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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author | devteam |
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date | Sun, 01 Mar 2020 12:23:22 +0000 |
parents | 5cabbe4cfaf4 |
children | 5b998d13de71 |
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<tool id="fasta2tab" name="FASTA-to-Tabular" version="1.1.1" profile="16.04"> <description>converter</description> <requirements> <requirement type="package" version="3.7">python</requirement> </requirements> <command> python '$__tool_directory__/fasta_to_tabular.py' '$input' '$output' $keep_first $descr_columns </command> <inputs> <param name="input" type="data" format="fasta" label="Convert these sequences"/> <param name="descr_columns" type="integer" value="1" min="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column"> </param> <param name="keep_first" type="integer" value="0" min="0" label="How many title characters to keep?" help="Applies only to the first column taken from the title string ('0' = keep the whole thing), useful when your sequence identifiers are all the same length."> </param> </inputs> <outputs> <data name="output" format="tabular"/> </outputs> <tests> <test> <param name="input" value="454.fasta" /> <param name="descr_columns" value="1"/> <param name="keep_first" value="0"/> <output name="output" file="fasta_to_tabular_out1.tabular" /> </test> <test> <param name="input" value="4.fasta" /> <param name="descr_columns" value="1"/> <param name="keep_first" value="0"/> <output name="output" file="fasta_to_tabular_out2.tabular" /> </test> <test> <param name="input" value="454.fasta" /> <param name="descr_columns" value="1"/> <param name="keep_first" value="14"/> <output name="output" file="fasta_to_tabular_out3.tabular" /> </test> <test> <param name="input" value="454.fasta" /> <param name="descr_columns" value="2"/> <param name="keep_first" value="0"/> <output name="output" file="fasta_to_tabular_out4.tabular" /> </test> <test> <param name="input" value="454.fasta" /> <param name="descr_columns" value="5"/> <param name="keep_first" value="0"/> <output name="output" file="fasta_to_tabular_out5.tabular" /> </test> <test> <param name="input" value="454.fasta" /> <param name="descr_columns" value="5"/> <param name="keep_first" value="10"/> <output name="output" file="fasta_to_tabular_out6.tabular" /> </test> </tests> <help><![CDATA[ **What it does** This tool converts FASTA formatted sequences to TAB-delimited format. Many tools consider the first word of the FASTA ">" title line to be an identifier, and any remaining text to be a free form description. It is therefore useful to split this text into two columns in Galaxy (identifier and any description) by setting **How many columns to divide title string into?** to **2**. In some cases the description can be usefully broken up into more columns -- see the examples . The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry. With the introduction of the **How many columns to divide title string into?** option this setting is of limited use, but does still allow you to truncate the identifier. ----- **Example** Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run:: >EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG >EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAA Running this tool with the default settings will produce this (2 column output): ========================================================================== ======================================= EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA ========================================================================== ======================================= Having the full title line (the FASTA ">" line text) as a column is not always ideal. The **How many characters to keep?** option is useful if your identifiers are all the same length. In this example the identifier is 14 characters, so setting **How many characters to keep?** to **14** (and leaving **How many columns to divide title string into?** as the default, **1**) will produce this (2 column output): ============== ======================================= EYKX4VC02EQLO5 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG EYKX4VC02D4GS2 AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA ============== ======================================= If however your FASTA file has identifiers of variable length, it is better to split the text into at least two columns. Running this tool with **How many columns to divide title string into?** to **2** will produce this (3 column output): ============== =========================================================== ======================================= EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA ============== =========================================================== ======================================= Running this tool with **How many columns to divide title string into?** to **5** will produce this (5 column output): ============== ========== ============ ======== ========================== ======================================= EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA ============== ========== ============ ======== ========================== ======================================= Running this tool with **How many columns to divide title string into?** to **5** and **How many characters to keep?** to **10** will produce this (5 column output). Notice that only the first column is truncated to 10 characters -- and be careful not to trim your sequence names too much (generally they should be unique): ========== ========== ============ ======== ========================== ======================================= EYKX4VC02E length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG EYKX4VC02D length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA ========== ========== ============ ======== ========================== ======================================= Note the sequences have been truncated for display purposes in the above tables. ]]></help> </tool>