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
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