view jbrowse_hub.xml @ 2:d048f9f9f9df draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty

<tool id="jbrowse_hub" name="JBrowse Hub Creator" version="1.0">
    <description>
        This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse
    </description>

    <requirements>
        <requirement type="package" version="1.9">numpy</requirement>
        <requirement type="package" version="1.68">biopython</requirement>
    </requirements>

    <stdio>
    </stdio>

    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/jbrowse_hub.py
        --fasta '$reference' 
        #for $f in $format
            #if $f.formatChoice.format_select == 'bed'
                #if $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option'
                    --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
                #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
                    --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
                #end if
            #end if
            #if $f.formatChoice.format_select == 'bam'
                --bam $f.formatChoice.BAM
            #end if
            #if $f.formatChoice.format_select == 'gff3'
                --gff3 $f.formatChoice.GFF3
            #end if
            #if $f.formatChoice.format_select == 'blastxml'
                --blastxml $f.formatChoice.BlastXML
            #end if
            #if $f.formatChoice.format_select == 'gtf'
                --gtf $f.formatChoice.GTF
            #end if
            #if $f.formatChoice.format_select == 'bigwig'
                --bigwig $f.formatChoice.BIGWIG
            #end if
       #end for
        --out $output
    ]]></command>

    <inputs>
        <param name="reference" type="data" format="fasta" label="Reference Genome" />
        <param name="output" type="text" size="30" value="unknown" label="Output folder" />
            <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"
                        />
                    </when>     
                    <when value="bed">
                        <conditional name="bedChoice">
                            <param name="bed_select" type="select" label="Bed Choice">
                                <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>
                            </param>
                            <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>
                        </conditional>
                    </when>
                    <when value="blastxml">
                        <param
                                format="blastxml"
                                name="BlastXML"
                                type="data"
                                label="Blast Alignments File"
                        />
                    </when>
                    <when value="bigwig">
                        <param
                                format="bigwig"
                                name="BIGWIG"
                                type="data"
                                label="BIGWIG File"
                        />
                    </when>
                    <when value="gff3">
                        <param
                                format="gff3"
                                name="GFF3"
                                type="data"
                                label="GFF3 File"
                        />
                    </when>
                    <when value="gtf">
                        <param
                                format="gtf"
                                name="GTF"
                                type="data"
                                label="GTF File"
                        />
                    </when>  
            </conditional>
        </repeat>
    </inputs>

    <outputs>
        <data format="tar" name="JBrowseHub" label="${tool.name} on ${output}" />
    </outputs>
    <tests>
        <test>
            <param name="reference" value="dbia3/raw/dbia3.fa" />
            <param name="output" value="hubtest" />
            <repeat name="format">
                <conditional name="formatChoice">
                    <param name="format_select" value="gff3"/>
                    <param name="GFF3" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
                </conditional>
            </repeat>
            <output name="JBrowseHub" file="hubtest.tar" />
        </test>
    </tests>
    <help>
        This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for
        JBrowse visualization.
    </help>
    <citations>
    </citations>
</tool>