<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.2">
    <description>
        This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.2">samtools</requirement>
        <requirement type="package" version="0.2.6">tabix</requirement>
        <requirement type="package" version="1.9">numpy</requirement>
        <requirement type="package" version="1.68">biopython</requirement>
        <requirement type="package" version="340">ucsc_hac</requirement>
        <requirement type="package" version="1.13.1">jbrowse_tools</requirement>
        <requirement type="package" version="1.0">gff3sort</requirement>
    </requirements>

    <stdio>
    </stdio>

    <command detect_errors="exit_code"><![CDATA[
        mkdir -p $output.extra_files_path;

        ## Dump the tool parameters into a JSON file
        python2 $json_file parameters.json;

        python2 $__tool_directory__/jbrowseArchiveCreator.py --data_json parameters.json -o $output
    ]]></command>
    <configfiles>
        <configfile name="json_file">
import json
import sys

file_path = sys.argv[1]
#set global data_parameter_dict = {}

## Ask the user to enter the genome name
#silent $data_parameter_dict.update({"genome_name": str($genome_name)})

## Function to retrieve the data of the inputs
#def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
    #set false_path = str($input_to_prepare)
    #set $data_dict = {"false_path": $false_path}

    #set name = str($input_to_prepare.name)
    #silent $data_dict.update({"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})

    #if $datatype in $data_parameter_dict
        #silent $data_parameter_dict[$datatype].append($data_dict)
    #else
        #set array_inputs = []
        #silent $array_inputs.append($data_dict)
        #silent $data_parameter_dict.update({$datatype: $array_inputs})
    #end if
#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 = {"track_color": $track_color,
                                "group_name": $group_name,
                                "long_label": $longLabel}
        #if $f.formatChoice.format_select == "bam"
            #set bam_index = $f.formatChoice.BAM.metadata.bam_index

            ## Add Bam format specific fields
            #silent $extra_data_dict.update({"index": $bam_index, "nameIndex": str($f.formatChoice.nameIndex)})

            #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
        #end if
        #if $f.formatChoice.format_select == "bed"
            #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.bedChoice.nameIndex)})
            #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
                #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED_generic, $index_track_final,
                                                $extra_data_dict)
            #end if
            #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
                #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
                                                $extra_data_dict)
            #end if
            #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
                #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
                                                $extra_data_dict)
            #end if
            #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
                #set database = str($f.formatChoice.bedChoice.database)
                #silent $extra_data_dict.update({"database": $database})
                #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
                                             $extra_data_dict)
            #end if
            #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
                #set database = str($f.formatChoice.bedChoice.database)
                #silent $extra_data_dict.update({"database": $database})
                #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
                                             $extra_data_dict)
            #end if
        #end if
        #if $f.formatChoice.format_select == "blastxml"
            #set database = str($f.formatChoice.database)
            #silent $extra_data_dict.update({"database": $database, "nameIndex": str($f.formatChoice.nameIndex)})
            #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final,
                                            extra_data_dict)
        #end if
        #if $f.formatChoice.format_select == "bigwig"
            #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
            #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
                                            $extra_data_dict)
        #end if
        #if $f.formatChoice.format_select == 'gff3'
            #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
            #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
                                            $extra_data_dict)
        #end if
        #if $f.formatChoice.format_select == "gtf"
            #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
            ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
            #silent $prepare_json("Gtf", $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 = {"false_path": str($fasta_file), "name": str($fasta_file.name)}
$data_parameter_dict.update({"fasta": $fasta_json})

## Retrieve the user email
#silent $data_parameter_dict.update({"user_email": str($__user_email__)})

#silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})

#silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})

#silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})

#silent $data_parameter_dict.update({"feature_tracks_type": str($advanced_options.feature_tracks_type)})

with open(file_path, 'w') as f:
    json.dump($data_parameter_dict, f)
        </configfile>
    </configfiles>

    <inputs>
        <param
                name="genome_name"
                type="text"
                size="30"
                value="unknown"
                label="JBrowse Hub Name"
        />
        <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="blastxml">BlastXML</option>
                        <option value="bigwig">BigWig</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="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                        <param name="longLabel" type="text" size="30" value = "Sequence Alignment" label="Track label" />
                        <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">BED Generic</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_generic"
                                        type="data"
                                        label="Bed File"
                                />
                                <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                            </when>
                            <when value="bed_simple_repeats_option">
                                <param
                                        format="bed"
                                        name="BED_simple_repeats"
                                        type="data"
                                        label="Bed Simple Repeats (Bed4+12) File"
                                />
                                <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                            </when>
                            <when value="bed_splice_junctions_option">
                                <param
                                        format="bed"
                                        name="BED_splice_junctions"
                                        type="data"
                                        label="Bed Splice Junctions (Bed12+1) File"
                                />
                                <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                            </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>
                                <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                            </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>
                                <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                            </when>
                        </conditional>
                        <param name="longLabel" type="text" size="30" label="Track label" />
                        <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="blastxml">
                        <param
                                format="blastxml"
                                name="BlastXML"
                                type="data"
                                label="Blast Alignments 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>
                        <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                        <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" />
                        <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="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                        <param name="longLabel" type="text" size="30" value="Sequence Coverage" label="Track label" />
                        <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="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                        <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" />
                        <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="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                        <param name="longLabel" type="text" size="30" value="Assembled Transcripts" label="Track name" />
                        <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>
            <when value="on">
                <param name="feature_tracks_type" type="select" label="Choose JBrowse feature tracks type">
                    <option value="CanvasFeatures" selected="true">CanvasFeatures</option>
                    <option value="HTMLFeatures">HTMLFeatures (Create a large number of range-indexed static JSON files. Don't choose this option if you want to upload/transfer output JBrowse hub to CyVerse Data Store!)
                    </option>
                </param>
                <param name="debug_mode" type="select" label="Activate debug mode">
                    <option value="false" selected="true">No</option>
                    <option value="true">Yes</option>
                    <help>
                        Use this option if you are a G-OnRamp developer
                    </help>
                </param>
            </when>
            <when value="off">
                <param name="debug_mode" type="hidden" value="false" />
                <param name="feature_tracks_type" type="hidden" value="CanvasFeatures" />
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data format="jbrowsehub" name="output" label="${tool.name}" />
    </outputs>
    <tests>
        <test>
            <param name="genome_name" value="Dbia3"/>
            <param name="fasta_file" value="common/dbia3.fa"/>
            <output name="output" file="only_genome/${tool.name}.html">
                <!-- Use macro to check the whole common structure without repeated code -->
                <expand macro="verify_hub_structure_no_track" test="only_genome" />
            </output>
        </test>
    </tests>
    <help>
        This Galaxy tool will prepare your files to be ready for visualization on JBrowse/Apollo.
    </help>
    <citations>
    </citations>
</tool>