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1 <?xml version="1.0"?>
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2
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3 <tool name="MGEScan-LTR" id="mgescan-ltr" version="0.0.1" workflow_compatible="false">
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4 <description>
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5 de novo identification of LTR retroelements
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6 </description>
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7 <!--
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8 <action module="galaxy.tools.actions.nonltr" class="nonltrToolAction"/>
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9 <requirements>
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10 <requirement type="package">HMMER</requirement>
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11 <requirement type="package">EMBOSS</requirement>
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12 </requirements>
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13 -->
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14 <command interpreter="bash">
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15 <!--
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16 /u/lee212/retrotminer/MGEScan_LTR/find_ltr.pl -genome=/u/lee212/retrotminer/MGEScan_nonLTR_v2/anoGam1/
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17 -data=/u/lee212/retrotminer/MGEScan_LTR/example/data/ -program=/u/lee212/retrotminer/MGEScan_LTR/
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18 -->
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19 <!--mgescan.sh $input $input.name $hmmver $output L None None None $ltr_gff3 None-->
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20 <!--mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None-->
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21 mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None $sw_rm "$scaffold" $min_dist $max_dist $min_len_ltr $max_len_ltr $ltr_sim_condition $cluster_sim_condition $len_condition $repeatmasker
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22 </command>
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23 <inputs>
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24 <!--
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25 <param name="genome" type="text" label="directory where input genome data exists" />
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26 <param name="data" type="text" label="directory of the output" />
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27 -->
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28 <param format="txt" name="input" type="data" label="From"/>
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29 <!--param name="hmmver" type="select" label="Hmmsearch version">
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30 <option selected="selected" value="3">3</option>
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31 <option value="2">2</option>
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32 </param-->
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33 <!-- path.conf -->
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34 <param name="sw_rm" type="select" display="checkboxes" multiple="True" label="enable repeatmasker, if necessary" help="Use this option if you are enable repeatmasker">
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35 <option value="Yes">Yes</option>
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36 </param>
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37 <param name="scaffold" type="text" label="path for the big file that has all scaffolds"/>
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38 <!-- value.conf -->
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39 <param name="min_dist" type="text" value="2000" label="minimum distance(bp) between LTRs" />
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40 <param name="max_dist" type="text" value="20000" label="maximum distance(bp) between LTRs" />
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41 <param name="min_len_ltr" type="text" value="130" label="minimum length(bp) of LTR"/>
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42 <param name="max_len_ltr" type="text" value="2000" label="maximum length(bp) of LTR"/>
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43 <param name="ltr_sim_condition" type="text" value="70" label="minimum similarity(%) for LTRs in an element"/>
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44 <param name="cluster_sim_condition" type="text" value="70" label="inimum similarity(%) for LTRs in a cluster"/>
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45 <param name="len_condition" type="text" value="70" label="minimum length(bp) for LTRs aligned in local alignment"/>
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46 </inputs>
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47 <outputs>
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48 <data format="ltr.out" name="output" />
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49 <data format="gff3" name="ltr_gff3" />
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50 <data format="repeatmasker" name="repeatmasker" >
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51 <filter>sw_rm == "Yes"</filter>
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52 </data>
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53 </outputs>
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54 <help>
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55 Running the program
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56 ===================
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57
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58 To run MGEScan-LTR, follow the steps below,
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59
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60 1. Specify options that you like to have:
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61
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62 * Check repeatmasker if you want to preprocess
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63 * Check scaffold if the input file has all scaffolds.
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64
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65 2. Update values:
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66
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67 * min_dist: minimum distance(bp) between LTRs.
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68 * max_dist: maximum distance(bp) between LTRS
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69 * min_len_ltr: minimum length(bp) of LTR.
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70 * max_len_ltr: maximum length(bp) of LTR.
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71 * ltr_sim_condition: minimum similarity(%) for LTRs in an element.
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72 * cluster_sim_condition: minimum similarity(%) for LTRs in a cluster
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73 * len_condition: minimum length(bp) for LTRs aligned in local alignment.
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74
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75 4. Click 'Execute'
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76
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77 * mask known repeats other than LTR retrotransposons
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78 * identify LTRs
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79
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80 Output
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81 ======
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82
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83 Upon completion, MGEScan-LTR generates a file ltr.out. This output file has information
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84 about clusters and coordinates of LTR retrotransposons identified. Each cluster of LTR
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85 retrotransposons starts with the head line of [cluster_number]---------, followed by
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86 the information of LTR retrotransposons in the cluster. The columns for LTR
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87 retrotransposons are as follows.
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88
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89 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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90 2. start position of 5 LTR.
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91 3. end position of 5 LTR.
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92 4. start position of 3 LTR.
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93 5. end position of 3 LTR.
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94 6. strand: + or -.
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95 7. length of 5 LTR.
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96 8. length of 3 LTR.
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97 9. length of the LTR retrotransposon.
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98 10. TSD on the left side of the LTR retotransposons.
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99 11. TSD on the right side of the LTR retrotransposons.
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100 12. di(tri)nucleotide on the left side of 5LTR
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101 13. di(tri)nucleotide on the right side of 5LTR
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102 14. di(tri)nucleotide on the left side of 3LTR
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103 15. di(tri)nucleotide on the right side of 3LTR
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104
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105 License
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106 ============
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107
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108 Copyright 2014 Mina Rho, Haixu Tang.
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109 You may redistribute this software under the terms of the GNU General Public License.
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110 </help>
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111 </tool>
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