--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/gap-rem.xml	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,57 @@
+<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.
+
+------
+
+**Inputs**
+
+Phylip
+
+------
+
+**Outputs**
+
+Text file
+
+------
+
+**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
+
+-------
+
+**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>