<tool id="remove_phytab_dupes" name="remove_phytab_dupes" version="1.0">
    <description> Finds duplicates in phytab format files </description>
    <command interpreter="perl">
        remove_phytab_dupes.pl $infile $keeplongest $ignoregaps $okfile $dupefile 
    </command>
    <inputs>
        <param format="tabular" name="infile" type="data" label="Phytab Input file" help=""/>
    <param name="keeplongest" type="select" optional="false" label="Keep which duplicate?">
      <option value="1">Keep Longest Duplicate</option>
      <option value="0">Keep First Duplicate in File</option>
    </param>
        <param name='ignoregaps' type='boolean' checked='true' falsevalue ='0' truevalue='1' label='Ignore Gaps' help='Whether to ignore gaps when calculating length for which duplicate to retain. Gaps not removed from file.'/>
    </inputs>
    <outputs>
	<data format="tabular" name="okfile" label="Unique phytab lines from ${on_string}" />
	<data format="tabular" name="dupefile" label="Duplicated phytab lines from ${on_string}" />
    </outputs>
    <help>
**What it does**

Finds lines with identical species (column 1) and partition (column 2) and writes on of the duplicates to one file, unique lines to another file.

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**Inputs**

1. PHYTAB format input file.
2. Choose whether to keep the longest or first sequence of a duplicated species in output file one. 
3. Choose whether to ignore gap characters (-) when comparing length of sequences for input #2.

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**Outputs**

Two PHYTAB format files. One contains only unique species. The other contains duplicates. 

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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>