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<tool id="VAPPER" name="VAPPER" version="1.0.0">
    <description>is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate</description>
	<requirements>
        <requirement type="package" version="1.2.10">velvet</requirement>
        <requirement type="package" version="3.1b2">HMMER</requirement>
        <requirement type="package" version="2.2.6">bowtie2</requirement>
        <requirement type="package" version="1.6">samtools</requirement>
        <requirement type="package" version="2.2.1">cufflinks</requirement>
        <requirement type="package" version="2.7.1">blast</requirement>
	</requirements>


    <command interpreter="python" detect_errors="exit_code">
        #if $TrypType.species == "Trypanosoma congolense":
            #if $TrypType.GT.analysis == "Genomic":
                #if $TrypType.GT.contigs.preassem == "Contig available":
                    <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 -->
                    Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path
                #else
                    <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 -->
                    Vap.py g_assemble $xname $P $TrypType.GT.contigs.kmers $TrypType.GT.contigs.inslen $TrypType.GT.contigs.covcut $TrypType.GT.contigs.forward $TrypType.GT.contigs.reverse $html_file $html_file.extra_files_path
                #end if
            #else
                <!-- name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 -->
                Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path
            #end if
        #else
            #if $TrypType.contigs.preassem == "Contig available":
                    <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 -->
                Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path
            #else
                    <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 -->
                Vap.py v_assemble $xname $P $TrypType.contigs.kmers $TrypType.contigs.inslen 0 $TrypType.contigs.forward $TrypType.contigs.reverse $html_file $html_file.extra_files_path
            #end if
        #end if

    </command>

    <inputs>
        <param name="xname" size = "30" type="text" value = "Test" label="Prefix Name" />
        <conditional name = "TrypType">
            <param name = "species" type = 'select' label="Select Species">
                <option value = "Trypanosoma congolense" selected="true"></option>
                <option value = "Trypanosoma vivax"></option>
            </param>
            <when value = "Trypanosoma congolense">
                <conditional name = "GT">
                    <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?">
                        <option value = "Genomic" selected = "true"></option>
                        <option value = "Transcriptomic"></option>
                    </param>
                    <when value = "Genomic">
                        <conditional name = "contigs">
                            <param name = "preassem" type = "select" label = "Contig file available?">
                                <option value = "Full assembly" selected = "true"></option>
                                <option value = "Contig available"></option>
                            </param>
                            <when value = "Full assembly">
                                <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param>
                                <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param>
                                <param name = "covcut" type="integer" value="5" min="1" max="999" label = "Coverage cut off"></param>
                                <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
                                <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
                            </when>
                            <when value = "Contig available">
                                <param name="contig" type="data" format="fasta" label="Contig file"/>
                            </when>
                        </conditional>
                    </when>
                    <when value = "Transcriptomic">
                        <param name = "strain" type="select" label = "Select Reference Strain">
                            <option value = "Tc148"></option>
                            <option value = "IL3000"></option>
                        </param>
                        <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
                        <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
                     </when>
                </conditional>
            </when>
            <when value="Trypanosoma vivax">
                <conditional name = "contigs">
                    <param name = "preassem" type = "select" label = "Contig file available?">
                        <option value = "Full assembly" selected = "true"></option>
                        <option value = "Contig available"></option>
                    </param>
                    <when value = "Full assembly">
                        <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param>
                        <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param>
                        <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
                        <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
                    </when>
                    <when value = "Contig available">
                        <param name="contig" type="data" format="fasta" label="Contig file"/>
                    </when>
                </conditional>
            </when>
        </conditional>

        <param name="P" type="boolean" truevalue='PDF_Yes' falsevalue='PDF_No' label="Export PDF of figures" />
    </inputs>

    <outputs>
        <data format="html" name = "html_file" label = "${xname.value}_html"/>
    </outputs>
    <tests>
		<test>
			<param name = "xname" value = "Test"/>
			<conditional name = "TrypType">
				<param name = "species" value = "Trypanosoma congolense"/>
			</conditional>
			<conditional name = "GT">
				<param name = "analysis" value = "Genomic"/>
			</conditional>
			<conditional name = "contigs">
				<param name = "preassem" value = "Contig available"/>
				<param name="contig" value = "Test.fa"/>
			</conditional>
			<param name = "P" value = 'PDF_No'/>
			<output name = "html_file" file = 'Test_html' ftype = 'html'/>
		</test>
	</tests>
</tool>