Mercurial > repos > devteam > fasta_formatter
diff fasta_formatter.xml @ 0:8f0ae92440b8
Uploaded tool tarball.
author | devteam |
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date | Wed, 25 Sep 2013 10:55:39 -0400 |
parents | |
children | 1dbb5181c327 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta_formatter.xml Wed Sep 25 10:55:39 2013 -0400 @@ -0,0 +1,89 @@ +<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>zcat -f '$input' | fasta_formatter -w $width -o $output</command> + <inputs> + <param format="fasta" version="1.0.0" name="input" type="data" label="Library to re-format" /> + + <param version="1.0.0" name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> + </inputs> + + <tests> + <test> + <!-- Re-format a FASTA file into a single line --> + <param version="1.0.0" name="input" value="fasta_formatter1.fasta" /> + <param version="1.0.0" name="width" value="0" /> + <output version="1.0.0" name="output" file="fasta_formatter1.out" /> + </test> + <test> + <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes --> + <param version="1.0.0" name="input" value="fasta_formatter1.fasta" /> + <param version="1.0.0" name="width" value="60" /> + <output version="1.0.0" name="output" file="fasta_formatter2.out" /> + </test> + </tests> + + <outputs> + <data format="input" version="1.0.0" name="output" metadata_source="input" /> + </outputs> + +<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>