comparison tests.xml @ 84:cb62314a6297 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty

84:cb62314a6297

<macro>
    <xml name="test_cases">
        <!-- Test with only the fasta file -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <output name="output" file="only_genome/only_genome.html">
                <!-- Use macro to check the whole common structure without repeated code -->
                <expand macro="verify_hub_structure_no_track" test="only_genome" />
            </output>
        </test>

        <!-- Test with Bam -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bam"/>
                        <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
                        <param name="longLabel" value="HISAT sequence alignment" />
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bam/bam.html">
                <!-- Verify tracks folder contains bam and bai -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
                             value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
                             value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
                             compare="sim_size"
                />
                <!-- Use macro to check the whole common structure without repeated code -->
                <expand macro="verify_hub_structure" test="bam" />
            </output>
        </test>

        <!-- Test with Bed Generic -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_generic"/>
                            <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
                            <param name="longLabel" value="TBLASTN alignment" />
                            <param name="track_color" value="#000000"/>
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bed_generic/bed_generic.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
                             value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="bed_generic" />
            </output>
        </test>

        <!-- Test with Bed Simple repeat -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_simple_repeats_option"/>
                            <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
                            <param name="longLabel" value="Simple repeat" />
                            <param name="track_color" value="#000000"/>
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
                             value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="bed_simple_repeats" />
            </output>
        </test>

        <!-- Test with Psl -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="psl"/>
                        <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
                        <param name="longLabel" value="BLAST Alignment" />
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="psl/psl_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
                             value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="psl" />
            </output>
        </test>

        <!-- Test with BigWig -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bigwig"/>
                        <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
                        <param name="longLabel" value="RNA-Seq Coverage" />
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bigwig/bigwig.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
                             value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="bigwig" />
                <!-- check additional trackDb settings for BigWig -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="autoScale"/>
                        <has_text text="maxHeightPixels"/>
                        <has_text text="windowingFunction"/>
                    </assert_contents>
                </extra_files>
            </output>
        </test>

        <!-- Test with GFF3 -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="gff3"/>
                        <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
                        <param name="longLabel" value="Augustus" />
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="gff3/gff3_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
                             value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="gff3" />
            </output>
        </test>

        <!-- Test with GTF -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="gtf"/>
                        <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
                        <param name="longLabel" value="StringTie transcripts" />
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="gtf/gtf_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="gtf" />
            </output>
        </test>

        <!-- Test with BLAT Alignment -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_blat_alignment_option"/>
                            <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
                            <param name="longLabel" value="BLAT alignment" />
                            <param name="track_color" value="#000000"/>
                            <param name="database" value="NCBI" />
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bed_blat_alignment/blat_alignment_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
                             value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="bed_blat_alignment" />
                <!-- check additional trackDb settings for BLAT -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="searchIndex"/>
                        <has_text text="url"/>
                        <has_text text="urlLabel"/>
                        <has_text text="iframeUrl"/>
                        <has_text text="iframeOptions"/>
                    </assert_contents>
                </extra_files>
            </output>
        </test>

        <!-- Test with BLAST Alignment -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_blast_alignment_option"/>
                            <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
                            <param name="longLabel" value="BLAST alignment" />
                            <param name="track_color" value="#000000"/>
                            <param name="database" value="NCBI" />
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bed_blast_alignment/blast_alignment_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
                             value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="bed_blast_alignment" />
                <!-- check additional trackDb settings for BLAST -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="searchIndex"/>
                        <has_text text="url"/>
                        <has_text text="urlLabel"/>
                        <has_text text="iframeUrl"/>
                        <has_text text="iframeOptions"/>
                    </assert_contents>
                </extra_files>
            </output>
        </test>

        <!-- Test with Regtools Splice Junctions -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_splice_junctions_option"/>
                            <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
                            <param name="longLabel" value="Splice junctions" />
                            <param name="track_color" value="#000000"/>
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bed_splice_junctions/splice_junctions_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/regtools_junctions.bb"
                             value="bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="bed_splice_junctions" />
            </output>
        </test>

        <!-- Test with Cytoband -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_cytoBand"/>
                            <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
                            <param name="longLabel" value="Cytoband" />
                            <param name="track_color" value="#000000"/>
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bed_cytoband/cytoband_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/Cytoband.bb"
                             value="bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="bed_cytoband" />
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="track cytoBandIdeo"/>
                    </assert_contents>
                </extra_files>
            </output>
        </test>

        <!-- Test with bigBed -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bigbed"/>
                        <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
                        <param name="longLabel" value="bigBed" />
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="big_bed/bigbed_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
                             value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="big_bed" />
            </output>
        </test>

        <!-- Test with one group and multiple tracks -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="gtf"/>
                        <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="gff3"/>
                        <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
                             value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="gtf_gff" />   
            </output>
        </test>

        <!-- Test with one group and all the supported datatypes -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bam"/>
                        <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed"/>
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_generic"/>
                            <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
                            <param name="track_color" value="#000000"/>
                        </conditional>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed"/>
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_simple_repeats_option"/>
                            <param name="BED_simple_repeats" ftype="bed"
                                   value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
                            <param name="track_color" value="#000000"/>
                        </conditional>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="psl"/>
                        <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bigwig"/>
                        <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="gff3"/>
                        <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="gtf"/>
                        <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_cytoBand"/>
                            <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
                            <param name="track_color" value="#000000"/>
                        </conditional>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_splice_junctions_option"/>
                            <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
                            <param name="track_color" value="#000000"/>
                        </conditional>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_blast_alignment_option"/>
                            <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
                            <param name="track_color" value="#000000"/>
                            <param name="database" value="NCBI" />
                        </conditional>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_blat_alignment_option"/>
                            <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
                            <param name="track_color" value="#000000"/>
                            <param name="database" value="NCBI" />
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
                <!-- verify tracks folder contains all the files -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
                             value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
                             value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
                             value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
                             value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
                             value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
                             value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
                             value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/Cytoband.bb"
                             value="all_datatypes/myHub/Dbia3/tracks/Cytoband.bb"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/regtools_junctions.bb"
                             value="all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
                             value="all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
                             value="all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="all_datatypes" />
            </output>
        </test>

         <!-- Test with two groups and no tracks -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
            </repeat>
            <repeat name="group">
                <param name="group_name" value="Other group"/>
            </repeat>
            <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
                <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" />
            </output>
        </test>

        <!-- Test with two groups and one track in first -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bigwig"/>
                        <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <repeat name="group">
                <param name="group_name" value="Other group"/>
            </repeat>
            <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
                <!-- Check tracks exist -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
                             value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="two_groups_one_track_first" />
            </output>
        </test>

        <!-- Test with two groups and one track in both -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bigwig"/>
                        <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <repeat name="group">
                <param name="group_name" value="Other group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="gtf"/>
                        <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
                <!-- Check tracks exist -->
                <!-- First group -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
                             value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
                             compare="sim_size"
                />

                <!-- Second group -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="two_groups_one_track_both" />
                <!-- Check the groups.txt exists and is properly populated -->
            </output>
        </test>

        <!-- Test with two groups and multiple tracks in both -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bigwig"/>
                        <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bam"/>
                        <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <repeat name="group">
                <param name="group_name" value="Other group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="gtf"/>
                        <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="gff3"/>
                        <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
                <!-- Check tracks exist -->
                <!-- First group -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
                             value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
                             value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
                             value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
                             compare="sim_size"
                />

                <!-- Second group -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             compare="sim_size"
                />
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
                             value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" />
            </output>
        </test>

        <!-- Test default color in a track -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bam"/>
                        <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="default_color/default_color_trackhub.html">
                <expand macro="verify_hub_structure" test="default_color" />
                <!-- Verify trackDb.txt contains the color 0,0,0 -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="color 0,0,0"/>
                    </assert_contents>
                </extra_files>

                <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
            </output>
        </test>

        <!-- Test changed color in a track -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bam"/>
                        <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
                        <param name="track_color" value="#8064a2"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="changed_color/changed_color_trackhub.html">
                <expand macro="verify_hub_structure" test="changed_color" />
                <!-- Verify trackDb.txt contains the color 128,100,162 -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="color 128,100,162"/>
                    </assert_contents>
                </extra_files>

                <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
            </output>
        </test>

        <!-- Test for StringTie Chromosome end coordinates -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="gtf"/>
                        <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" />

                <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
            </output>
        </test>

        <!-- Test default label in a track -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bam"/>
                        <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="default_color/default_color_trackhub.html">
                <expand macro="verify_hub_structure" test="default_color" />
                <!-- Verify trackDb.txt contains default label -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="longLabel HISAT2 Accepted Hits.bam"/>
                    </assert_contents>
                </extra_files>

                <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
            </output>
        </test>

        <!-- Test customized label in a track -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bam"/>
                        <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
                        <param name="longLabel" value="HISAT sequence alignment" />
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="changed_label/changed_label_trackhub.html">
                <expand macro="verify_hub_structure" test="changed_label" />
                <!-- Verify trackDb.txt contains the customized label -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="longLabel HISAT sequence alignment"/>
                    </assert_contents>
                </extra_files>

                <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
            </output>
        </test>

        <!-- Test TrixIndex for Blat alignment track -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_blat_alignment_option"/>
                            <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
                            <param name="longLabel" value="BLAT alignment" />
                            <param name="track_color" value="#000000"/>
                            <param name="database" value="NCBI" />
                            <conditional name="add_trix_index">
                                <param name="add_trix_index_selector" value="yes" />
                                <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
                            </conditional>
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <param name="debug_mode" value="true" />
            <output name="output" file="trix_index_files/blat_alignment_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
                             value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="bed_blat_alignment" />
                <!-- check additional trackDb settings for BLAT -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="searchIndex"/>
                        <has_text text="searchTrix"/>
                        <has_text text="url"/>
                        <has_text text="urlLabel"/>
                        <has_text text="iframeUrl"/>
                        <has_text text="iframeOptions"/>
                    </assert_contents>
                </extra_files>
                <!-- check Trix index directory -->
                <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix"
                             value="trix_index/blat_out.ix" />
                <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx"
                             value="trix_index/blat_out.ixx" />
            </output>
        </test>

        <!-- Test TrixIndex for BLAST Alignment -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bed" />
                        <conditional name="bedChoice">
                            <param name="bed_select" value="bed_blast_alignment_option"/>
                            <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
                            <param name="longLabel" value="BLAST alignment" />
                            <param name="track_color" value="#000000"/>
                            <param name="database" value="NCBI" />
                            <conditional name="add_trix_index">
                                <param name="add_trix_index_selector" value="yes" />
                                <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
                            </conditional>
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <param name="debug_mode" value="true" />
            <output name="output" file="trix_index_files/blast_alignment_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
                             value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="bed_blast_alignment" />
                <!-- check additional trackDb settings for BLAST -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="searchIndex"/>
                        <has_text text="searchTrix"/>
                        <has_text text="url"/>
                        <has_text text="urlLabel"/>
                        <has_text text="iframeUrl"/>
                        <has_text text="iframeOptions"/>
                    </assert_contents>
                </extra_files>
                <!-- check Trix index directory -->
                <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix"
                             value="trix_index/blast_out.ix" />
                <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx"
                             value="trix_index/blast_out.ixx" />
            </output>
        </test>

        <!-- Test TrixIndex for BigBed -->
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <repeat name="group">
                <param name="group_name" value="Default group"/>
                <repeat name="format">
                    <conditional name="formatChoice">
                        <param name="format_select" value="bigbed"/>
                        <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
                        <param name="longLabel" value="bigBed" />
                        <param name="track_color" value="#000000"/>
                        <conditional name="add_trix_index">
                            <param name="add_trix_index_selector" value="yes" />
                            <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
                            <param name="trix_id" value="name" />
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <param name="debug_mode" value="true" />
            <output name="output" file="trix_index_files/bigbed_trackhub.html">
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
                             value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
                             compare="sim_size"
                />
                <expand macro="verify_hub_structure" test="big_bed">
                    <has_text text="searchIndex"/>
                    <has_text text="searchTrix"/>
                </expand>

                <!-- check Trix index directory -->
                <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix"
                             value="trix_index/blat_out.ix" />
                <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx"
                             value="trix_index/blat_out.ixx" />
            </output>
        </test>

        <!-- Test for big files? -->

        <!-- Find tests that should fail -->
    </xml>
</macro>