diff --git a/results/all_tools.tsv b/results/all_tools.tsv index 69e9c4f2..654e46a1 100644 --- a/results/all_tools.tsv +++ b/results/all_tools.tsv @@ -329,7 +329,7 @@ epicseg 245.0 5.0 epicseg_segment EpiCSeg is a tool for conducting chromatin seg fastq_info 5765.0 679.0 fastq_info FASTQ info allows to validate single or paired fastq files To update https://github.com/nunofonseca/fastq_utils Fastq Manipulation fastq_info bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 0.25.1 fastq_utils 0.25.2 (1/1) (0/1) (1/1) file_manipulation bg_uniq This tool returns all unique lines from a tab-separated file. To update https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation Text Manipulation unique bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python (0/1) (0/1) (1/1) find_subsequences 763.0 31.0 bg_find_subsequences To update find_subsequences bgruening 0.3 biopython 1.70 (1/1) (0/1) (1/1) -flye 20904.0 1499.0 flye Assembly of long and error-prone reads. To update https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.1 flye 2.9.3 (1/1) (1/1) (1/1) +flye 20904.0 1499.0 flye Assembly of long and error-prone reads. Up-to-date https://github.com/fenderglass/Flye/ Assembly flye bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye 2.9.3 flye 2.9.3 (1/1) (1/1) (1/1) footprint 57.0 footprint Find transcription factor footprints To update https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ Epigenetics footprint rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint 1.0.0 footprint 1.0.1 (0/1) (0/1) (1/1) format_cd_hit_output 166.0 20.0 format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file To update Fasta Manipulation format_cd_hit_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ 1.0.0+galaxy1 (0/1) (0/1) (1/1) format_metaphlan2_output 5588.0 166.0 format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels format_metaphlan2_output Format metaphlan2 output """This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains)."" - Galaxy tool wrapper" Formatting Taxonomy, Metagenomics To update Metagenomics format_metaphlan2_output bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ 0.2.0 (0/1) (0/1) (1/1) @@ -561,6 +561,7 @@ clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-perfor clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins " clustal2 " Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) +cnv-phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv_phenopacket iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket 1.0.2 cnv-phenopacket (0/1) (0/1) (0/1) cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. To update https://pypi.org/project/cnv-phenopacket/ Variant Analysis cnv-vcf2json iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json 1.0.4 cnv-vcf2json (0/1) (0/1) (0/1) cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target detecting copy number variants and alterations genome-wide from high-throughput sequencing cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. Variant calling DNA structural variation Up-to-date https://github.com/etal/cnvkit Variant Analysis cnvkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit 0.9.10 cnvkit 0.9.10 (0/17) (0/17) (17/17) codeml 60901.0 29.0 codeml Detects positive selection paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) @@ -604,7 +605,7 @@ disco 369.0 42.0 disco DISCO is a overlap-layout-consensus (OLC) metagenome asse dnabot dnabot DNA assembly using BASIC on OpenTrons To update https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT Synthetic Biology dnabot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot 3.1.0 dnabot (0/1) (0/1) (0/1) dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. Up-to-date https://github.com/Edinburgh-Genome-Foundry/DnaWeaver Synthetic Biology dnaweaver iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver 1.0.2 dnaweaver_synbiocad 1.0.2 (0/1) (0/1) (0/1) dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes Gene functional annotation Metagenomics, Biological databases, Molecular genetics To update https://github.com/WrightonLabCSU/DRAM Metagenomics dram iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram 1.3.5 dram 1.4.6 (0/5) (0/5) (5/5) -drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis Up-to-date https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep 3.4.5 drep 3.4.5 (0/2) (0/2) (2/2) +drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Genome comparison Metagenomics, Genomics, Sequence analysis To update https://github.com/MrOlm/drep Metagenomics drep iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep 3.4.5 drep 3.5.0 (0/2) (0/2) (2/2) dropletutils 3934.0 126.0 dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Transcriptomics, Sequence Analysis dropletutils iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ 1.10.0 bioconductor-dropletutils 1.22.0 (1/1) (1/1) (1/1) ebi_tools ebi_metagenomics_run_downloader, ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases To update http://www.ebi.ac.uk/services/all Web Services, Data Source ebi_tools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools 0.1.0 six (2/2) (0/2) (2/2) edger 18522.0 945.0 edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger 3.36.0 bioconductor-edger 4.0.2 (1/1) (1/1) (1/1) @@ -1297,7 +1298,7 @@ sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Sin sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.0.5 r-sceasy 0.0.7 (1/1) (0/1) (1/1) scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.6.3 scmap-cli 0.1.0 (0/7) (0/7) (7/7) scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 1.0.2 scpred-cli 0.1.0 (0/4) (0/4) (4/4) -seurat 1543.0 66.0 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_normalise_data, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_scale_data De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ 0.3.0 seurat-scripts 4.0.0 (0/13) (0/13) (12/13) +seurat 1543.0 66.0 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 Up-to-date https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa 4.0.0 seurat-scripts 4.0.0 (0/19) (0/19) (12/19) ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml 1.0.0+galaxy1 ucsc-cell-browser 1.2.5 (0/1) (0/1) (1/1) biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 (0/1) (1/1) (1/1) filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) diff --git a/results/index.html b/results/index.html index 59fc2011..92d93957 100644 --- a/results/index.html +++ b/results/index.html @@ -7011,10 +7011,10 @@ flye - 2.9.1 + 2.9.3 2.9.3 flye - To update + Up-to-date @@ -7022,7 +7022,7 @@ Assembly of long and error-prone reads. - To update + Up-to-date https://github.com/fenderglass/Flye/ Assembly flye @@ -11838,6 +11838,27 @@ devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw + + + cnv-phenopacket + 1.0.2 + + cnv-phenopacket + To update + + + + + cnv-phenopacket Converts TSV metadata file to JSON. + + + To update + https://pypi.org/project/cnv-phenopacket/ + Variant Analysis + cnv_phenopacket + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket + cnv-vcf2json @@ -12703,9 +12724,9 @@ drep 3.4.5 - 3.4.5 + 3.5.0 drep - Up-to-date + To update drep dRep Genome comparison @@ -12713,7 +12734,7 @@ dRep compares and dereplicates genome sets Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. - Up-to-date + To update https://github.com/MrOlm/drep Metagenomics drep @@ -27045,10 +27066,10 @@ seurat - 0.3.0 + 4.0.0 4.0.0 seurat-scripts - To update + Up-to-date @@ -27056,12 +27077,12 @@ De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 - To update - + Up-to-date + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa - https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ +