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fetch all tools bot - step merge
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10 changes: 5 additions & 5 deletions results/all_tools.tsv
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Expand Up @@ -451,7 +451,7 @@ column_arrange_by_header 3781.0 179.0 bg_column_arrange_by_header Column arrange
join_files_on_column_fuzzy 2448.0 117.0 join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. To update Text Manipulation join_files_on_column_fuzzy bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 1.0.1 python (0/1) (1/1) (1/1)
split_file_on_column 5507.0 159.0 tp_split_on_column Split a file on a specific column. To update Text Manipulation split_file_on_column bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 0.6 gawk (1/1) (0/1) (1/1)
split_file_to_collection 15358.0 412.0 split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. To update Text Manipulation split_file_to_collection bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.1 python (1/1) (1/1) (1/1)
text_processing 3864895.0 15048.0 tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 9.3 coreutils 8.25 (19/20) (19/20) (19/20)
text_processing 3864895.0 15048.0 tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. To update https://www.gnu.org/software/ Text Manipulation text_processing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 9.3 coreutils 8.25 (19/20) (19/20) (20/20)
tgsgapcloser 460.0 36.0 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 (0/1) (0/1) (1/1)
tool_recommendation_model create_tool_recommendation_model Create model to recommend tools To update https://github.com/bgruening/galaxytools Machine Learning create_tool_recommendation_model bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model 0.0.5 python (1/1) (0/1) (1/1)
trim_galore 238699.0 2334.0 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1)
Expand Down Expand Up @@ -808,7 +808,7 @@ nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based
obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10)
ococo 1877.0 32.0 ococo Variant detection of SNVs Up-to-date https://github.com/karel-brinda/ococo Variant Analysis ococo iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo 0.1.2.6 ococo 0.1.2.6 (1/1) (0/1) (1/1)
odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ 0.3 odgi 0.8.4 (0/2) (0/2) (2/2)
omark omark Proteome quality assessment software To update https://github.com/DessimozLab/OMArk Sequence Analysis omark iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ 0.3.0 (0/1) (0/1) (0/1)
omark omark Proteome quality assessment software To update https://github.com/DessimozLab/OMArk Sequence Analysis omark iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ 0.3.0 (0/1) (0/1) (1/1)
ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 (0/4) (0/4) (4/4)
onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. Up-to-date http://search.cpan.org/~easr/ONTO-PERL-1.45/ Ontology Manipulation onto_toolkit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit 1.45 perl-onto-perl 1.45 (0/18) (0/18) (17/18)
optdoe optdoe Optimal Design Of Experiment To update https://github.com/pablocarb/doebase Synthetic Biology optdoe iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe v2.0.2 doebase (0/1) (0/1) (0/1)
Expand All @@ -831,7 +831,7 @@ pharokka 2565.0 74.0 pharokka rapid standardised annotation tool for bacteriopha
" (0/1) (1/1) (1/1)
phyloseq phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics To update https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html Metagenomics phyloseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq 1.38.0 bioconductor-phyloseq 1.46.0 (0/3) (0/3) (3/3)
phyml 1770.0 104.0 phyml PhyML is a phylogeny software based on the maximum-likelihood principle. phyml PhyML Phylogenetic estimation software using Maximum Likelihood Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Up-to-date http://www.atgc-montpellier.fr/phyml/ Phylogenetics phyml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml 3.3.20220408 phyml 3.3.20220408 (0/1) (1/1) (1/1)
picard 379429.0 3956.0 picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_fastqtosam picard_fastqtosam Create an unaligned BAM file. Formatting Sequencing To update http://broadinstitute.github.io/picard/ SAM picard devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard 2.18.2 picard 3.1.1 (31/31) (31/31) (31/31)
picard 379429.0 3956.0 picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. picard_fastqtosam picard_fastqtosam Create an unaligned BAM file. Formatting Sequencing Up-to-date http://broadinstitute.github.io/picard/ SAM picard devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard 3.1.1 picard 3.1.1 (31/31) (31/31) (31/31)
pick_value 116.0 2.0 pick_value Compose a text parameter value using text, integer and float values To update Text Manipulation pick_value iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 0.2.0 (1/1) (0/1) (1/1)
picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing To update https://picrust.github.io/picrust/ Metagenomics picrust iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust 1.1.1 picrust 1.1.4 (0/6) (6/6) (5/6)
picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7)
Expand Down Expand Up @@ -870,7 +870,7 @@ quickmerge quickmerge Merge long-read and hybrid assemblies to increase contig
raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 0.2.3 r-raceid 0.1.3 (5/5) (5/5) (5/5)
ragtag 2833.0 237.0 ragtag Reference-guided scaffolding of draft genomes tool. ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Genome assembly Sequence assembly Up-to-date https://github.com/malonge/RagTag Assembly ragtag iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag 2.1.0 ragtag 2.1.0 (0/1) (0/1) (1/1)
rapidnj 176.0 14.0 rapidnj Galaxy wrapper for the RapidNJ tool rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. Phylogenetic tree generation Phylogeny Up-to-date https://birc.au.dk/software/rapidnj/ Phylogenetics rapidnj iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj 2.3.2 rapidnj 2.3.2 (1/1) (0/1) (1/1)
rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa Produces an unbiased subsample of your reads Up-to-date https://github.com/mbhall88/rasusa Sequence Analysis rasusa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa 0.8.0 rasusa 0.8.0 (0/1) (0/1) (0/1)
rasusa rasusa Randomly subsample sequencing reads to a specified coverage rasusa rasusa Produces an unbiased subsample of your reads Up-to-date https://github.com/mbhall88/rasusa Sequence Analysis rasusa iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa 0.8.0 rasusa 0.8.0 (0/1) (0/1) (1/1)
raven 6902.0 262.0 raven Raven is a de novo genome assembler for long uncorrected reads. To update https://github.com/lbcb-sci/raven Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven 1.8.0 raven-assembler 1.8.3 (0/1) (1/1) (1/1)
raxml 6808.0 383.0 raxml RAxML - A Maximum Likelihood based phylogenetic inference raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Sequence analysis, Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://www.exelixis-lab.org/web/software/raxml/ Phylogenetics raxml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml 8.2.12 raxml 8.2.13 (1/1) (1/1) (1/1)
rcorrector 569.0 30.0 rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Sequencing error detection RNA, RNA-Seq, Sequencing To update https://github.com/mourisl/Rcorrector Fastq Manipulation rcorrector iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector 1.0.3+galaxy1 rcorrector 1.0.6 (0/1) (0/1) (1/1)
Expand Down Expand Up @@ -1222,7 +1222,7 @@ high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plottin
justdiff justdiff Unix diff To update http://artbio.fr Text Manipulation justdiff artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 3.10+galaxy0 diffutils (0/1) (0/1) (0/1)
justgzip justgzip Compress fastq sequence files To update http://artbio.fr Convert Formats justgzip artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 2.8+galaxy0 pigz (0/1) (0/1) (0/1)
lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow To update http://artbio.fr Variant Analysis lumpy_smoove artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0.2.8+galaxy1 svtyper 0.7.1 (0/2) (0/2) (0/2)
manta 93.0 8.0 manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta 1.6 manta 1.6.0 (0/1) (0/1) (0/1)
manta 93.0 8.0 manta Structural variant and indel caller for mapped sequencing data To update http://artbio.fr Variant Analysis manta artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta 1.6 manta 1.6.0 (0/1) (0/1) (1/1)
mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file To update http://artbio.fr Sequence Analysis, Statistics mapping_quality_stats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0.22.0 r-optparse 1.3.2 (0/1) (0/1) (0/1)
mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts 1.6 tar (0/1) (1/1) (0/1)
mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs Up-to-date http://artbio.fr Variant Analysis mutational_patterns artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 3.12.0 bioconductor-mutationalpatterns 3.12.0 (0/1) (0/1) (0/1)
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6 changes: 3 additions & 3 deletions results/index.html
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Expand Up @@ -17259,18 +17259,18 @@
<tr>
<td></td>
<td>picard</td>
<td>2.18.2</td>
<td>3.1.1</td>
<td>3.1.1</td>
<td>picard</td>
<td>To update</td>
<td>Up-to-date</td>
<td>picard_fastqtosam</td>
<td>picard_fastqtosam</td>
<td>Formatting</td>
<td>Sequencing</td>
<td>Picard SAM/BAM manipulation tools.</td>
<td>Create an unaligned BAM file.</td>
<td></td>
<td>To update</td>
<td>Up-to-date</td>
<td>http://broadinstitute.github.io/picard/</td>
<td>SAM</td>
<td>picard</td>
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