Manipulation toolsΒΆ

Subsection Tool Galaxy wrapper
Name Revision
Manipulate file 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 745871c0b055
Change case of selected columns change_case ecf91530d461
Column join column_join 6bb6c0a30c67
Compute an expression on every row column_maker 626658afe4cb
Concatenate multiple datasets tail-to-head concatenate_multiple 1e06fa2771f9
Convert delimiters to TAB convert_characters 8a53d7f02ce4
Cut columns from a table cut_columns cec635fab700
Merge columns together merge_cols f2aac0c5c60d
Column regex find and replace regex_find_replace 209b7c5ee9d7
Regex find and replace
Remove beginning of a file remove_beginning b3d762515db4
Select first lines from a dataset show_beginning b5af46a99f6e
Select last lines from a dataset show_tail ae45155543e1
Split file according to the values of a column split_file_on_column b60f2452580e
Unique occurrences of each record unique 7ce75adb93be
Normalize a dataset by row or column sum normalize_dataset 72633301cc0d
Extract lines corresponding with minimum and maximum values of a column extract_min_max_lines 90fc00b34716
Manipulate sequence files Filter sequences by id from a tabular file seq_filter_by_id 832c1fd57852
Rename sequences with id mapping from a tabular file seq_rename 7c0642fc57ad
Select sequences by id from a tabular file seq_select_by_id 91f55ee8fea5
FastQ to FastA converter fastq_to_fasta 186b8d913e6c
FastA to Tabular converter fasta_to_tabular 7e801ab2b70e
Split paired end reads split_paired_reads 36163bff76cc
Convert/ Extract information from a sequence file, with possible constraints convert_extract_sequence_file 01c2b74b3a21
Add barcodes to Fasta sequences fasta_add_barcode 04699558a38a
Manipulate BAM/SAM files Copy SAM/BAM header between datasets suite_samtools_1_2 5b673ccc8747
Remove PCR duplicates
Slice BAM by genomic regions
Recalculate MD/NM tags
Generate statistics for BAM dataset
Convert SAM to BAM
Calculate read depth for a set of genomic intervals
Sort BAM dataset
Tabulate descriptive stats for BAM dataset
Convert BAM to SAM
Split BAM dataset on readgroups
Tabulate mapping statistics for BAM dataset
Call variants
Manipulate BIOM files Add metadata to a BIOM table suite_biom_format 8eda049e45c2
Convert BIOM