File and meta tools

Data retrieval

Name Version Galaxy wrapper
EBISearch 0.0.3 suite_ebi_tools
ENASearch 0.1.1 suite_enasearch
NCBI Entrez E-Utilties   suite_ncbi_entrez
NCBI SRA 2.8.1 sra_tools

Text manipulation

Name Version Galaxy wrapper
Paste two files side by side    
Select random lines from a file    
Line/Word/Character count of a dataset    
Filter data on any column using simple expressions    
Sort data in ascending or descending order    
Select lines that match an expression    
Join two datasets side by side on a specified file    
Compare two datasets to find common or distinct rows    
Group data by a column and perform aggregate operation on other columns    
Add column to an existing dataset   add_value
Change case of selected columns   change_case
Column join   column_join
Column Join on Collections   collection_column_join
Compute an expression on every row   column_maker
Concatenate multiple datasets tail-to-head   concatenate_multiple
Convert delimiters to TAB   convert_characters
Cut columns from a table   cut_columns
Merge columns together   merge_cols
Column regex find and replace   regex_find_replace
Remove beginning of a file   remove_beginning
Select first lines from a dataset   show_beginning
Select last lines from a dataset   show_tail
Split file according to the values of a column   split_file_on_column
Unique occurrences of each record   unique
Text processing tools using the GNU coreutils, sed, awk and friends 8.25 text_processing
GNU datamash 1.0.6 suite_datamash

BAM/SAM file manipulation

Name Version Galaxy wrapper
SAMTools 1.2 suite_samtools_1_2

BIOM file manipulation

Name Version Galaxy wrapper
BIOM Format 2.1.5 suite_biom_format


[1]Erik Aronesty. Ea-utils : “Command-line tools for processing biological sequencing data”. 2011. URL:
[2]Daniel Blankenberg, Assaf Gordon, Gregory Von Kuster, Nathan Coraor, James Taylor, Anton Nekrutenko, and the Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics, 26(14):1783–1785, July 2010. URL:, doi:10.1093/bioinformatics/btq281.