<tool id="genomeindex" name="genomePrepare" workflow_compatible="false" version="20.05">
    <!-- <description>get genome sequences, annotation and file path (built-in or uploaded)</description> -->

    <command><![CDATA[
        bash ${__tool_directory__}/scripts/obtainSpecies.sh
            --curpath ${__tool_directory__}
            #if $genometype.datainput == "UploadData":
                --name "$genometype.speciename"
                --genome $genometype.genomeData
                --gff $genometype.annotationData
                --otherrna $genometype.otherrna
                --transcript $genometype.transcriptsData
                --protein $genometype.proteinsData
                --speciesout $filePath
                --infout $infout1
            #else
                --ensembl "$genometype.buildplant"
                --verorder "$genometype.version"

                --outgenome $outgenome
                --outgff3 $outgff3
                --outtranscript $outtranscript
                --outtrsnsnoRNA $outtrsnsnoRNA
                --outprotein $outprotein

                --speciesout $builtinPath
                --infout $infout2
            #end if

    ]]></command>

    <inputs>
        <conditional name="genometype">
            <!-- <param name="datainput" type="boolean"  truevalue="yes" falsevalue="no" checked="true"
                label="Upload your own genome data?" help ="User can also select built-in species by clicking the button-No " /> -->
            <param type="select" name="datainput" display="radio" multiple="false" help="Note: for 'upload from local disk', please upload files by uploadFile function first."
                label="Two ways for preparing genome data:" >
                <option value="BuiltinSpecies" selected="true" > Download from EnsemblPlants database</option>
		             <option value="UploadData"> Upload from local disk</option>
            </param>

            <when value="BuiltinSpecies">
                <param name="buildplant" type="select"
                    label="Species (support for 61 species)"
                    help="">
                    <options from_data_table="ensembl_plant" >
                        <!-- <filter type="sort_by" column="1"/>
                        <validator type="no_options" message="No indexes are available for the selected input dataset"/> -->
                    </options>
                </param>

                <param name="version" type="select"
                    label="Database version"
                    help="">
                    <options from_data_table="ensembl_plant_version">
                        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                    </options>
                </param>

            </when>

            <when value="UploadData">
                <param type="text" name="speciename" value=""
                    label="Species"
                    help="e.g. Arabidopsis thaliana" />

                <param name="genomeData" type="data" format="fasta" optional="true" label="Genome sequences (.fasta)" />
                <param name="annotationData" type="data" format="gff3" optional="true" label="Annotation file (.gff3)" />
                <param name="otherrna" type="data" format="fasta" optional="true" label="t/r/sn/snoRNA sequences (.fasta)" />
                <param name="transcriptsData" type="data" format="fasta" optional="true" label="cDNA sequences (.fasta)" />
                <param name="proteinsData" type="data" format="fasta" optional="true" label="Optional: Protein sequences (.fasta)" />
            </when>
        </conditional>
    </inputs>

    <stdio><exit_code range="1:" level="fatal" description="Error when running ${tool.name}"/></stdio>

    <outputs>
        <data format="simple" name="filePath" label="${genometype.speciename.value}">
            <filter> genometype['datainput'] == "UploadData" </filter>
        </data>
        <data format="pdf" name="infout1" label="${genometype.speciename.value} | ${tool.name} | Summary of genomic features">
            <filter> genometype['datainput'] == "UploadData" </filter>
        </data>
        <data format="simple" name="builtinPath" label="${genometype.buildplant.value}_${genometype.version.value}">
            <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
        </data>
        <data format="pdf" name="infout2" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | Summary of genomic features">
            <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
        </data>
        <data format="gz" name="outgenome" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | Genome sequences ">
            <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
        </data>
        <data format="fasta" name="outtrsnsnoRNA" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | t/r/sn/snoRNA sequences">
            <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
        </data>
        <data format="gff3" name="outgff3" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | GFF3 annotations">
            <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
        </data>
        <data format="fasta" name="outtranscript" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | cDNA sequences">
            <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
        </data>
        <data format="fasta" name="outprotein" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | Protein sequences">
            <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
        </data>

    </outputs>

    <tests>
        <test>
            <param name="genomeData" value="Arabidopsis_genome.fa" ftype="fasta" />
            <param name="annotationData" value="Arabidopsis_annotation.gff3" ftype="fasta" />
            <output name="filePath" file="genomePrepare: References_of_Arabidopsis_thaliana.simple" ftype="simple" />
        </test>

    </tests>


<help><![CDATA[

.. class:: donemark

**What it does**

This tool provides two ways for preparing genome data:

    1. Automatically download genomes, annotations, t/r/sn/snoRNAs (i.e. tRNAs, rRNAs, snRNAs, and snoRNAs), cDNAs, and proteins from `EnsemblPlants database`_.
    2. Upload genomic data for species not included in EnsemblPlants.

.. class:: infomark

**Outputs**

    - A file containing the path of formatted genome sequences and annotations. Index files of the reference genome and t/r/sn/snoRNA sequences in this path are used for 'miRNAPredict' analysis.
    - Summary of the number and length of genomic features.
    - Genome sequences, annotation file in GFF3 format, t/r/sn/snoRNA sequences, cDNAs, and protein sequences.

.. _`EnsemblPlants database`: ftp://ftp.ensemblgenomes.org/pub/plants

|

    ]]></help>

    <citations>
        <citation type="doi">10.1007/978-1-4939-6658-5_1</citation>
    </citations>

</tool>