<tool id="databases" name="miRNARetrival " version="20.05">
    <!-- <description>aggregates annotated miRNAs provided by different miRNA databases</description> -->

    <command><![CDATA[

        bash ${__tool_directory__}/scripts/databases_mining.sh ${__tool_directory__} "$plant" $database $htmlreport1 $filelist

    ]]></command>

    <inputs>
        <param name="plant" type="select" value="Choose" label="Species (support for 192 species)"
            help="">
            <options from_data_table="miRNA_species" >
                <!-- <filter type="sort_by" column="1"/> -->
                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
            </options>
        </param>

        <param type="select" name="database" display="checkboxes" multiple="true"
            label="miRNA databases"
            help ="">
            <option value="miRBase" selected="true">miRBase</option>
            <option value="PmiREN" selected="true">PmiREN</option>
            <option value="sRNAanno" selected="true">sRNAanno</option>
            <option value="PlantsmallRNAgenes" selected="true">Plant small RNA genes</option>
        </param>
    </inputs>

    <stdio><exit_code range="1:" level="fatal" description="Error Running miRNARetrival"/></stdio>

    <outputs>
        <data format="html" name="htmlreport1" label="${plant.value} | ${tool.name} | Overview of already annotated miRNAs in public databases" />
        <data format="zip" name="filelist" label="${plant.value} | ${tool.name} | Collection of ${plant.value} miRNAs from public databases" />
    </outputs>

<help>

|

.. class:: donemark

**What it does**

This tool is designed to integrate four representative miRNA databases (`miRBase`_, `PmiREN`_, `sRNAanno`_, and `Plant small RNA genes`_) into
a unified HTML document, which contains the size, length distribution, and composition of the first base of miRNA families, enabling users to easily perform comparative analysis.

.. class:: infomark

**Inputs**

- **miRNA databases**: Choose miRNA databases (at least one).

.. class:: infomark

**Outputs**

- **Overview of already annotated miRNAs in public databases**: An HTML document recording the comprehensive information of already annotated miRNAs reported in selected databases.
- **Collection of {species} miRNAs from public databases**: A packaged file containing miRNAs in each database.

.. _`miRBase`: http://www.mirbase.org/
.. _`PmiREN`: http://www.pmiren.com/
.. _`sRNAanno`: http://plantsrnas.org/
.. _`Plant small RNA genes`: http://plantsmallrnagenes.science.psu.edu/
.. _`GMAP`: https://academic.oup.com/bioinformatics/article/21/9/1859/409207

.. class:: infomark

**About**

- **miRBase:** The miRBase database is the central online repository of published miRNA sequences and annotations.

- **PmiREN (Plant miRNA ENcyclopedia):** The PmiREN is a comprehensive functional plant miRNA database. In current version, PmiREN contains 20,388 miRNA loci (MIRs) belonging to 5,757 families, 1,365 clusters, 1,668 syntenic blocks and 141,327 predicted miRNA-target pairs in 88 species phylogenetically ranging from chlorophytes to angiosperms. In addition, 1,537 deeply sequenced small RNA libraries were used in quantification of miRNA expression pattern.

- **sRNAanno:** The sRNAanno hosts a large collection of miRNA, phasiRNA- and hc-siRNA-generating loci annotated from ~140 plants using consistent and high-confidence criteria.

- **Plant small RNA genes:** The 'Plant small RNA genes' database analyzed a large data set of published and newly generated sRNA sequencing data (1,333 sRNA-seq libraries containing more than 20 billion reads) and used a uniform bioinformatic pipeline to produce comprehensive sRNA loci annotations of 47 diverse plants, yielding more than 2.7 million sRNA loci.

For details, please see the following table：

+-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
|  **Database**         | **Date** | **Version** |  **Species**                                                                                                                                | **Small RNA type**                         |
+-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
| miRBase               | 2019     |  v22.1      | 86 plants (1 chlorophytes, 3 mosses, 4 gymnosperms, 1 basal angiosperm, 14 monocotyledons, and 63 eudicotyledons)                           | miRNA                                      |
+-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
| PmiREN                | 2019     |  v1.0       | 88 plants (2 chlorophytes, 1 moss, 1 lycophyte, 2 gymnosperms, 1 basal angiosperm, 1 magnoliidae, 18 monocotyledons, and 62 eudicotyledons) | miRNA                                      |
+-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
| sRNAanno              | 2020     |  v1.0       | 143 plants (2 chlorophytes, 3 mosses, 2 fernes, 2 gymnosperms, 1 basal angiosperm, 2 Magnoliids,  28 monocotyledons, and 103 eudicotyledons)| miRNA, phasiRNA, hc-siRNA                  |
+-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
| Plant small RNA genes | 2019     |  v1.0       | 47 plants (2 mosses, 1 gymnosperm, 1 basal angiosperm, 9 monocotyledons, and 34 eudicotyledons)                                             | miRNA, nearMIRNA, 20-24nt siRNA,  otherRNA |
+-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+

|

    </help>

    <citations>
        <citation type="doi">10.1093/nar/gky1141</citation>
        <citation type="doi">10.1093/nar/gkz894</citation>
        <citation type="doi">10.1101/gr.256750.119</citation>
        <citation type="doi">10.1101/771121</citation>
        <!-- <citation type="doi">10.1093/bioinformatics/bti310</citation> -->
    </citations>

</tool>