<?xml version="1.0"?>
<macros>
    <token name="@VERSION@">0.26.0</token>
    <xml name="citations">
        <citations>
            <citation type="doi">add citation</citation>
        </citations>
    </xml>
    <xml name="index">
        <conditional name="refTranscriptSource">
            <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?">
                <option value="history">Use an index from your history</option>
                <option value="built" selected="True">Built one </option>
            </param>
            <when value="history">
                <section name="h_index" title="Select the index files from your history:" expanded="true">
                    <param name="index_file" type="data" format="kallisto.idx" label="kb index file (.idx)"/>
                    <param name="t2g_file" type="data" format="txt" label="Transcript to gene (t2g) file"/>
                    <section name="history_lamanno" title="Additional index files" expanded="false">
                        <param name="cdna_t2c" optional="true" type="data" format="txt" label="-c1 cDNA transcripts-to-captures (t2c) file (only needed with workflow==lamanno or nucleus)"/>
                        <param name="intron_t2c" optional="true" type="data" format="txt" label="-c2 intron transcripts-to-captures (t2c) file (only needed with workflow==lamanno or nucleus)"/>
                    </section>
                </section>
            </when>
            <when value="built">
                <section name="s_index" title="Kb index" expanded="true">
                    <param name="genomic_fasta" type="data" optional="true" format="fasta" label="Genomic fasta file (leave empty when: workflow = kite)"/>
                    <param name="genomic_gtf" type="data" optional="true" format="gtf" label="Genomic gtf file (leave empty when: workflow = kite)"/>
                    <param name="kite_table" type="data" label="Kite table of feature barcodes and IDs (only required when workflow = kite)" optional="true" format="tabular"/>
                </section>
            </when>
        </conditional>
    </xml>
    <xml name="tests">
    		<!-- Test1: Test with pre-built index provided by user and generating report -->
		<test>
			<conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="h_index">
                    <param name="index_file" value="GRCm39.gencode.chr19_sub.kb_ref.idx"/>
					<param name="t2g_file" value="GRCm39.gencode.chr19_sub.t2g.txt"/>
                </section>
            </conditional>
			<param name="technology" value="10XV2"/>
			<param name="workflow" value="standard"/>
			<param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
			<param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
			<param name="extra_dtype" value="none"/>
			<output name="barcodes" file="barcodes.tsv" compare="sim_size" delta="100000" ftype="txt"/>
			<output name="genes" file="genes.tsv" compare="sim_size" delta="100000"   ftype="txt"/>
			<output name="matrix" file="matrix.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
		</test>
		<!--Test2: Test with building the index on the fly, before kb count.-->
		<test>
			<conditional name="refTranscriptSource">
				<param name="TranscriptSource" value="built"/>
				<section name="s_index">
					<param name="genomic_fasta" value="GRCm39.chr19_100k.fa.gz"/>
					<param name="genomic_gtf" value="gencode.VM26.chr19_10k.gtf.gz"/>
				</section>
			</conditional>
			<param name="technology" value="10XV2"/>
			<param name="workflow" value="standard"/>
			<param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
			<param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
			<param name="extra_dtype" value="none"/>
			<output name="barcodes" file="barcodes.tsv" compare="sim_size" delta="100000" ftype="txt"/>
			<output name="genes" file="genes.tsv" compare="sim_size" delta="100000"   ftype="txt"/>
			<output name="matrix" file="matrix.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
		</test>
		<!--Test3: Test lamanno workflow with pre-built index.-->	
		<test>
			<conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="h_index">
                    <param name="index_file" value="kb_ref.lamanno.idx"/>
					<param name="t2g_file" value="t2g.lamanno.txt"/>
					<section name="history_lamanno">
						<param name="cdna_t2c" value="cdna_t2c.lamanno.txt"/>
						<param name="intron_t2c" value="intron_t2c.lamanno.txt"/>
					</section>
                </section>
            </conditional>
			<param name="technology" value="10XV2"/>
			<param name="workflow" value="lamanno"/>
			<param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
			<param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
			<param name="extra_dtype" value="none"/>
			<output name="barcodes" file="barcodes.lamanno.tsv" compare="sim_size" delta="100000" ftype="txt"/>
			<output name="genes" file="genes.lamanno.tsv" compare="sim_size" delta="100000"   ftype="txt"/>
			<output name="matrix" file="matrix.lamanno.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
		</test>
		<!--Test:4 Test lamanno workflow with building the index on the fly, before kb count.-->	
		<test>
			<conditional name="refTranscriptSource">
				<param name="TranscriptSource" value="built"/>
					<section name="s_index">
						<param name="genomic_fasta" value="GRCm39.chr19_100k.fa.gz"/>
						<param name="genomic_gtf" value="gencode.VM26.chr19_10k.gtf.gz"/>
					</section>
			</conditional>
			<param name="technology" value="10XV2"/>
			<param name="workflow" value="lamanno"/>
			<param name="FASTQ1" value="SRR8599150_S1_L001_R1_001.100k_lines.fastq.gz"/>
			<param name="FASTQ2" value="SRR8599150_S1_L001_R2_001.100k_lines.fastq.gz"/>
			<param name="extra_dtype" value="none"/>
			<output name="barcodes" file="barcodes.lamanno.tsv" compare="sim_size" delta="100000" ftype="txt"/>
			<output name="genes" file="genes.lamanno.tsv" compare="sim_size" delta="100000"   ftype="txt"/>
			<output name="matrix" file="matrix.lamanno.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
		</test>
        <!--Test:5 Test kite workflow with pre-built index.-->	
		<test>
			<conditional name="refTranscriptSource">
				<param name="TranscriptSource" value="history"/>
                    <section name="h_index">
                        <param name="index_file" value="mismatch.idx"/>
                        <param name="t2g_file" value="t2g.kite.txt"/>
					</section>
			</conditional>
			<param name="technology" value="10XV3"/>
			<param name="workflow" value="kite"/>
			<param name="FASTQ1" value="pbmc_1k_protein_v3_antibody_S2_L001_R1_001.100k_sub.fastq.gz"/>
			<param name="FASTQ2" value="pbmc_1k_protein_v3_antibody_S2_L001_R2_001.100k_sub.fastq.gz"/>
			<param name="extra_dtype" value="none"/>
			<output name="barcodes" file="barcodes.kite.tsv" compare="sim_size" delta="100000" ftype="txt"/>
			<output name="genes" file="genes.kite.tsv" compare="sim_size" delta="100000"   ftype="txt"/>
			<output name="matrix" file="matrix.kite.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
		</test>
        <!--Test:6 Test kite workflow with building the index on the fly, before kb count.-->	
		<test>
			<conditional name="refTranscriptSource">
				<param name="TranscriptSource" value="built"/>
					<section name="s_index">
						<param name="kite_table" value="kite_features.tsv"/>
					</section>
			</conditional>
			<param name="technology" value="10XV3"/>
			<param name="workflow" value="kite"/>
			<param name="FASTQ1" value="pbmc_1k_protein_v3_antibody_S2_L001_R1_001.100k_sub.fastq.gz"/>
			<param name="FASTQ2" value="pbmc_1k_protein_v3_antibody_S2_L001_R2_001.100k_sub.fastq.gz"/>
			<param name="extra_dtype" value="none"/>
			<output name="barcodes" file="barcodes.kite.tsv" compare="sim_size" delta="100000" ftype="txt"/>
			<output name="genes" file="genes.kite.tsv" compare="sim_size" delta="100000"   ftype="txt"/>
			<output name="matrix" file="matrix.kite.mtx" compare="sim_size" delta="100000" ftype="mtx"/>
		</test>
    </xml>
</macros>