.. _framework-tools-manipulation: =================== 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 `_ | +-------------------------------------------------------------------------+---------+-----------------------------------------------------------------------------------------------------+ Sequence file manipulation ========================== +-----------------------------------------------------------------------------------------------------+---------+--------------------------------------------------------------------------------------------------------------+ | 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 :cite:`blankenberg_manipulation_2010` | 0.0.3 | `fastq_paired_end_joiner `_ | +-----------------------------------------------------------------------------------------------------+---------+--------------------------------------------------------------------------------------------------------------+ | FastQ-join :cite:`aronesty_ea-utils_2011` | 0.1.1 | `fastq_join `_ | +-----------------------------------------------------------------------------------------------------+---------+--------------------------------------------------------------------------------------------------------------+ 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 `_ | +---------------------------------------------------------+---------+-----------------------------------------------------------------------------------+ .. rubric:: References .. bibliography:: /assets/references.bib :cited: :style: plain :filter: docname in docnames