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view fasta_formatter.xml @ 2:9457a20156db draft
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author | devteam |
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date | Mon, 12 Oct 2015 10:15:31 -0400 |
parents | 1dbb5181c327 |
children | 859422bcb689 |
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<tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width"> <description>formatter</description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> <!-- Note: fasta_formatter also has a tabular output mode (-t), but Galaxy already contains such a tool, so no need to offer the user a duplicated tool. So this XML tool only changes the width (line-wrapping) of a FASTA file. --> <command> <![CDATA[ zcat -f < '$input' | fasta_formatter -w $width -o '$output' ]]> </command> <inputs> <param format="fasta" name="input" type="data" label="Library to re-format" /> <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> </inputs> <outputs> <data format="fasta" name="output" metadata_source="input" /> </outputs> <tests> <test> <!-- Re-format a FASTA file into a single line --> <param name="input" value="fasta_formatter1.fasta" /> <param name="width" value="0" /> <output name="output" file="fasta_formatter1.out" /> </test> <test> <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes --> <param name="input" value="fasta_formatter1.fasta" /> <param name="width" value="60" /> <output name="output" file="fasta_formatter2.out" /> </test> </tests> <help> **What it does** This tool re-formats a FASTA file, changing the width of the nucleotides lines. **TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line. -------- **Example** Input FASTA file (each nucleotides line is 50 characters long):: >Scaffold3648 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT >Scaffold9299 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG aactggtctttacctTTAAGTTG Output FASTA file (with width=80):: >Scaffold3648 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA ATTTTAATGAACATGTAGTAAAAACT >Scaffold9299 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG Output FASTA file (with width=0 => single line):: >Scaffold3648 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT >Scaffold9299 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> </tool>