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1 <tool id="databases" name="miRNARetrival " version="20.05">
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2 <!-- <description>aggregates annotated miRNAs provided by different miRNA databases</description> -->
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3
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4 <command><![CDATA[
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5
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6 bash ${__tool_directory__}/scripts/databases_mining.sh ${__tool_directory__} "$plant" $database $htmlreport1 $filelist
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7
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8 ]]></command>
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9
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10 <inputs>
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11 <param name="plant" type="select" value="Choose" label="Species (support for 192 species)"
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12 help="">
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13 <options from_data_table="miRNA_species" >
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14 <!-- <filter type="sort_by" column="1"/> -->
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15 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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16 </options>
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17 </param>
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18
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19 <param type="select" name="database" display="checkboxes" multiple="true"
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20 label="miRNA databases"
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21 help ="">
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22 <option value="miRBase" selected="true">miRBase</option>
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23 <option value="PmiREN" selected="true">PmiREN</option>
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24 <option value="sRNAanno" selected="true">sRNAanno</option>
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25 <option value="PlantsmallRNAgenes" selected="true">Plant small RNA genes</option>
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26 </param>
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27 </inputs>
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28
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29 <stdio><exit_code range="1:" level="fatal" description="Error Running miRNARetrival"/></stdio>
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30
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31 <outputs>
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32 <data format="html" name="htmlreport1" label="${plant.value} | ${tool.name} | Overview of already annotated miRNAs in public databases" />
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33 <data format="zip" name="filelist" label="${plant.value} | ${tool.name} | Collection of ${plant.value} miRNAs from public databases" />
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34 </outputs>
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35
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36 <help>
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37
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38 |
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39
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40 .. class:: donemark
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41
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42 **What it does**
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43
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44 This tool is designed to integrate four representative miRNA databases (`miRBase`_, `PmiREN`_, `sRNAanno`_, and `Plant small RNA genes`_) into
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45 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.
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46
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47 .. class:: infomark
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48
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49 **Inputs**
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50
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51 - **miRNA databases**: Choose miRNA databases (at least one).
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52
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53 .. class:: infomark
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54
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55 **Outputs**
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56
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57 - **Overview of already annotated miRNAs in public databases**: An HTML document recording the comprehensive information of already annotated miRNAs reported in selected databases.
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58 - **Collection of {species} miRNAs from public databases**: A packaged file containing miRNAs in each database.
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59
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60 .. _`miRBase`: http://www.mirbase.org/
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61 .. _`PmiREN`: http://www.pmiren.com/
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62 .. _`sRNAanno`: http://plantsrnas.org/
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63 .. _`Plant small RNA genes`: http://plantsmallrnagenes.science.psu.edu/
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64 .. _`GMAP`: https://academic.oup.com/bioinformatics/article/21/9/1859/409207
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65
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66 .. class:: infomark
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67
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68 **About**
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69
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70 - **miRBase:** The miRBase database is the central online repository of published miRNA sequences and annotations.
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71
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72 - **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.
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73
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74 - **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.
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75
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76 - **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.
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77
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78 For details, please see the following tableļ¼
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79
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80 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
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81 | **Database** | **Date** | **Version** | **Species** | **Small RNA type** |
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82 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
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83 | miRBase | 2019 | v22.1 | 86 plants (1 chlorophytes, 3 mosses, 4 gymnosperms, 1 basal angiosperm, 14 monocotyledons, and 63 eudicotyledons) | miRNA |
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84 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
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85 | 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 |
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86 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
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87 | 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 |
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88 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
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89 | 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 |
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90 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
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91
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92 |
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93
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94 </help>
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95
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96 <citations>
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97 <citation type="doi">10.1093/nar/gky1141</citation>
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98 <citation type="doi">10.1093/nar/gkz894</citation>
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99 <citation type="doi">10.1101/gr.256750.119</citation>
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100 <citation type="doi">10.1101/771121</citation>
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101 <!-- <citation type="doi">10.1093/bioinformatics/bti310</citation> -->
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102 </citations>
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103
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104 </tool>
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