view jbrowseArchiveCreator.xml @ 28:0c075fac6719 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty

<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="1.0.1">
    <description>
        This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
    </description>

    <requirements>
        <requirement type="package" version="1.2">samtools</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="3.0.3">apollo_api</requirement>
        <requirement type="package" version="1.12.1">jbrowse_tools</requirement>
    </requirements>

    <stdio>
    </stdio>

    <command detect_errors="exit_code"><![CDATA[
        mkdir -p $output.extra_files_path;
        
        ## Dump the tool parameters into a JSON file 
        python $json_file parameters.json;

        python $__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)})
#silent $data_parameter_dict.update({"apollo_host": str($apollo_host)})
if $apollo_users_settings.apollo_users_selector == "yes":
    #set apollo_user = {"firstname": str($apollo_users_settings.firstname), "lastname": str($apollo_users_settings.lastname), "password": str($apollo_users_settings.password), "user_email": str($apollo_users_settings.user_email)}
    $data_parameter_dict.update({"apollo_user": $apollo_user})

## 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})

            #silent $prepare_json("Bam", $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"
                #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED, $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"
                #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
        #end if
        #if $f.formatChoice.format_select == "bigwig"
            #set pos_color = str($f.formatChoice.pos_color)
            #set neg_color = str($f.formatChoice.neg_color)
            #silent $extra_data_dict.update({"style" : {"pos_color" : $pos_color, "neg_color" : $neg_color}})
            #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
                                            $extra_data_dict)
        #end if
        #if $f.formatChoice.format_select == 'gff3'
            #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_generic'
                #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
                                            $extra_data_dict)
            #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript'
                #silent $prepare_json("Gff3_transcript", $f.formatChoice.GFF3, $index_track_final,
                                            $extra_data_dict)
            #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_mrna'
                #silent $prepare_json("Gff3_mrna", $f.formatChoice.GFF3, $index_track_final,
                                            $extra_data_dict)
            #end if
        #end if
        #if $f.formatChoice.format_select == "gtf"
            ## 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)})

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"
        />
        <param
                name="apollo_host"
                type="text"
                label="Apollo host"
        />
        <conditional name="apollo_users_settings">
            <param name="apollo_users_selector" type="select" label="Create or specify your Apollo account">
                <option value="no" selected="true">Use exist demo user account (will use your galaxy email address for apollo, password: gonramp) </option>
                <option value="yes">Create or use your own Apollo account</option>
            </param>
            <!-- TODO: Avoid redundancy here -->
            <when value="yes">
                <param
                    name="firstname"
                    type="text"
                    label="First Name"
                />
                <param
                    name="lastname"
                    type="text"
                    label="Last Name"
                />
                <param
                    name="user_email"
                    type="text"
                    label="Email Address"
                />
                <param
                    name="password"
                    type="text"
                    label="Password"
                />
            </when>
            <when value="no">
                <param name="default_user" type="hidden"
                       value="false">
                </param>
            </when>
        </conditional>
        
        <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="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 format</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"
                                />
                            </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"
                                />
                            </when>
                            <when value="bed_blat_alignment_option">
                                <param
                                        format="bed"
                                        name="BED_blat_alignment"
                                        type="data"
                                        label="Bed BLAT Alignments (bigPsl) File"
                                />
                            </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="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="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">
                        <conditional name="gff3Choice">
                            <param name="gff3_select" type="select" label="gff3 type">
                                <option value="gff3_generic">GFF3 format</option>
                                <option value="gff3_transcript">GFF3 format output from gene prediction tools (e.g. Augustus), structure: gene->transcription->CDS</option>
                                <option value="gff3_mrna">GFF3 format output from gene prediction tools (e.g. SNAP), structure: gene->mRNA->CDS</option>
                            </param>
                            <when value="gff3_generic">
                                <param
                                        format="gff3"
                                        name="GFF3_generic"
                                        type="data"
                                        label="GFF3 File"
                                />
                            </when>
                            <when value="gff3_transcript">
                                <param
                                        format="gff3"
                                        name="GFF3_transcript"
                                        type="data"
                                        label="GFF3 File from gene prediction"
                                />
                            </when>
                            <when value="gff3_mrna">
                                <param
                                        format="gff3"
                                        name="GFF3_mrna"
                                        type="data"
                                        label="GFF3 File from gene prediction"
                                />
                            </when>
                        </conditional>
                        <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" />
                        <param name="track_color" type="color" label="Track color" value="#daa520">
                            <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="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>
            <!-- TODO: Avoid redundancy here -->
            <when value="on">
                <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>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data format="jbrowsehub" name="output" label="${tool.name}" />
    </outputs>
    <tests>
        <test>
            <param name="reference" value="dbia3/raw/dbia3.fa" />
            <param name="genome_name" value="unknown" />
            <param name="group_name" value="Default group"/>
            <param name="format_select" value="bam" />
            <param name="BAM" value="dbia3/raw/HISAT.bam" />
            <param name="label" value="" />             
            <output name="output" file="JBrowse_Archive_Creator_html.html" />
        </test>
    </tests>
    <help>
        This Galaxy tool will create a jbrowse hub which including binary datasets and json datasets that can be used for
        JBrowse visualization.
    </help>
    <citations>
    </citations>
</tool>