root/galaxy-central/tools/fastx_toolkit/fasta_formatter.xml @ 3

<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
</help>
</tool>