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1 <?xml version="1.0"?>
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2
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3 <tool name="MGEScan" id="mgescan" version="0.0.1" workflow_compatible="false">
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4 <description>
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5 MGEScan
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6 </description>
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7 <command interpreter="bash">
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8 mgescan.sh $input '$input.name' 3 $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3
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9 <!-- mgescan.sh $input $input.name $hmmver $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3 -->
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10 </command>
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11 <inputs>
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12 <param format="txt" name="input" type="data" label="From"/>
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13 <!--param name="hmmver" type="select" label="Hmmsearch version">
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14 <option selected="selected" value="3">3</option>
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15 <option value="2">2</option>
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16 </param-->
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17 <param name="program" type="select" label="MGEScan">
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18 <option selected="selected" value="B">Both</option>
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19 <option value="L">LTR</option>
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20 <option value="N">nonLTR</option>
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data format="ltr.out" name="output">
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25 <filter>program != "N"</filter>
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26 </data>
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27 <data format="fasta" name="clade">
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28 <filter>program != "L"</filter>
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29 </data>
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30 <data format="qfile" name="qvalue_en">
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31 <filter>program != "L"</filter>
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32 </data>
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33 <data format="qfile" name="qvalue_rt">
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34 <filter>program != "L"</filter>
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35 </data>
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36 <data format="gff3" name="ltr_gff3">
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37 <filter>program != "N"</filter>
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38 </data>
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39 <data format="gff3" name="nonltr_gff3">
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40 <filter>program != "L"</filter>
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41 </data>
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42
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43 </outputs>
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44 <help>
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45 Running the program
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46 ===================
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47
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48 To run MGEScan, select input genome data in From select box, and select program either LTR, nonLTR or both.
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49
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50 Click 'Execute' button.
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51
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52 If you like to have more options to run LTR or nonLTR progrma, use separated tools on the left panel.
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53 In LTR > MGEScan-LTR, preprocessing by repeatmasker and setting other variables are available e.g. distance(bp) between LTRs.
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54
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55 Output
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56 ============
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57 A. MGEScan_LTR:
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58 Upon completion, MGEScan-LTR generates a file "ltr.out". This output file has information
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59 about clusters and coordinates of LTR retrotransposons identified. Each cluster of LTR
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60 retrotransposons starts with the head line of "[cluster_number]---------", followed by
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61 the information of LTR retrotransposons in the cluster. The columns for LTR
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62 retrotransposons are as follows.
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63
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64 1. LTR_id: unique id of LTRs identified. It consist of two components, sequence file name and id in the file. For example, chr1_2 is the second LTR retrotransposon in the chr1 file.
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65 2. start position of 5’ LTR.
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66 3. end position of 5’ LTR.
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67 4. start position of 3’ LTR.
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68 5. end position of 3’ LTR.
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69 6. strand: + or -.
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70 7. length of 5’ LTR.
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71 8. length of 3’ LTR.
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72 9. length of the LTR retrotransposon.
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73 10. TSD on the left side of the LTR retotransposons.
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74 11. TSD on the right side of the LTR retrotransposons.
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75 12. di(tri)nucleotide on the left side of 5’LTR
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76 13. di(tri)nucleotide on the right side of 5’LTR
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77 14. di(tri)nucleotide on the left side of 3’LTR
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78 15. di(tri)nucleotide on the right side of 3’LTR
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79
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80 B. MGEScan_nonLTR:
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81 Upon completion, MGEScan-nonLTR generates the directory, "info" in the data directory you
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82 specified. In this "info" directory, two sub-directories ("full" and "validation") are
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83 generated.
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84
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85 - The "full" directory is for storing sequences of elements. Each subdirectory in "full"
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86 is the name of clade. In each directory of clade, the DNA sequences of nonLTRs identified
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87 are listed. Each sequence is in fasta format. The header contains the position
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88 information of TEs identified:
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89 [genome_file_name]_[start position in the sequence]
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90
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91 For example, >chr1_333 means that this element start at 333bp in the "chr1" file.
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92
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93 - The "validation" directory is for storing Q values. In the files "en" and "rt", the first column corresponds to the element name and the last column Q value.
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94
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95 License
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96 ============
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97 Copyright 2014 Mina Rho, Haixu Tang.
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98 You may redistribute this software under the terms of the GNU General Public License.
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99
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100 </help>
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101 </tool>
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