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comparison miRNARetrival.xml @ 0:aa09089f2c31 draft

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author 19zhang
date Tue, 13 Oct 2020 03:16:51 +0000
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1 <tool id="databases" name="miRNARetrival " version="20.05">
2 <!-- <description>aggregates annotated miRNAs provided by different miRNA databases</description> -->
3
4 <command><![CDATA[
5
6 bash ${__tool_directory__}/scripts/databases_mining.sh ${__tool_directory__} "$plant" $database $htmlreport1 $filelist
7
8 ]]></command>
9
10 <inputs>
11 <param name="plant" type="select" value="Choose" label="Species (support for 192 species)"
12 help="">
13 <options from_data_table="miRNA_species" >
14 <!-- <filter type="sort_by" column="1"/> -->
15 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
16 </options>
17 </param>
18
19 <param type="select" name="database" display="checkboxes" multiple="true"
20 label="miRNA databases"
21 help ="">
22 <option value="miRBase" selected="true">miRBase</option>
23 <option value="PmiREN" selected="true">PmiREN</option>
24 <option value="sRNAanno" selected="true">sRNAanno</option>
25 <option value="PlantsmallRNAgenes" selected="true">Plant small RNA genes</option>
26 </param>
27 </inputs>
28
29 <stdio><exit_code range="1:" level="fatal" description="Error Running miRNARetrival"/></stdio>
30
31 <outputs>
32 <data format="html" name="htmlreport1" label="${plant.value} | ${tool.name} | Overview of already annotated miRNAs in public databases" />
33 <data format="zip" name="filelist" label="${plant.value} | ${tool.name} | Collection of ${plant.value} miRNAs from public databases" />
34 </outputs>
35
36 <help>
37
38 |
39
40 .. class:: donemark
41
42 **What it does**
43
44 This tool is designed to integrate four representative miRNA databases (`miRBase`_, `PmiREN`_, `sRNAanno`_, and `Plant small RNA genes`_) into
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.
46
47 .. class:: infomark
48
49 **Inputs**
50
51 - **miRNA databases**: Choose miRNA databases (at least one).
52
53 .. class:: infomark
54
55 **Outputs**
56
57 - **Overview of already annotated miRNAs in public databases**: An HTML document recording the comprehensive information of already annotated miRNAs reported in selected databases.
58 - **Collection of {species} miRNAs from public databases**: A packaged file containing miRNAs in each database.
59
60 .. _`miRBase`: http://www.mirbase.org/
61 .. _`PmiREN`: http://www.pmiren.com/
62 .. _`sRNAanno`: http://plantsrnas.org/
63 .. _`Plant small RNA genes`: http://plantsmallrnagenes.science.psu.edu/
64 .. _`GMAP`: https://academic.oup.com/bioinformatics/article/21/9/1859/409207
65
66 .. class:: infomark
67
68 **About**
69
70 - **miRBase:** The miRBase database is the central online repository of published miRNA sequences and annotations.
71
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.
73
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.
75
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.
77
78 For details, please see the following tableļ¼š
79
80 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
81 | **Database** | **Date** | **Version** | **Species** | **Small RNA type** |
82 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
83 | miRBase | 2019 | v22.1 | 86 plants (1 chlorophytes, 3 mosses, 4 gymnosperms, 1 basal angiosperm, 14 monocotyledons, and 63 eudicotyledons) | miRNA |
84 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
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 |
86 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
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 |
88 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
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 |
90 +-----------------------+----------+-------------+---------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------+
91
92 |
93
94 </help>
95
96 <citations>
97 <citation type="doi">10.1093/nar/gky1141</citation>
98 <citation type="doi">10.1093/nar/gkz894</citation>
99 <citation type="doi">10.1101/gr.256750.119</citation>
100 <citation type="doi">10.1101/771121</citation>
101 <!-- <citation type="doi">10.1093/bioinformatics/bti310</citation> -->
102 </citations>
103
104 </tool>