<tool id="gap-rem" name="Sequence Gap Remover" version="1.0">
	<description>Removes gap in sequences</description>
	<command interpreter="perl">seqfill.pl $file $question_mark $hyphen $N $usePart $pfile</command>
	<inputs>
		<param format="phylipnon" name="file" type="data" label="File" />
		<param type ="boolean" name="usePart" checked="true" truevalue="true" falsevalue="false" label="Also use Partition File -- if unchecked, it will be ignored." />
		<param format="txt" name="pfile" checked="true" type="data" label="Partition file" />
		<param type="boolean" name="question_mark" checked="true" truevalue="true" falsevalue="false" label="'?' signifies gap" />
		<param type="boolean" name="hyphen" checked="true" truevalue="true" falsevalue="false" label="'-' signifies gap" />
		<param type="boolean" name="N" checked="true" truevalue="true" falsevalue="false" label="'N' signifies gap"/>
	</inputs>

	<outputs>
		<data from_work_dir="out.phylipnon" format="phylipnon" name="out1" label="DATA ${tool.name}" />
		<data from_work_dir="partOut.txt" format="txt" name="out2" label="PARTITION ${tool.name}" />
	</outputs>

	<help>
**What it does**
Sequence Gap Remover

Gaps across all species are introduced by phylocatenator when selecting pre-aligned datasets

Takes an input phylip file and removes any specified gap characters that exist in the same columns of containing sequences.

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**Inputs**

Phylip

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**Outputs**

Text file

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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>