<tool id="beautify_fasta" name="Beautify_FASTA" version="1.0">
    <description>Converts interleaved FASTA to non-interleaved</description>
    <command interpreter="perl">
		beautify_fasta.pl $infile $outfile $delpipes $convgi $delslash $renumber $space
    </command>
    <inputs>
	    <param name="infile" type="data" format="fasta" label="Input File" help="fasta file to convert" />
	    <param name='delpipes' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Convert Pipes' help='Convert pipe symbols in fasta sequence id to space.'/>
	    <param name='convgi' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Convert gi|' help='Converts instances of gi| to gi_.'/>
	    <param name='delslash' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Convert slash \ ' help='Converts instances of \ to _.'/>
	    <param name='renumber' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Add a unique number' help='Sequentially add a unique number to beginning of each sequence.'/>
	    <param name='space' type='boolean' checked='no' truevalue='yes' falsevalue='no' label='Add a unique number' help='Add a space after the unique number.'/>
    </inputs>
    <outputs>
	<data format="fasta" name="outfile" label="${tool.name} on ${on_string}: Out file" />
    </outputs>
    <help>**What it does**

Input an interleaved FASTA file. Beautify_FASTA converts interleaved FASTA to
non-interleaved (full sequence on one line). In addition, you can choose to
convert symbols from the FASTA ID. The FASTA ID is the descriptor from the >
to the first space. The FASTA description (first line after any space) is not changed.

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**Inputs**

Interleaved FASTA file.

------

**Outputs**

Non-interleaved FASTA file with optional modifications to the FASTA ID.

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**Additional Information**

Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the 
osiris_phylogenetics site at bitbucket.org

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**Citations**

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please 
consider citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html

    </help>
</tool>