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ToolShed/Contributions/2015_08

August 2015 Tool Shed Contributions

Galaxy ToolShed
Tools contributed to the Galaxy Project Tool Shed in August 2015.

In no particular order:

New Tools

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  • From rnateam:

    • sortmerna: (Planemo upload) for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty. SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. SortMeRNA_ is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity. http://bioinfo.lifl.fr/RNA/sortmerna/

    • mea: (Planemo upload) commit 6f0b360c2f718f0d3bd436db0f89af3805d7c332-dirty. Maximum expected accuracy prediction

  • From saskia-hiltemann:

    • virtual_normal_analysis: Compare variants to a large set of normal genomes Compare variants to a large set of normal genomes from healthy, unrelated individuals

    • igv_screenshot Create an IGV screenshot. Given the build, tracks, region, and viewing preferences, creates an IGV screenshot and outputs it as a png image.

  • From anmoljh:

  • From reditama:

    • smart_rda Workflow for RNA-Seq differential expression analysis

  • From lecorguille:

  • From mmonsoor:

    • camera_combinexsannos: (Planemo upload) [W4M][GC-MS] CAMERA R Package - Annotation - combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode Part of the W4M project: http://workflow4metabolomics.org

      • CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html
        This function check annotations of ion species with the help of a sample from opposite ion mode. As first step it searches for pseudospectra from the positive and the negative sample within a retention time window. For every result the m/z differences between both samples are matched against specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion mode with recalculated annotations.
        BEWARE: this tool don't come with its script. You will need to install the dedicated package_camara_w4m_script too

  • From yhoogstrate:

    • crossmap: (Planemo upload) for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb CrossMap: Convert genome coordinates or annotation files between genome assemblies

      • CrossMap is versatile tool to convert genome coordinates or annotation files between genome assemblies. It supports mostly commonly used file types, including BAM, BED, BigWig, GFF, GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF and VCF, reading from remote servers and file compression are supported.
        http://crossmap.sourceforge.net/

    • segmentation_fold: (Planemo upload) for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36 RNA-Folding including predefined segments including K-turns Segmentation-fold is a bioinformatics application that predicts RNA 2D-structure with an extended version of the Zuker algorithm. This modification contains a new "structure element" named a segment and is capable of folding a pre-defined substructure with multiple canonical or non-canonical pairings.

      • This allows folding of more complex structures like the K-turns, which are also part of the implemented free energy tables. These thermodynamic parameters (free Gibbs energy levels) have been estimated using a computational approach and therefore lack accuracy.
  • From devteam:

  • From damion:

    • versioned_data first version This tool enables retrieval of FASTA format databases (by date or version id) that can be set up in a number of archive formats. As well one can trigger workflows like makeblastdb to generate BLAST databases. Results can be cached for reuse by other users who make the same requests. This tool can be used on a server both via the command line and via the Galaxy bioinformatics workflow platform using the "Versioned Data" tool. Different kinds of content are suited to different archiving technologies, so the system provides a few storage system choices. Results are cached so that subsequent requests for the same versioned database or derived data (like a BLAST database) are immediately satisfied.

  • From tgac:

  • From jcl:

    • jclgrr An effort to run grr An effort to run GRR

  • From deleury:

    • wcr WCR experiment WCR experiment

tool_dependency_definition

  • From anmoljh:

  • From cmonjeau:

    • package_stacks_1_18: Imported from capsule None Contains a tool dependency definition that downloads and compiles version 1.18 of Stacks Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

  • From lecorguille:

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tool_dependency_definition