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1 <?xml version="1.0"?>
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2 <tool name="MGEScan" id="mgescan" version="3.0.0">
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3 <description>
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4 MGEScan
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5 </description>
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6 <requirements>
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7 <requirement type="package" version="3.0.0">mgescan</requirement>
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8 <requirement type="package" version="4.0">tandem_repeats_finder</requirement>
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9 <requirement type="package" version="5.0.0">emboss</requirement>
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10 <requirement type="package" version="3.1b1">hmmer</requirement>
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11 </requirements>
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12 <version_command>mgescan --version</version_command>
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13 <command interpreter="bash">
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14 mgescan.sh $input '$input.name' 3 $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3 $both_gff3 $mpi_yn.nmpi
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15 <!-- mgescan.sh $input $input.name $hmmver $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3 -->
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16 </command>
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17 <inputs>
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18 <param format="fasta,tabular,data" name="input" type="data" label="Input FASTA file(s)"/>
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19 <!--param name="hmmver" type="select" label="Hmmsearch version">
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20 <option selected="selected" value="3">3</option>
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21 <option value="2">2</option>
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22 </param-->
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23 <param name="program" type="select" label="MGEScan">
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24 <option selected="selected" value="B">Both</option>
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25 <option value="L">LTR</option>
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26 <option value="N">nonLTR</option>
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27 </param>
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28 <conditional name="mpi_yn">
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29 <param name="mpi_select" type="select" label="Enable MPI">
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30 <option value="no_mpi">No</option>
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31 <option value="yes_mpi">Yes</option>
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32 </param>
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33 <when value="yes_mpi">
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34 <param name="nmpi" format="txt" type="text" value="1" label="Number of MPI Processes"/>
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35 </when>
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36 <when value="no_mpi">
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37 <param name="nmpi" type="hidden" value="0"/>
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38 </when>
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39 </conditional>
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40 </inputs>
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41 <outputs>
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42 <data format="ltr.out" name="output" label="LTR Results (ltr.out)">
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43 <filter>program != "N"</filter>
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44 </data>
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45 <data format="fasta" name="clade" label="clade file (FASTA)">
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46 <filter>program != "L"</filter>
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47 </data>
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48 <data format="qfile" name="qvalue_en" label="qvalue_en">
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49 <filter>program != "L"</filter>
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50 </data>
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51 <data format="qfile" name="qvalue_rt" label="qvalue_rt">
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52 <filter>program != "L"</filter>
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53 </data>
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54 <data format="gff3" name="ltr_gff3" label="GFF3 for LTR">
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55 <filter>program != "N"</filter>
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56 </data>
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57 <data format="gff3" name="nonltr_gff3" label="GFF3 for nonLTR">
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58 <filter>program != "L"</filter>
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59 </data>
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60 <data format="gff3" name="both_gff3" label="GFF3 for LTR and nonLTR">
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61 <filter>program == "B"</filter>
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62 </data>
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63
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64 </outputs>
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65 <help>
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66 How to Run MGEScan
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67 ===================
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68
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69 * Select an input genome data from the select box, and choose a program. Both LTR and nonLTR of MGEScan is default.
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70 * Click 'Execute' button.
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71 * MPI will be enabled depending on your system support.
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72
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73 If you like to have more options to run LTR or nonLTR program, use separated tools on the left panel.
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74
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75 For example, in LTR > MGEScan-LTR, preprocessing by repeatmasker and setting other variables are available e.g. distance(bp) between LTRs.
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76
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77 Output
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78 ============
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79
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80 A. MGEScan_LTR:
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81
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82 Upon completion, MGEScan-LTR generates a file "ltr.out". This output file has information
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83 about clusters and coordinates of LTR retrotransposons identified. Each cluster of LTR
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84 retrotransposons starts with the head line of "[cluster_number]---------", followed by
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85 the information of LTR retrotransposons in the cluster. The columns for LTR
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86 retrotransposons are as follows.
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87
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88 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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89 2. start position of 5’ LTR.
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90 3. end position of 5’ LTR.
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91 4. start position of 3’ LTR.
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92 5. end position of 3’ LTR.
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93 6. strand: + or -.
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94 7. length of 5’ LTR.
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95 8. length of 3’ LTR.
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96 9. length of the LTR retrotransposon.
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97 10. TSD on the left side of the LTR retotransposons.
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98 11. TSD on the right side of the LTR retrotransposons.
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99 12. di(tri)nucleotide on the left side of 5’LTR
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100 13. di(tri)nucleotide on the right side of 5’LTR
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101 14. di(tri)nucleotide on the left side of 3’LTR
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102 15. di(tri)nucleotide on the right side of 3’LTR
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103
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104 B. MGEScan_nonLTR:
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105 Upon completion, MGEScan-nonLTR generates the directory, "info" in the data directory you
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106 specified. In this "info" directory, two sub-directories ("full" and "validation") are
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107 generated.
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108
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109 * The "full" directory is for storing sequences of elements. Each subdirectory in "full"
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110 is the name of clade. In each directory of clade, the DNA sequences of nonLTRs identified
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111 are listed. Each sequence is in fasta format. The header contains the position
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112 information of TEs identified: [genome_file_name]_[start position in the sequence]
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113
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114 For example, >chr1_333 means that this element start at 333bp in the "chr1" file.
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115
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116 * The "validation" directory is for storing Q values.
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117 In the files "en" and "rt", the first column corresponds to the element name and the last column Q value.
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118
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119 License
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120 ============
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121 Copyright 2015.
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122 You may redistribute this software under the terms of the GNU General Public License.
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123
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124 </help>
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125 </tool>
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