protk-galaxytools

Galaxy tool wrappers for protk tools. All tools are available on the Galaxy toolshed.

The Tools

• make_protein_decoys: Generate randomised amino acid sequences with the same composition as those from a provided set
• mascot: Run a Mascot search from within Galaxy via your local Mascot server and convert results to pepXML. Toolshed Link
• msgfplus: Run a tandem ms search using the ms-gf+ search engine. Toolshed Link
• omssa: Run a tandem ms search using the omssa search engine. Toolshed Link
• protk-proteogenomics: Map peptides and proteins from a tandem ms search to genomic coordinates.
• sixframe-translate: Generate 6-frame translations of nucleic acid sequences.
• tpp-prophets: Calculate peptide and protein probabilities from tandem ms search results using the TPP tools, peptide prophet, iProphet and protein prophet. Toolshed Link
• xtandem: Run a tandem ms search using the X!Tandem search engine. Toolshed Link
• spectrast: (In Development) Create and filter splib files using spectrast

Datatypes

Many of the tools in this suite depend on the proteomics datatypes repository. If tools are installed via the toolshed this will be automatically installed as well.

Other dependencies

All tools in this repository depend on the protk ruby gem and a wide variety of other open source proteomics software. While protk provides an installer for most of these tools, an easier way to ensure that all these dependencies are satisfied is to enable running tools within Docker on your Galaxy instance. If Galaxy is configured to run tools within docker containers these tools will automatically fetch an appropriate docker image. For details on how we build this image, refer to the protk-dockerfile created by Simon Belluzzo.