<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.4.2">
    <description>
        This Galaxy tool permits to prepare your files to be ready for
        Assembly Hub visualization.
    </description>

    <requirements>
        <requirement type="package" version="340">ucsc_hac</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
        <requirement type="package" version="340">ucsc_bigwig</requirement>
        <requirement type="package" version="340">ucsc_bigbed</requirement>
    </requirements>

    <stdio>
        <regex match="^pass1"
               source="stderr"
               level="log"
               description="bedToBigBed"/>
        <!-- TODO: Add the case pass1 and 0 chroms -->
        <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
    </stdio>

    <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p $output.extra_files_path;

        python $__tool_directory__/hubArchiveCreator.py

        ## Ask the user to enter the genome name
        --genome_name '$genome_name'

        #import json

        #set global data_parameter_dict = {}

        ## Function to retrieve the data of the inputs
        #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
            #set false_path = str($input_to_prepare)
            #set name = $input_to_prepare.name

            #set data_dict = {"name": $name}
            #silent data_dict.update($extra_data_dict)

            ## Add the ordering by taking the tool form indexes
            #silent $data_dict.update({"order_index": $order_index})

            #silent $data_parameter_dict.update({$false_path: $data_dict})

        #end def


        ## Get the number of digits from tracks, to have a unique integer from group index and track index

        #set temp_max_digit = 0

        #for $g in $group
            #if len($g.format) > $temp_max_digit
                #silent temp_max_digit = len($g.format)
            #end if
        #end for

        #set nb_digits_max_track = len(str($temp_max_digit))

        ## END Get the number of digits

        #for $i_g, $g in enumerate( $group )
            #for $i, $f in enumerate( $g.format )
                ## Create the order index using index_group+1 concatenated with index_track
                #set index_group_final = str($i_g + 1)
                #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)

                ## For each format, we have a few mandatory fields we store in a dict
                #set track_color = str($f.formatChoice.track_color)
                #set group_name = str($g.group_name)
                #set longLabel = str($f.formatChoice.longLabel)
                #set extra_data_dict = {"database": "",
                                        "track_color": $track_color,
                                        "group_name": $group_name,
                                        "long_label": $longLabel}

                #if $f.formatChoice.format_select == "bam"
                    --bam $f.formatChoice.BAM
                    #set bam_index = $f.formatChoice.BAM.metadata.bam_index

                    ## Add Bam format specific fields
                    #silent extra_data_dict.update({"index": $bam_index})

                    #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)
                #end if
                #if $f.formatChoice.format_select == "bed"
                    #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
                        --bed $f.formatChoice.bedChoice.BED
                        #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,
                                                extra_data_dict)
                    #end if
                    #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand"
                        --cytoBand $f.formatChoice.bedChoice.BED_cytoBand
                        #silent $prepare_json($f.formatChoice.bedChoice.BED_cytoBand, $index_track_final,
                                                extra_data_dict)
                    #end if
                    #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
                        --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
                        #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
                                                extra_data_dict)
                    #end if
                    #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
                        --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
                        #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
                                                extra_data_dict)
                    #end if
                    #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
                        --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
                        #set database = str($f.formatChoice.bedChoice.database)
                        #silent extra_data_dict.update({"database": $database})
                        #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
                                             extra_data_dict)
                    #end if
                    #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
                        --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment
                        #set database = str($f.formatChoice.bedChoice.database)
                        #silent extra_data_dict.update({"database": $database})
                        #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
                                             extra_data_dict)
                    #end if
                #end if
                #if $f.formatChoice.format_select == "psl"
                    --psl $f.formatChoice.PSL
                    #silent $prepare_json($f.formatChoice.PSL, $index_track_final,
                                           extra_data_dict)
                #end if
                #if $f.formatChoice.format_select == "bigwig"
                    --bigwig $f.formatChoice.BIGWIG
                    #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
                                            extra_data_dict)
                #end if
                #if $f.formatChoice.format_select == "bigbed"
                    --bigbed $f.formatChoice.BIGBED
                    #silent $prepare_json($f.formatChoice.BIGBED, $index_track_final,
                                            extra_data_dict)
                #end if
                #if $f.formatChoice.format_select == "gff3"
                    --gff3 $f.formatChoice.GFF3
                    #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
                                            extra_data_dict)
                #end if
                #if $f.formatChoice.format_select == "gtf"
                    ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
                    --gtf $f.formatChoice.GTF
                    #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
                                             extra_data_dict)
                #end if
            #end for
        #end for

        ## We combine the fasta file dataset name with his false path in a JSON object
        #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
        -f '$fasta_json'

        ## Dump the final json
        #set all_data_json = json.dumps($data_parameter_dict)

        --data_json '$all_data_json'

        ## Retrieve the user email
        --user_email $__user_email__

        -d $__tool_directory__

        -e $output.extra_files_path

        $advanced_options.debug_mode

        -o $output;

    ]]></command>

    <inputs>
        <param
                name="genome_name"
                type="text"
                size="30"
                value="unknown"
                label="UCSC Genome Browser assembly ID"
        />
        <param
                format="fasta"
                name="fasta_file"
                type="data"
                label="Reference genome"
        />
        <repeat name="group" title="New group">
            <param type="text" name="group_name" label="Group name" value="Default group"/>
            <repeat name="format" title="New track">
                <conditional name="formatChoice">
                    <param name="format_select" type="select" label="Format">
                        <option value="bam" selected="true">BAM</option>
                        <option value="bed">BED</option>
                        <option value="psl">PSL</option>
                        <option value="bigwig">BIGWIG</option>
                        <option value="bigbed">BIGBED</option>
                        <option value="gff3">GFF3</option>
                        <option value="gtf">GTF</option>
                    </param>

                    <when value="bam">
                        <param
                                format="bam"
                                name="BAM"
                                type="data"
                                label="BAM File"
                        />
                        <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
                        <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
                        <param name="track_color" type="color" label="Track color" value="#000000">
                            <sanitizer>
                                <valid initial="string.letters,string.digits">
                                    <add value="#"/>
                                </valid>
                            </sanitizer>
                        </param>
                    </when>
                    <when value="bed">
                        <conditional name="bedChoice">
                            <param name="bed_select" type="select" label="Bed Choice">
                                <option value="bed_generic" selected="true">BED Generic (bed4)</option>
                                <option value="bed_cytoBand">cytoBand Track (bed4+1)</option>
                                <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
                                <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
                                <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
                                <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
                            </param>
                            <when value="bed_generic">
                                <param
                                        format="bed"
                                        name="BED"
                                        type="data"
                                        label="Generic Bed File Choice"
                                />

                            </when>
                            <when value="bed_cytoBand">
                                <param
                                        format="bed"
                                        name="BED_cytoBand"
                                        type="data"
                                        label="cytoBand Track (Bed4)"
                                />
                            </when>
                            <when value="bed_simple_repeats_option">
                                <param
                                        format="bed"
                                        name="BED_simple_repeats"
                                        type="data"
                                        label="Bed Simple Repeats (Bed4+12) File"
                                />
                            </when>
                            <when value="bed_splice_junctions_option">
                                <param
                                        format="bed"
                                        name="BED_splice_junctions"
                                        type="data"
                                        label="Bed Splice Junctions (Bed12+1) File"
                                />
                            </when>
                            <when value="bed_blast_alignment_option">
                                <param
                                        format="bed"
                                        name="BED_blast_alignment"
                                        type="data"
                                        label="Bed Blast Alignments (Bed12+12) File"
                                />
                                <param name="database" type="select" label="Protein database">
                                    <option value="NCBI" selected="true">NCBI</option>
                                    <option value="UniProt">UniProt</option>
                                    <option value="FlyBase">FlyBase</option>
                                    <option value="Others">Others</option>
                                </param>
                            </when>
                            <when value="bed_blat_alignment_option">
                                <param
                                        format="bed"
                                        name="BED_blat_alignment"
                                        type="data"
                                        label="Bed BLAT Alignments (bigPsl) File"
                                />
                                <param name="database" type="select" label="mRNA database">
                                    <option value="NCBI" selected="true">NCBI</option>
                                    <option value="Others">Others</option>
                                </param>
                            </when>
                        </conditional>
                        <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
                        <param name="track_color" type="color" label="Track color" value="#000000">
                            <sanitizer>
                                <valid initial="string.letters,string.digits">
                                    <add value="#"/>
                                </valid>
                            </sanitizer>
                        </param>
                    </when>
                    <when value="psl">
                        <param
                                format="psl"
                                name="PSL"
                                type="data"
                                label="PSL File"
                        />
                        <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
                        <param name="track_color" type="color" label="Track color" value="#000000">
                            <sanitizer>
                                <valid initial="string.letters,string.digits">
                                    <add value="#"/>
                                </valid>
                            </sanitizer>
                        </param>
                    </when>
                    <when value="bigwig">
                        <param
                                format="bigwig"
                                name="BIGWIG"
                                type="data"
                                label="BIGWIG File"
                        />
                        <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
                        <param name="track_color" type="color" label="Track color" value="#000000">
                            <sanitizer>
                                <valid initial="string.letters,string.digits">
                                    <add value="#"/>
                                </valid>
                            </sanitizer>
                        </param>
                    </when>
                    <when value="bigbed">
                        <param
                                format="bigbed"
                                name="BIGBED"
                                type="data"
                                label="BIGBED File"
                        />
                        <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
                        <param name="track_color" type="color" label="Track color" value="#000000">
                            <sanitizer>
                                <valid initial="string.letters,string.digits">
                                    <add value="#"/>
                                </valid>
                            </sanitizer>
                        </param>
                    </when>
                    <when value="gff3">
                        <param
                                format="gff3"
                                name="GFF3"
                                type="data"
                                label="GFF3 File"
                        />
                        <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
                        <param name="track_color" type="color" label="Track color" value="#000000">
                            <sanitizer>
                                <valid initial="string.letters,string.digits">
                                    <add value="#"/>
                                </valid>
                            </sanitizer>
                        </param>
                    </when>
                    <when value="gtf">
                        <param
                                format="gtf"
                                name="GTF"
                                type="data"
                                label="GTF File"
                        />
                        <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
                        <param name="track_color" type="color" label="Track color" value="#000000">
                            <sanitizer>
                                <valid initial="string.letters,string.digits">
                                    <add value="#"/>
                                </valid>
                            </sanitizer>
                        </param>
                    </when>
                </conditional>
            </repeat>
        </repeat>
        <conditional name="advanced_options">
            <param name="advanced_options_selector" type="select" label="Advanced options">
                <option value="off" selected="true">Hide advanced options</option>
                <option value="on">Display advanced options</option>
            </param>
            <!-- TODO: Avoid redundancy here -->
            <when value="on">
                <param name="debug_mode" type="boolean"
                       label="Activate debug mode" checked="false"
                       truevalue="--debug_mode" falsevalue="">
                    <help>
                        Use this option if you are a G-OnRamp developer
                    </help>
                </param>
            </when>
            <when value="off">
                <param name="debug_mode" type="hidden"
                       value="">
                </param>
            </when>
    </conditional>
</inputs>

    <outputs>
        <data format="trackhub" name="output"/>
    </outputs>

    <tests>
        <!-- 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">
                <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />
                <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />
                <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
                <!-- Email could be different, but we need to ensure we still have the email line -->
                <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
                    <assert_contents>
                        <has_text text="email"/>
                    </assert_contents>
                </extra_files>
                <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
                </extra_files>
                <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
            </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="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"
                />
                <!-- Verify trackDb.txt contains the basic fields for a bam -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">
                    <assert_contents>
                        <has_text text="track"/>
                        <has_text text="longLabel"/>
                        <has_text text="shortLabel"/>
                        <has_text text="bigDataUrl"/>
                        <has_text text="type"/>
                        <has_text text="visibility"/>
                        <has_text text="thickDrawItem"/>
                        <has_text text="priority"/>
                        <has_text text="color"/>
                        <has_text text="group"/>
                    </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 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="track_color" value="#000000"/>
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bed_generic/bed_generic.html">
                <!-- Verify tracks folder contains bam and bai -->
                <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"
                />
            </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="track_color" value="#000000"/>
                        </conditional>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
                <!-- Verify tracks folder contains bam and bai -->
                <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"
                />
            </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="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="psl/psl_trackhub.html">
                <!-- Verify tracks folder contains bam and bai -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
                             value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
                             compare="sim_size"
                />
                <!-- Verify trackDb.txt contains the basic fields for a bam -->
                <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
            </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_Summary"/>
                        <param name="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="bigwig/bigwig.html">
                <!-- Verify tracks folder contains bam and bai -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
                             value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
                             compare="sim_size"
                />
                <!-- Verify trackDb.txt contains the basic fields for a bam -->
                <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
            </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="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="gff3/gff3_trackhub.html">
                <!-- Verify tracks folder contains bam and bai -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
                             value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
                             compare="sim_size"
                />
                <!-- Verify trackDb.txt contains the basic fields for a bam -->
                <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
            </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="track_color" value="#000000"/>
                    </conditional>
                </repeat>
            </repeat>
            <output name="output" file="gtf/gtf_trackhub.html">
                <!-- Verify tracks folder contains bam and bai -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
                             compare="sim_size"
                />
                <!-- Verify trackDb.txt contains the basic fields for a bam -->
                <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
            </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">
                <!-- verify tracks folder contains bam and bai -->
                <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"
                />
                <!-- verify trackdb.txt contains the basic fields for a bam -->
                <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
            </output>
        </test>

        <!-- Test with one group and all the supported datatypes on 10/04/2016 -->
        <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_Summary"/>
                        <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>
            <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_Summary.bigwig"
                             value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.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"
                />
                <!-- verify trackdb.txt contains the basic fields for a bam -->
                <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
            </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">
                <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/>
                <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>
                <!-- Email could be different, but we need to ensure we still have the email line -->
                <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">
                    <assert_contents>
                        <has_text text="email"/>
                    </assert_contents>
                </extra_files>
                <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
                </extra_files>
                <extra_files type="file" name="myHub/Dbia3/description.html"
                             value="two_groups_no_track/myHub/Dbia3/description.html"/>
            </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_Summary"/>
                        <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 myHub structure -->
                <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>
                <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>
                <!-- Email could be different, but we need to ensure we still have the email line -->
                <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">
                    <assert_contents>
                        <has_text text="email"/>
                    </assert_contents>
                </extra_files>
                <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
                </extra_files>
                <extra_files type="file" name="myHub/Dbia3/description.html"
                             value="two_groups_one_track_first/myHub/Dbia3/description.html"/>

                <!-- Check tracks exist -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
                             value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
                             compare="sim_size"
                />

                <!-- Check the groups.txt exists and is properly populated -->
            </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_Summary"/>
                        <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 myHub structure -->
                <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>
                <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>
                <!-- Email could be different, but we need to ensure we still have the email line -->
                <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"
                             lines_diff="2">
                    <assert_contents>
                        <has_text text="email"/>
                    </assert_contents>
                </extra_files>
                <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
                </extra_files>
                <extra_files type="file" name="myHub/Dbia3/description.html"
                             value="two_groups_one_track_both/myHub/Dbia3/description.html"/>

                <!-- Check tracks exist -->
                <!-- First group -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
                             value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.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"
                />
                <!-- 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_Summary"/>
                        <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 myHub structure -->
                <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>
                <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>
                <!-- Email could be different, but we need to ensure we still have the email line -->
                <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"
                             lines_diff="2">
                    <assert_contents>
                        <has_text text="email"/>
                    </assert_contents>
                </extra_files>
                <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
                </extra_files>
                <extra_files type="file" name="myHub/Dbia3/description.html"
                             value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>

                <!-- Check tracks exist -->
                <!-- First group -->
                <extra_files type="file"
                             name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
                             value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.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"
                />
                <!-- Check the groups.txt exists and is properly populated -->
            </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">
                <!-- Verify trackDb.txt contains the color 0,0,0 -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/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">
                <!-- Verify trackDb.txt contains the color 128,100,162 -->
                <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/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"
                />

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

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

        <!-- Find tests that should fail -->

    </tests>

    <help>
        This Galaxy tool permits to prepare your files to be ready for
        Assembly Hub visualization.
    </help>

    <citations>
        <citation type="doi">10.7490/f1000research.1112719.1</citation>
    </citations>
</tool>