/tools/fastx_toolkit/fasta_formatter.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 87 lines · 57 code · 19 blank · 11 comment · 0 complexity · 8b921702d94023ab58dc11d8f4df842c MD5 · raw file
- <tool id="cshl_fasta_formatter" name="FASTA Width">
- <description>formatter</description>
- <requirements><requirement type="package">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" 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>
- <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>
- <outputs>
- <data format="input" 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>