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April 2015 Tool Shed Contributions

Tools contributed to the Galaxy Project Tool Shed in April 2015.

In no particular order:

New Tools


  • From arkarachai-fungtammasan:

    • str_fm: Pipeline to profile and genotype microsatellites from short read data This repository contains three sets of tools: 1 create microsatellite length profile, 2 correct for sequencing errors and report genotype, 3 estimate minimum sequencing read depth.

  • From peterjc:

    • blast_top_hit_species: v0.0.1 Workflow to count species of top nr BLASTX hits of a transcriptome This is a non-trivial example workflow using the NCBI BLAST+ wrappers, intended only for crude crude contamination assessment of a transcriptome assembly.
      This would ideally include a visualisation of the finally tally table as a Pie Chart, currently not possible with the Galaxy Visualization Framework.

  • From devteam:

  • From yutaka-saito:

    • bisulfighter: A pipeline for accurate detection of methylated cytosines and differentially methylated regions A pipeline for accurate detection of methylated cytosines and differentially methylated regions

  • From mir-bioinf:

    • multi_join_left: Joins multiple files serially Use this tool to join multiple tab-delimited files serially on one column; performs a left-join starting with the first file specified (first specified file is printed in full, then only matching lines are printed from each subsequent file).

    • heatmap_colormanipulation: Initial upload Generates heatmap with nonlinear color mapping options Uses R's heatmap.2 function and gplots package. Good for visualization of disparate data.

    • fix_excel_date_symbols: Initial upload Can recover human or mouse gene symbols from dates (usually caused by Excel) When Excel sees a gene symbol like SEPT9, it thinks to itself 'must be a date' and automatically converts it to the date 9-Sep (permanent conversion). As an 'after-the-fact' remedy, this tool converts dates like 9-Sept, 3-March, etc, in the chosen column(s) back to the gene symbols SEPT9 and MARCH3, etc. (respectively).

    • column_range_string_generator: Initial upload Generates column string for input to Cut Columns tool Use this tool to generate a string that can be copied to the buffer then pasted into the Cut Column tool to save time (rather than needing to individually type out C1,C2,C3..... etc.).

  • From galaxyp:


  • From arkarachai-fungtammasan:

  • From devteam:

    • suite_samtools_1_2: A suite of Galaxy utilities associated with version 1.2 of the SAMtools package. SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. This repository suite associates selected repositories containing Galaxy utilities that require version 1.2 of the SAMTools package. These associated Galaxy utilities consist of a Galaxy Data Manager contained in the repository named data_manager_sam_fasta_index_builder and Galaxy tools contained in several separate repositories.


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