<?xml version="1.0" encoding="utf-8"?>
<tool id="gff_unique_count" name="Count unique seq in GFF" version="@VERSION@">
  <description>Gives the non-redundant count of sequences</description>
  <macros>
    <import>motif_tools_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command><![CDATA[
  perl $__tool_directory__/CountUniqueIDs.pl $input $output
  ]]></command>
  <inputs>
    <param format="gff" name="input" type="data" label="GFF file" help="Select a GFF file."/>
  </inputs>
  <outputs>
    <data format="txt" name="output" />
  </outputs>

  <help>
.. class:: infomark

**What it does**

This tool counts the number non-redundant sequence identifiers (seqname) in a GFF file.  The tool was originally written to read a GFF file containing set of motif matches and report the number of sequences that contain one or more instances of the scanned motif.

----

.. class:: infomark

**Options**

A GFF formated file is required.

----

.. class:: infomark

**Credits**

This Galaxy tool has been developed within the Bioinformatics Core Facility at the University of Manchester. It runs the CountUniqueIDs.pl Perl script that was written by Ian Donaldson.

Please kindly acknowledge both this Galaxy tool and CountUniqueIDs.pl if you use it.
  </help>

</tool>