<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.9">python</requirement>
            <requirement type="package" version="1.81">biopython</requirement>
            <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@WRAPPER_VERSION@">2.4.0</token>
    <xml name="citation/gepard">
        <citation type="doi">10.1093/bioinformatics/btm039</citation>
    </xml>
    <token name="@XMFA_INPUT@">
		'$xmfa'
	</token>
    <xml name="xmfa_input" token_formats="xmfa">
        <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
    </xml>
    <token name="@XMFA_FA_INPUT@">
		'$sequences'
	</token>
    <xml name="xmfa_fa_input">
        <param type="data" format="fasta" name="sequences" label="Sequences in alignment" help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/>
    </xml>
    <xml name="genome_selector">
        <conditional name="reference_genome">
            <param name="reference_genome_source" type="select" label="Reference Genome">
                <option value="history" selected="True">From History</option>
                <option value="cached">Locally Cached</option>
            </param>
            <when value="cached">
                <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
                    <options from_data_table="all_fasta"/>
                </param>
            </when>
            <when value="history">
                <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
            </when>
        </conditional>
    </xml>
    <xml name="gff3_input">
        <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
    </xml>
    <xml name="input/gff3+fasta">
        <expand macro="gff3_input"/>
        <expand macro="genome_selector"/>
    </xml>
    <xml name="citation/mijalisrasche">
        <citation type="doi">10.1371/journal.pcbi.1008214</citation>
        <citation type="bibtex">@unpublished{galaxyTools,
		author = {E. Mijalis, H. Rasche},
		title = {CPT Galaxy Tools},
		year = {2013-2017},
		note = {https://github.com/tamu-cpt/galaxy-tools/}
		}
		</citation>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
            <citation type="bibtex">
			@unpublished{galaxyTools,
				author = {E. Mijalis, H. Rasche},
				title = {CPT Galaxy Tools},
				year = {2013-2017},
				note = {https://github.com/tamu-cpt/galaxy-tools/}
			}
			</citation>
            <yield/>
        </citations>
    </xml>
    <xml name="citations-crr">
        <citations>
            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
            <citation type="bibtex">
			@unpublished{galaxyTools,
				author = {C. Ross},
				title = {CPT Galaxy Tools},
				year = {2020-},
				note = {https://github.com/tamu-cpt/galaxy-tools/}
			}
			</citation>
            <yield/>
        </citations>
    </xml>
    <xml name="citations-2020">
        <citations>
            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
            <citation type="bibtex">
			@unpublished{galaxyTools,
				author = {E. Mijalis, H. Rasche},
				title = {CPT Galaxy Tools},
				year = {2013-2017},
				note = {https://github.com/tamu-cpt/galaxy-tools/}
			}
			</citation>
            <citation type="bibtex">
			@unpublished{galaxyTools,
				author = {A. Criscione},
				title = {CPT Galaxy Tools},
				year = {2019-2021},
				note = {https://github.com/tamu-cpt/galaxy-tools/}
			}
                        </citation>
            <yield/>
        </citations>
    </xml>
    <xml name="citations-2020-AJC-solo">
        <citations>
            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
            <citation type="bibtex">
			@unpublished{galaxyTools,
				author = {A. Criscione},
				title = {CPT Galaxy Tools},
				year = {2019-2021},
				note = {https://github.com/tamu-cpt/galaxy-tools/}
			}
                        </citation>
            <yield/>
        </citations>
    </xml>
    <xml name="citations-clm">
        <citations>
            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
            <citation type="bibtex">
			@unpublished{galaxyTools,
				author = {C. Maughmer},
				title = {CPT Galaxy Tools},
				year = {2017-2020},
				note = {https://github.com/tamu-cpt/galaxy-tools/}
			}
			</citation>
            <yield/>
        </citations>
    </xml>
    <xml name="sl-citations-clm">
        <citation type="bibtex">
			@unpublished{galaxyTools,
				author = {C. Maughmer},
				title = {CPT Galaxy Tools},
				year = {2017-2020},
				note = {https://github.com/tamu-cpt/galaxy-tools/}
			}
			</citation>
        <yield/>
    </xml>
    <token name="@INPUT_GFF@">
	    '$gff3_data'
	</token>
    <token name="@INPUT_FASTA@">
    #if str($reference_genome.reference_genome_source) == 'cached':
            '${reference_genome.fasta_indexes.fields.path}'
    #else if str($reference_genome.reference_genome_source) == 'history':
            genomeref.fa
    #end if
	</token>
    <token name="@GENOME_SELECTOR_PRE@">
    #if $reference_genome.reference_genome_source == 'history':
            ln -s '$reference_genome.genome_fasta' genomeref.fa;
    #end if
	</token>
    <token name="@GENOME_SELECTOR@">
    #if str($reference_genome.reference_genome_source) == 'cached':
            '${reference_genome.fasta_indexes.fields.path}'
    #else if str($reference_genome.reference_genome_source) == 'history':
            genomeref.fa
    #end if
	</token>
</macros>