diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml index 05b771f4..8f5c0469 100644 --- a/communities/microgalaxy/lab/sections/5_tools.yml +++ b/communities/microgalaxy/lab/sections/5_tools.yml @@ -8,703 +8,703 @@ tabs: description_md: |- Tools to compute and analyse biodiversity metrics - title_md: TreeBest description_md: |- TreeBeST best - title_md: abacas description_md: |- Order and Orientate Contigs - title_md: abricate description_md: |- Mass screening of contigs for antiobiotic resistance genes - title_md: abritamr description_md: |- A pipeline for running AMRfinderPlus and collating results into functional classes - title_md: abyss description_md: |- Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler - title_md: aldex2 description_md: |- Performs analysis Of differential abundance taking sample variation into account - title_md: amplican description_md: |- AmpliCan is an analysis tool for genome editing. - title_md: amrfinderplus description_md: |- "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms. - title_md: ancombc description_md: |- Performs analysis of compositions of microbiomes with bias correction. - title_md: antismash description_md: |- Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters - title_md: artic description_md: |- The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building - title_md: assemblystats description_md: |- Summarise an assembly (e.g. N50 metrics) - title_md: bakta description_md: |- "Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis." - title_md: bamtools description_md: |- Operate on and transform BAM datasets in various ways using bamtools - title_md: bandage description_md: |- Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily - title_md: bayescan description_md: |- Detecting natural selection from population-based genetic data - title_md: bbtools description_md: |- BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. - title_md: bigscape description_md: |- Construct sequence similarity networks of BGCs and groups them into GCF - title_md: binning_refiner description_md: |- Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. - title_md: biohansel description_md: |- Heidelberg and Enteritidis SNP Elucidation - title_md: biom_format description_md: |- The biom-format package provides a command line interface and Python API for working with BIOM files. - title_md: biotradis description_md: |- Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. - title_md: blast2go description_md: |- Maps BLAST results to GO annotation terms - title_md: blast_rbh description_md: |- BLAST Reciprocal Best Hits (RBH) from two FASTA files - title_md: blastxml_to_top_descr description_md: |- Make table of top BLAST match descriptions - title_md: bracken description_md: |- Bayesian Reestimation of Abundance with KrakEN - title_md: busco description_md: |- BUSCO assess genome and annotation completeness - title_md: cat description_md: |- Contig Annotation Tool (CAT) - title_md: cd_hit_dup description_md: |- simple tool for removing duplicates from sequencing reads - title_md: cdhit description_md: |- Cluster or compare biological sequence datasets - title_md: cemitool description_md: |- Gene co-expression network analysis tool - title_md: checkm description_md: |- Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes - title_md: clair3 description_md: |- Symphonizing pileup and full-alignment for high-performance long-read variant calling - title_md: clinod description_md: |- NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins - title_md: clustalw description_md: |- ClustalW multiple sequence alignment program for DNA or proteins - title_md: cmsearch_deoverlap description_md: |- removes lower scoring overlaps from cmsearch results. - title_md: codeml description_md: |- Detects positive selection - title_md: cojac description_md: |- co-occurrence of mutations on amplicons - title_md: combine_assembly_stats description_md: |- Combine multiple Assemblystats datasets into a single tabular report - title_md: combine_metaphlan_humann description_md: |- Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances - title_md: compare_humann2_output description_md: |- Compare outputs of HUMAnN2 for several samples and extract similar and specific information - title_md: compleasm description_md: |- Compleasm: a faster and more accurate reimplementation of BUSCO - title_md: concoct description_md: |- CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. - title_md: coverm description_md: |- CoverM genome and contig wrappers - title_md: cryptogenotyper description_md: |- CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. - title_md: cutadapt description_md: |- Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). - title_md: dada2 description_md: |- DADA2 wrappers - title_md: das_tool description_md: |- DAS Tool for genome resolved metagenomics - title_md: deseq2 description_md: |- Differential gene expression analysis based on the negative binomial distribution - title_md: diamond description_md: |- DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. - title_md: disco description_md: |- DISCO is a overlap-layout-consensus (OLC) metagenome assembler - title_md: dram description_md: |- DRAM for distilling microbial metabolism to automate the curation of microbiome function - title_md: drep description_md: |- dRep compares and dereplicates genome sets - title_md: ectyper description_md: |- EC-Typer - in silico serotyping of Escherichia coli species - title_md: effectiveT3 description_md: |- Find bacterial type III effectors in protein sequences - title_md: eggnog_mapper description_md: |- eggnog-mapper fast functional annotation of novel sequences - title_md: emboss_5 description_md: |- Galaxy wrappers for EMBOSS version 5.0.0 tools - title_md: ete description_md: |- Analyse phylogenetic trees using the ETE Toolkit - title_md: export2graphlan description_md: |- export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn - title_md: ez_histograms description_md: |- ggplot2 histograms and density plots - title_md: fargene description_md: |- fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) - title_md: fastani description_md: |- Fast alignment-free computation of whole-genome Average Nucleotide Identity - title_md: fastk description_md: |- FastK: A K-mer counter (for HQ assembly data sets) - title_md: fastp description_md: |- Fast all-in-one preprocessing for FASTQ files - title_md: fastqe description_md: |- FASTQE - title_md: fasttree description_md: |- FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL - title_md: featurecounts description_md: |- featureCounts counts the number of reads aligned to defined masked regions in a reference genome - title_md: filter_spades_repeats description_md: |- Remove short and repeat contigs/scaffolds - title_md: filtlong description_md: |- Filtlong - Filtering long reads by quality - title_md: flashlfq description_md: |- FlashLFQ mass-spectrometry proteomics label-free quantification - title_md: flye description_md: |- Assembly of long and error-prone reads. - title_md: format_metaphlan2_output description_md: |- Format MetaPhlAn2 output to extract abundance at different taxonomic levels - title_md: fraggenescan description_md: |- Tool for finding (fragmented) genes in short read - title_md: freyja description_md: |- lineage abundances estimation - title_md: frogs description_md: |- Suite for metabarcoding analysis - title_md: funannotate description_md: |- Funannotate is a genome prediction, annotation, and comparison software package. - title_md: getmlst description_md: |- Download MLST datasets by species from pubmlst.org - title_md: ggplot2 description_md: |- ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. - title_md: gi2taxonomy description_md: |- Fetch taxonomic representation - title_md: glimmer description_md: |- Glimmer makes gene predictions. - title_md: glimmer_hmm description_md: |- @@ -715,169 +715,169 @@ tabs: description_md: |- Performs GO Enrichment analysis. - title_md: goseq description_md: |- goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data - title_md: graphlan description_md: |- GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees - title_md: graphmap description_md: |- Mapper for long, error-prone reads. - title_md: gtdbtk description_md: |- GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. - title_md: gubbins description_md: |- Gubbins - bacterial recombination detection - title_md: hamronization description_md: |- Convert AMR gene detection tool output to hAMRonization specification format. - title_md: hansel description_md: |- Heidelberg and Enteritidis SNP Elucidation - title_md: hifiasm_meta description_md: |- A hifiasm fork for metagenome assembly using Hifi reads. - title_md: hivtrace description_md: |- An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. - title_md: hmmer3 description_md: |- HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). - title_md: humann description_md: |- HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution - title_md: hyphy description_md: |- Hypothesis Testing using Phylogenies - title_md: hypo description_md: |- Super Fast & Accurate Polisher for Long Read Genome Assemblies - title_md: icescreen description_md: |- ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. - title_md: idba_ud description_md: |- Wrappers for the idba assembler variants. - title_md: infernal description_md: |- Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. - title_md: instrain description_md: |- InStrain is a tool for analysis of co-occurring genome populations from metagenomes - title_md: integron_finder description_md: |- "IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching" - title_md: interproscan description_md: |- Interproscan queries the interpro database and provides annotations. - title_md: iprscan5 description_md: |- @@ -888,1441 +888,1441 @@ tabs: description_md: |- Efficient phylogenomic software by maximum likelihood - title_md: isescan description_md: |- "ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements." - title_md: itsx description_md: |- ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. - title_md: ivar description_md: |- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing - title_md: jbrowse description_md: |- JBrowse Genome Browser integrated as a Galaxy Tool - title_md: jellyfish description_md: |- Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA - title_md: kat_filter description_md: |- Filtering kmers or reads from a database of kmers hashes - title_md: kc-align description_md: |- Kc-Align custom tool - title_md: khmer description_md: |- In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more - title_md: kleborate description_md: |- Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) - title_md: kofamscan description_md: |- Gene function annotation tool based on KEGG Orthology and hidden Markov model - title_md: kraken description_md: |- Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. - title_md: kraken2 description_md: |- Kraken2 for taxonomic designation. - title_md: kraken2tax description_md: |- Convert Kraken output to Galaxy taxonomy data. - title_md: kraken_biom description_md: |- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) - title_md: kraken_taxonomy_report description_md: |- Kraken taxonomy report - title_md: krakentools description_md: |- KrakenTools is a suite of scripts to be used alongside the Kraken - title_md: krocus description_md: |- Predict MLST directly from uncorrected long reads - title_md: lca_wrapper description_md: |- Find lowest diagnostic rank - title_md: legsta description_md: |- Performs in silico Legionella pneumophila sequence based typing. - title_md: lighter description_md: |- Lighter is a kmer-based error correction method for whole genome sequencing data - title_md: limma_voom description_md: |- Perform RNA-Seq differential expression analysis using limma voom pipeline - title_md: lineagespot description_md: |- Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) - title_md: lorikeet description_md: |- Tools for M. tuberculosis DNA fingerprinting (spoligotyping) - title_md: lotus2 description_md: |- LotuS2 OTU processing pipeline - title_md: m6anet description_md: |- m6anet to detect m6A RNA modifications from nanopore data - title_md: maaslin2 description_md: |- MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. - title_md: mafft description_md: |- Multiple alignment program for amino acid or nucleotide sequences - title_md: make_nr description_md: |- Make a FASTA file non-redundant - title_md: maker description_md: |- MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. - title_md: mapseq description_md: |- fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. - title_md: mash description_md: |- Fast genome and metagenome distance estimation using MinHash - title_md: maxbin2 description_md: |- clusters metagenomic contigs into bins - title_md: maxquant description_md: |- wrapper for MaxQuant - title_md: mcl description_md: |- The Markov Cluster Algorithm, a cluster algorithm for graphs - title_md: medaka description_md: |- Sequence correction provided by ONT Research - title_md: megahit description_md: |- An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. - title_md: megahit_contig2fastg description_md: |- A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) - title_md: megan description_md: |- MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). - title_md: meningotype description_md: |- Assign sequence type to N. meningitidis genome assemblies - title_md: merqury description_md: |- Merqury is a tool for evaluating genomes assemblies based of k-mer operations. - title_md: meryl description_md: |- Meryl a k-mer counter. - title_md: metabat2 description_md: |- MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. - title_md: metaeuk description_md: |- MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. - title_md: metagene_annotator description_md: |- MetaGeneAnnotator gene-finding program for prokaryote and phage - title_md: metagenomeseq description_md: |- metagenomeSeq Normalization - title_md: metanovo description_md: |- Produce targeted databases for mass spectrometry analysis. - title_md: metaphlan description_md: |- MetaPhlAn for Metagenomic Phylogenetic Analysis - title_md: metaquantome description_md: |- quantitative analysis of microbiome taxonomy and function - title_md: metawrapmg description_md: |- A flexible pipeline for genome-resolved metagenomic data analysis - title_md: minia description_md: |- Short-read assembler based on a de Bruijn graph - title_md: miniasm description_md: |- Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) - title_md: minipolish description_md: |- Polishing miniasm assemblies - title_md: miniprot description_md: |- Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. - title_md: mitos description_md: |- de-novo annotation of metazoan mitochondrial genomes - title_md: mlst description_md: |- Scan contig files against PubMLST typing schemes - title_md: mob_suite description_md: |- MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies - title_md: mothur description_md: |- Mothur wrappers - title_md: mrbayes description_md: |- A program for the Bayesian estimation of phylogeny. - title_md: msconvert description_md: |- msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container - title_md: msstatstmt description_md: |- MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling - title_md: multigsea description_md: |- GSEA-based pathway enrichment analysis for multi-omics data - title_md: multiqc description_md: |- MultiQC aggregates results from bioinformatics analyses across many samples into a single report - title_md: mykrobe description_md: |- Antibiotic resistance predictions - title_md: mykrobe_parser description_md: |- RScript to parse the results of mykrobe predictor. - title_md: mz_to_sqlite description_md: |- Creates a SQLite database for proteomics data - title_md: nanocompore description_md: |- Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. - title_md: nanoplot description_md: |- Plotting tool for long read sequencing data and alignments - title_md: nanopolishcomp description_md: |- NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. - title_md: ncbi_blast_plus description_md: |- NCBI BLAST+ - title_md: ncbi_fcs_gx description_md: |- FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). - title_md: newick_utils description_md: |- Perform operations on Newick trees - title_md: nextclade description_md: |- Identify differences between your sequences and a reference sequence used by Nextstrain - title_md: nextdenovo description_md: |- String graph-based de novo assembler for long reads - title_md: nonpareil description_md: |- Estimate average coverage in metagenomic datasets - title_md: nucleosome_prediction description_md: |- Prediction of Nucleosomes Positions on the Genome - title_md: nugen_nudup description_md: |- Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. - title_md: obisindicators description_md: |- Compute biodiveristy indicators for marine data from obis - title_md: obitools description_md: |- OBITools is a set of programs developed to simplify the manipulation of sequence files - title_md: omark description_md: |- Proteome quality assessment software - title_md: orfipy description_md: |- Galaxy wrapper for ORFIPY - title_md: orthofinder description_md: |- Accurate inference of orthologous gene groups made easy - title_md: peptideshaker description_md: |- PeptideShaker and SearchGUI - title_md: pfamscan description_md: |- Search a FASTA sequence against a library of Pfam HMM. - title_md: pharokka description_md: |- rapid standardised annotation tool for bacteriophage genomes and metagenomes - title_md: phyloseq description_md: |- Handling and analysis of high-throughput microbiome census data - title_md: phyml description_md: |- PhyML is a phylogeny software based on the maximum-likelihood principle. - title_md: picrust description_md: |- PICRUSt wrappers - title_md: picrust2 description_md: |- PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States - title_md: plasflow description_md: |- PlasFlow - Prediction of plasmid sequences in metagenomic contigs. - title_md: plasmidfinder description_md: |- "PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage" - title_md: plasmidspades description_md: |- Genome assembler for assemblying plasmid - title_md: polypolish description_md: |- "Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." - title_md: prodigal description_md: |- A protein-coding gene prediction software tool for bacterial and archaeal genomes - title_md: prokka description_md: |- Rapid annotation of prokaryotic genomes - title_md: promer description_md: |- Aligns two sets of contigs and reports amino acid substitutions between them - title_md: proteinortho description_md: |- Proteinortho is a tool to detect orthologous proteins/genes within different species. - title_md: pycoqc description_md: |- QC metrics for ONT Basecalling - title_md: pygenometracks description_md: |- pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. - title_md: qiime_add_on description_md: |- QIIME to perform microbial community analysis - title_md: qiime_core description_md: |- QIIME to perform microbial community analysis - title_md: qualimap description_md: |- Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. - title_md: quast description_md: |- Quast (Quality ASsessment Tool) evaluates genome assemblies. - title_md: quickmerge description_md: |- Merge long-read and hybrid assemblies to increase contiguity - title_md: rRNA description_md: |- Identification of ribosomal RNA genes in metagenomic fragments. - title_md: racon description_md: |- Consensus module for raw de novo DNA assembly of long uncorrected reads. - title_md: rasusa description_md: |- Randomly subsample sequencing reads to a specified coverage - title_md: raxml description_md: |- RAxML - A Maximum Likelihood based phylogenetic inference - title_md: read_it_and_keep description_md: |- Rapid decontamination of SARS-CoV-2 sequencing reads - title_md: reago description_md: |- Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. - title_md: recentrifuge description_md: |- "With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." - title_md: repeatexplorer2 description_md: |- Tool for annotation of repeats from unassembled shotgun reads. - title_md: roary description_md: |- Roary the pangenome pipeline - title_md: rseqc description_md: |- an RNA-seq quality control package - title_md: salmon description_md: |- Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. - title_md: sarscov2formatter description_md: |- sarscov2formatter custom script - title_md: sarscov2summary description_md: |- sarscov2summary custom script - title_md: scoary description_md: |- Scoary calculates the assocations between all genes in the accessory genome and the traits. - title_md: semibin description_md: |- SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks - title_md: seqkit description_md: |- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation - title_md: seqprep description_md: |- Tool for merging paired-end Illumina reads and trimming adapters. - title_md: seqsero2 description_md: |- Salmonella serotype prediction from genome sequencing data - title_md: shorah description_md: |- Reconstruct haplotypes using ShoRAH in amplicon mode - title_md: shovill description_md: |- Faster de novo assembly pipeline based around Spades - title_md: sistr_cmd description_md: |- SISTR in silico serotyping tool - title_md: smallgenomeutilities description_md: |- Set of utilities for manipulating small viral genome data. - title_md: smalt description_md: |- SMALT aligns DNA sequencing reads with a reference genome. - title_md: snap description_md: |- SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. - title_md: snippy description_md: |- Contains the snippy tool for characterising microbial snps - title_md: sonneityping description_md: |- Scripts for parsing Mykrobe predict results for Shigella sonnei. - title_md: sortmerna description_md: |- SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. - title_md: spades description_md: |- SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. - title_md: spotyping description_md: |- SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads - title_md: sr_bowtie description_md: |- bowtie wrapper tool to align small RNA sequencing reads - title_md: srst2 description_md: |- Short Read Sequence Typing for Bacterial Pathogens - title_md: srst2 description_md: |- SRST2 Short Read Sequence Typing for Bacterial Pathogens - title_md: staramr description_md: |- Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. - title_md: stringmlst description_md: |- Rapid and accurate identification of the sequence type (ST) - title_md: structure description_md: |- for using multi-locus genotype data to investigate population structure. - title_md: suite_qiime2__alignment description_md: |- nan - title_md: suite_qiime2__composition description_md: |- nan - title_md: suite_qiime2__cutadapt description_md: |- nan - title_md: suite_qiime2__dada2 description_md: |- nan - title_md: suite_qiime2__deblur description_md: |- nan - title_md: suite_qiime2__demux description_md: |- nan - title_md: suite_qiime2__diversity description_md: |- nan - title_md: suite_qiime2__diversity_lib description_md: |- nan - title_md: suite_qiime2__emperor description_md: |- nan - title_md: suite_qiime2__feature_classifier description_md: |- nan - title_md: suite_qiime2__feature_table description_md: |- nan - title_md: suite_qiime2__fragment_insertion description_md: |- nan - title_md: suite_qiime2__longitudinal description_md: |- nan - title_md: suite_qiime2__metadata description_md: |- nan - title_md: suite_qiime2__phylogeny description_md: |- nan - title_md: suite_qiime2__quality_control description_md: |- nan - title_md: suite_qiime2__quality_filter description_md: |- nan - title_md: suite_qiime2__rescript description_md: |- nan - title_md: suite_qiime2__sample_classifier description_md: |- nan - title_md: suite_qiime2__taxa description_md: |- nan - title_md: suite_qiime2__vsearch description_md: |- nan - title_md: suite_qiime2_core description_md: |- @@ -2333,167 +2333,167 @@ tabs: description_md: |- nan - title_md: t2ps description_md: |- Draw phylogeny - title_md: t2t_report description_md: |- Summarize taxonomy - title_md: t_coffee description_md: |- T-Coffee - title_md: taxonomy_krona_chart description_md: |- Krona pie chart from taxonomic profile - title_md: tb-profiler description_md: |- Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. - title_md: tooldistillator description_md: |- ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files - title_md: transit description_md: |- TRANSIT - title_md: transtermhp description_md: |- Finds rho-independent transcription terminators in bacterial genomes - title_md: trim_galore description_md: |- Trim Galore adaptive quality and adapter trimmer - title_md: trycycler description_md: |- Trycycler toolkit wrappers - title_md: unicycler description_md: |- Unicycler is a hybrid assembly pipeline for bacterial genomes. - title_md: unipept description_md: |- Unipept retrieves metaproteomics information - title_md: uniprotxml_downloader description_md: |- Download UniProt proteome in XML or fasta format - title_md: usher description_md: |- UShER toolkit wrappers - title_md: valet description_md: |- A pipeline for detecting mis-assemblies in metagenomic assemblies. - title_md: vapor description_md: |- Classify Influenza samples from raw short read sequence data - title_md: varvamp description_md: |- Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses - title_md: vegan description_md: |- an R package fo community ecologist - title_md: velvet description_md: |- de novo genomic assembler specially designed for short read sequencing technologies - title_md: velvet_optimiser description_md: |- Automatically optimize Velvet assemblies - title_md: virAnnot description_md: |- virAnnot wrappers - title_md: vsearch description_md: |- VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. - title_md: wtdbg description_md: |- WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. diff --git a/sources/bin/populate_labs.py b/sources/bin/populate_labs.py index 6327c4a1..45a697d7 100644 --- a/sources/bin/populate_labs.py +++ b/sources/bin/populate_labs.py @@ -58,7 +58,7 @@ def main() -> None: # Create the base URL template for each tool link url_template = ( - "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu/{owner}/{wrapper_id}/{tool_id}" + "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%Frepos%{owner}%{wrapper_id}%{tool_id}" ) # Build HTML list items with links