This repository contains tools that can be installed from the Galaxy Tool Shed Galaxy Tool Shed for use within Galaxy.

• Corals - Baums lab at Penn State University

  • affy_ids_for_genotyping - extracts the Affymetrix ids from a VCF file for genotyping.
  • coral_multilocus_genotype - renders the unique combination of the alleles for two or more loci for each individual. The multilocus genotypes are critically important for tracking dispersal and population structure of organisms, especially those that reproduce clonally (plants, sponges, cnidarians, flatworms, annelids, sea stars, and many more).
  • ensure_synced - compares a list of Affymetrix ids from a vcf file with those in a database table for equivalency.
  • export_all_sample_data - generates a tabular dataset of all samples and associated metadata in the stag database.
  • genotype_population_info - generates the genotype population information file for use as input to the coral_multilocus_genotype tool.
  • queue_genotype_workflow - uses the Galaxy REST API to execute the complete multilocus genotype pipeline for corals or symbiants.
  • update_stag_database - updates the corals (stag) database tables from a dataset collection.
  • validate_affy_metadata - validates an Affymetrix metadata file for 96 well plate data.

• ChIP-seq - Mahony lab at Penn State University

  • MultiGPS - a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing differential binding events between conditions. MultiGPS encourages consistency in the reported binding event locations across conditions and provides accurate estimation of ChIP enrichment levels at each event.

• Entomology - Fleischer lab at Penn State University

  • Temperature data for insect phenology model - data source tool for retrieving temperature data from the remote data source Pestwatch
  • Insect phenology model - an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
  • Extract date interval from insect phenology model data - extracts a date interval from the data produced by the Insect Phenology Model tool, providing a "zoomed in" view of the plots.

• PlantTribes - PlantTribes pipelines from the DePamphillis lab at Penn State University.

  • Load PlantTribes Scaffold - analyzes scaffolds installed into Galaxy by the PlantTribes Scaffolds Downloader data manager tool and inserts information about them into the Galaxy PlantTribes database for querying and additional analysis.
  • Update PlantTribes Scaffold - adds a new genome to a scaffold installed into Galaxy by the PlantTribes Scaffolds Downloader data manager tool.
  • AssemblyPostProcessor - post-processes de novo assembled transcripts into putative coding sequences and their corresponding amino acid translations and optionally assigns transcripts to circumscribed gene families (orthogroups).
  • GeneFamilyClassifier - classifies gene coding sequences either produced by the AssemblyPostProcessor tool or from an external source into pre-computed orthologous gene family clusters (orthogroups) of a PlantTribes scaffold.
  • GeneFamilyIntegrator - integrates PlantTribes scaffold orthogroup backbone gene models with gene coding sequences classified into the scaffold by the GeneFamilyClassifier tool.
  • GeneFamilyAligner - estimates protein and codon multiple sequence alignments of integrated orthologous gene family fasta files produced by the GeneFamilyIntegrator tool.
  • GeneFamilyPhylogenyBuilder - performs gene family phylogenetic inference of multiple sequence alignments produced by the GeneFamilyAligner tool.
  • KaKsAnalysis - estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates for a set of gene coding sequences either produced by the AssemblyPostProcessor tool or from an external source.
  • KsDistribution - uses the analysis results produced by the KaKsAnalysis tool to plot the distribution of synonymous substitution (Ks) rates and fit the estimated significant normal mixtures component(s) onto the distribution.

• Epigenetics - IDEAS pipeline from the Zhang lab at Penn State University

  • IDEAS Preprocessor - maps a list of epigenetic datasets to a common genomic coordinate in a selected assembly, producing datasets for use as input to IDEAS.
  • IDEAS - an Integrateive and Discriminitive Epigenome Annotation System that identifies de novo regulatory functions from epigenetic data in multiple cell types jointly.
  • IDEAS Genome Tracks - creates UCSC Genome Browser Track Hubs for vizualizing IDEAS outputs.

• Sequence Analysis - USDA vSNP

  • vSNP sample names - accepts fastqsanger sample files, extracts a unique portion of the file name as the sample name, and writes it to the output. The output text file can be consumed by the Parse parameter value expression tool to provide workflow parameter values to the Read group identifier (ID) and the Sample name identifier (SM) parameters in the Map with BWA-MEM tool.
  • vSNP add zero coverafge - accepts a combination of single BAM and associated VCF files (or associated collections of each) to produce a VCF file for each combination whose positions with no coverage are represented as "N". These outputs are restricted to SNPs and those regions along the reference with no coverage.
  • vSNP determine reference from data - accepts a single fastqsanger read, a set of paired reads, or a collection of single or paired reads (bacterial samples) and inspects the data to discover the best reference genome for aligning the reads.
  • vSNP statistics - accepts associated fastq files, SAMtools idxstats files and vSNP add zero coverage metrics files and extracts information from them to produce an Excel spreadsheet containing statistics for each sample.
  • vSNP get SNPs - accepts a zero coverage VCF file produced by the vSNP: add zero coverage tool (or a collection of them) along with a collection of zero coverage VCF files that have been aligned with the same reference and contain SNPs called between closely related isolate groups. The tool produces fasta files containing SNP alignments, json files containing the SNP positions and additional json files containing the average map quality values.
  • vSNP build tables - accepts a combination of single SNPs json, average MQ json and newick files (or associated collections of each) to produce annotated SNPs tables in the form of Excel spreadsheets.