cf9
• arriba_draw_fusions was updated to 7acb00fc980a
• arriba_get_filters was updated to 7a5a2d28c539
• cherri_train was updated to 2f7daa5d2d82
• deseq2 was updated to 6f91b8ce6e07
• trinity_abundance_estimates_to_matrix was updated to 2e21a7c28b38
• trinity_abundance_estimates_to_matrix was updated to 442e3696c634
• trinity_abundance_estimates_to_matrix was updated to 59fff1388bc2
• trinity_abundance_estimates_to_matrix was updated to cdde9062b49c
• trinity_align_and_estimate_abundance was updated to 00719b8004c9
• trinity_align_and_estimate_abundance was updated to 75f4e1859ed7
• trinity_filter_low_expr_transcripts was updated to 17101429bf0d
• tximport was updated to 0bcc35b10569

Gemini

• gemini_db_info was updated to bc8b01d1b496

RAD-seq

• stacks_procrad was updated to 57910d476be9
• stacks_ustacks was updated to a4ec4f620a77

FASTA/FASTQ

• fastq_trimmer was updated to 2d0d13b0b0f1
• fasta_merge_files_and_filter_unique_sequences was updated to 650d553c1fda
• falco was updated to 959a14c1f2dd
• umi_tools_count was updated to 9570563fb686
• umi_tools_dedup was updated to 04e09969d376
• umi_tools_extract was updated to 015cf18f4a15
• umi_tools_group was updated to 257be15474a7
• umi_tools_whitelist was updated to 4c8a1c7d3608
• cutadapt was updated to 02c5a84971c8

Proteomics

• maxquant was updated to 74f5d355d156
• maxquant_mqpar was updated to 256cc0e17454
• openms_databasefilter was updated to 0c98acedb17a
• openms_openswathmzmlfilecacher was updated to e7c43d17e3dc
• openms_qcexporter was updated to adf7f5301284
• openms_rtevaluation was updated to 0cf2a9047a17

Assembly

• racon was updated to 7c847ec300b8

Machine Learning

• keras_batch_models was updated to 7f6079deac6f

Statistics

• scipy_sparse was updated to 6d1a9fae57eb

Annotation

• busco was updated to 2a5b8b9936bf
• chewbbaca_allelecallevaluator was updated to b4467818950a
• chewbbaca_createschema was updated to ae1374a5ecdf
• chewbbaca_downloadschema was updated to f502e55c34a3
• chewbbaca_extractcgmlst was updated to 9c4c2191b550
• chewbbaca_joinprofiles was updated to e3cba867efd4
• chewbbaca_nsstats was updated to 7c84b3b83def
• chewbbaca_prepexternalschema was updated to d8c1dcd7418c
• roary was updated to e02e9af2743f
• tsebra was updated to 69dcd75c0f5f
• sortmerna was updated to 185effcdfb68

Metagenomic Analysis

• concoct_cut_up_fasta was updated to f80e693468d8
• humann was updated to c2803012bbb3
• humann_barplot was updated to 5fea25ee6275
• humann_join_tables was updated to f01ca38fb6c5
• humann_reduce_table was updated to 60749924ad62
• humann_regroup_table was updated to 8237a0f225db
• humann_rename_table was updated to aabf8cfb8fef
• humann_renorm_table was updated to 2bdd84912a2b
• humann_split_table was updated to 81c5dd1c777f
• instrain_compare was updated to dff92aac9f75
• nonpareil was updated to 45210df786b9

Climate Analysis

• cds_essential_variability was updated to b9d9fe0c2ce7

Mapping

• bwa was updated to 48f306c57611

Imaging

• 2d_feature_extraction was updated to 6fdb3542a406
• 2d_local_threshold was updated to c90b91f4a07b
• colocalization_viz was updated to fc85eb253163
• colorize_labels was updated to 5907be5a8d7c
• coordinates_of_roi was updated to 0d30ffea8874
• imagecoordinates_flipaxis was updated to d0960e1b25a8
• imagej2_adjust_threshold_binary was updated to 2b007b1e6c1b
• imagej2_adjust_threshold_binary was updated to f1ba33cd9edf
• imagej2_analyze_skeleton was updated to bb84f130a4e1
• imagej2_binary_to_edm was updated to 91b8f4730a93
• imagej2_bunwarpj_adapt_transform was updated to 706af1d7028a
• imagej2_bunwarpj_align was updated to 711adedc5bb8
• imagej2_bunwarpj_align was updated to ab54024c0a88
• imagej2_bunwarpj_compare_elastic_raw was updated to da91b5eaf92d
• imagej2_bunwarpj_compare_raw was updated to b0da913f048e
• imagej2_bunwarpj_compose_elastic was updated to e781a17b3c14
• imagej2_bunwarpj_compose_raw_elastic was updated to 1bf7e70e67f9
• imagej2_bunwarpj_convert_to_raw was updated to 95fb6fa70c2f
• imagej2_bunwarpj_convert_to_raw was updated to bd2aadf0f589
• imagej2_bunwarpj_elastic_transform was updated to f72f8e6787cd
• imagej2_bunwarpj_raw_transform was updated to 69e951528a0b
• imagej2_create_image was updated to dc3935a0165a
• imagej2_enhance_contrast was updated to 1f92b1da556b
• imagej2_find_maxima was updated to 4409f9eb9433
• imagej2_make_binary was updated to 1cf9771e0e53
• imagej2_shadows was updated to f7ae316b00e4
• imagej2_skeletonize3d was updated to 5f5b7185bc16
• imagej2_smooth was updated to c11777ffe5b1
• landmark_registration was updated to a71239f3543a
• morphological_operations was updated to f10112b317a1
• overlay_images was updated to ca362a9bfa20
• permutate_axis was updated to 5b82f2186244
• points2binaryimage was updated to 5411384e5e1d

Evolution

• tn93 was updated to 2fd21f5b16bc
• tn93_filter was updated to 1aa73004ba9b
• tn93_readreduce was updated to c176164dc8a5

HiCExplorer

• hicexplorer_hicmergematrixbins was updated to d5e27e6cfa59

Nanopore

• medaka_consensus was updated to 22f6a0e7424f

Single-cell

• sinto_barcode was updated to d0f56ac6bb60

Mothur

• mothur_venn was updated to e4f4c1c0d193

Peak Calling

• macs2 was updated to c33686854b19

Phylogenetics

• hyphy_absrel was updated to 181f5b9f139f

Variant Calling

• artic_minion was updated to f212134e204c
• bbtools_callvariants was updated to 8eace8923202
• bcftools_annotate was updated to 2436e3bef247
• bcftools_annotate was updated to 3f62d4939d54
• bcftools_consensus was updated to 147de996e34f
• bcftools_norm was updated to 1ca7418e46ee
• bcftools_plugin_color_chrs was updated to 36960e552ddc
• beacon2_biosamples was updated to 7cea4f9c4d8f
• beacon2_biosamples was updated to 7e8a31232cdb
• beacon2_cohorts was updated to 64718ff8785c
• beacon2_datasets was updated to 5cab12440f5e
• beacon2_individuals was updated to 3033822b7bb0
• beacon2_runs was updated to b960f8955623
• ucsc_fatovcf was updated to 3c19c84fbce2

Text Manipulation

• join was updated to a10f49d9218a
• table_compute was updated to 93a3ce78ce55

Operate on Genomic Intervals

• subtract was updated to 0145969324c4

None

• data_manager_diamond_database_builder was updated to 4a08b7b76b78

Spatial Omics

• mesmer was updated to c60b810d570d