File and meta tools¶

Data retrieval¶

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

Name	Version	Galaxy wrapper
Filter sequences by id from a tabular file		seq_filter_by_id
Rename sequences with id mapping from a tabular file		seq_rename
Select sequences by id from a tabular file		seq_select_by_id
FastQ to FastA converter		fastq_to_fasta
FastA to Tabular converter		fasta_to_tabular
Split paired end reads		split_paired_reads
Add barcodes to Fasta sequences		fasta_add_barcode
Combine FASTA and QUAL into FASTQ	1.1.0	fastq_combiner
Filter FASTQ reads by quality score and length	1.1.0	fastq_filter
Convert between various FASTQ quality formats	1.1.0	fastq_groomer
Manipulate FASTQ reads on various attributes	1.1.0	fastq_manipulation
FASTQ Masker by quality score	1.1.0	fastq_masker_by_quality
FASTQ de-interlacer on paired end reads	1.1.0	fastq_paired_end_deinterlacer
FASTQ interlacer on paired end reads	1.1.0	fastq_paired_end_interlacer
FASTQ splitter on joined paired end reads	1.1.0	fastq_paired_end_splitter
FASTQ Summary Statistics by column	1.1.0	fastq_stats
FASTQ to Tabular converter	1.1.0	fastq_to_tabular
FASTQ Trimmer by quality	1.1.0	fastq_trimmer
FASTQ to FASTA converter	1.1.0	fastqtofasta
Tabular to FASTQ converter	1.1.0	tabular_to_fastq
FastQ joiner [2]	0.0.3	fastq_paired_end_joiner
FastQ-join [1]	0.1.1	fastq_join

Name	Version	Galaxy wrapper
SAMTools	1.2	suite_samtools_1_2

Name	Version	Galaxy wrapper
BIOM Format	2.1.5	suite_biom_format

References

[1]	Erik Aronesty. Ea-utils : “Command-line tools for processing biological sequencing data”. 2011. URL: http://code.google.com/p/ea-utils.

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: http://bioinformatics.oxfordjournals.org/content/26/14/1783, doi:10.1093/bioinformatics/btq281.