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<?xml version="1.1"?>
<tool id="edu.tamu.cpt2.gff3.remove_fasta" name="Remove FASTA Sequences from .gff3 File" version="1.1">
    <description>Removes FASTA sequences at the end of .gff3 file. All lines after '##FASTA' deleted</description>
    <macros>
		<import>macros.xml</import>
		<import>cpt-macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/gff3_remove_fasta_sequences.py
$gff3
--ogff3 $ogff3

]]></command>
    <inputs>
        <param label="Input .gff3 file" name="gff3" type="data" format="gff3" />
    </inputs>
    <outputs>
	<data format="gff3" name="ogff3" label="Output file"/>
    </outputs>
    <help><![CDATA[
**What it does**
This program removes the lines after '##FASTA' in a .gff3 to be compliant with standard .gff3 format

        ]]></help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1008214</citation>
        <citation type="bibtex">
        @unpublished{galaxyTools, 
            author = {A. Holt},
            title = {CPT Galaxy Tools},
            year = {2020},
            note = {https://github.com/tamu-cpt/galaxy-tools/}
        }
        </citation>
    </citations>
</tool>