annotate macros.xml @ 4:abba05ead5d7 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 85b3b324f510d5f3c9322ecbdd9636e0c2cb8c07

<macros>
    <token name="@TOOL_VERSION@">1.2.0</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">agat</requirement>
        </requirements>
    </xml>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">agat</xref>
        </xrefs>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.5281/zenodo.3552717</citation>
        </citations>
    </xml>
    <xml name="ANNOTATION_INPUT" token_format="gff,gtf,gff3,gff3.gz">
        <param argument="--gff" type="data" format="@FORMAT@" label="Annotation file" help="Input GTF/GFF file" />
    </xml>
    <xml name="AGAT_CONFIG">
        <conditional name="output_format">
            <param name="selector" type="select" label="Output format">
                <option value="GFF">GFF</option>
                <option value="GTF">GTF</option>
            </param>
            <when value="GFF">
                <param name="version" type="select" label="Format version">
                    <option value="1">1</option>
                    <option value="2">2</option>
                    <option value="2.5">2.5</option>
                    <option value="3" selected="true">3</option>
                </param>
            </when>
            <when value="GTF">
                <param name="version" type="select" label="Format version">
                    <option value="1">1 = ("CDS", "start_codon", "stop_codon", "exon", "intron")</option>
                    <option value="2">2 = ("CDS", "start_codon", "stop_codon", "exon")</option>
                    <option value="2.1">2.1 = ("CDS", "start_codon", "stop_codon", "exon", "5UTR", "3UTR")</option>
                    <option value="2.2">2.2 = ("CDS", "start_codon", "stop_codon", "5UTR", "3UTR", "inter", "inter_CNS", "intron_CNS", "exon")</option>
                    <option value="2.5">2.5 = ("gene", "transcript", "exon", "CDS", "UTR", "start_codon", "stop_codon", "Selenocysteine")</option>
                    <option value="3">3 = ("gene", "transcript", "exon", "CDS", "Selenocysteine", "start_codon", "stop_codon", "three_prime_utr", "five_prime_utr")</option>
                    <option value="relax" selected="true">Relax = All feature types will be accepted</option>
                </param>
            </when>
        </conditional>
        <param name="merge_loci" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge loci" help="Should overlapping loci (at CDS level) be merged in a single locus. Only one gene is kept, and the mRNA features become isoforms." />
        <param name="create_exon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Create exon when l2 do not have children"/>
    </xml>
    
    <xml name="REFERENCE_FASTA">
        <conditional name="reference_genome">
            <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
                <option value="indexed" selected="true">Use a built-in genome</option>
                <option value="history" selected="true">Use a genome from history</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
                    <options from_data_table="fasta_indexes">
                        <filter type="sort_by" column="2" />
                        <validator type="no_options" message="No genomes are available for the selected input dataset" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
            </when>
        </conditional>
    </xml>
    <token name="@input_annotation_single@"><![CDATA[
        #set $input_annotation = 'annotation.' + str($tool.gff.ext)
        ln -s '${tool.gff}' $input_annotation &&
    ]]></token>
    <token name="@input_reference@"><![CDATA[
        #if $tool.reference_genome.source == 'history':
            #set $ref_genome = 'reference.fasta'
            ln -s -f '${tool.reference_genome.history_item}' '$ref_genome' &&
        #else:
            #set $ref_genome = $tool.reference_genome.index.fields.path
        #end if
    ]]></token>
    <token name="@input_annotation_double@"><![CDATA[
        #set $input1 = 'annotation1.' + str($tool.input_annotation1.ext)
        #set $input2 = 'annotation2.' + str($tool.input_annotation2.ext)
        ln -s '${tool.input_annotation1}' '$input1' &&
        ln -s '${tool.input_annotation2}' '$input2' &&
    ]]></token>
</macros>