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1 <tool id="annotate_contigs" name="Format Repeat Library" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="2.60.0">bioconductor-biostrings</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 $__tool_directory__/annotate_contigs.R '$contigs' '$cluster_table' '$annotated_contigs'
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7 ]]></command>
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8 <inputs>
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9 <param type="data" name="contigs" format="fasta" label="Contigs - Library of Repeats from TAREAN/RepeatExplorer pipeline" />
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10 <param type="data" name="cluster_table" format="txt" label="CLUSTER_TABLE from RepeatExplorer pipeline" help="CLUSTER_TABLE which contain annotation of clusters from RepeatExplorer pipeline"/>
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11 </inputs>
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12 <outputs>
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13 <data name="annotated_contigs" format="fasta" label="Annotated Repeat Library based on ${contigs.hid} and ${cluster_table.hid}" />
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14 </outputs>
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15 <help><![CDATA[
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16 **What this tool does**
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17
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18 Contigs from RepeatExplorer archive are annotated based on the classification of repeats from cluster_table.
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19
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20 Preformated CLUSTER_TABLE can be extracted from RepeatExplorer archive and modified accordingly. By default, "Final_annotation" column is used to append annotation to contigs in repeat library (based on the cluster id). If "Final_annotation" column is incomplete, "Automatic_annotation" column is used instead.
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21
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22 Example of tab delimited CLUSTER_TABLE::
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23
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24
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25 "Number_of_reads_in_clusters" 3886
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26 "Number_of_clusters" 822
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27 "Number_of_superclusters" 821
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28 "Number_of_singlets" 6114
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29 "Number_of_analyzed_reads" 10000
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30
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31 "Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation" "TAREAN_annotation" "Final_annotation"
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32 1 1 260 260 "All/repeat/satellite" "Putative satellites (low confidence)" ""
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33 2 2 157 157 "All/repeat/satellite" "Putative satellites (low confidence)" ""
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34 3 4 100 100 "All" "Other" ""
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35 4 5 83 83 "All" "Other" ""
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36 5 3 77 77 "All" "Other" ""
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37 6 3 65 65 "All" "Other" ""
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38 7 6 61 61 "All" "Other" ""
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39 8 7 58 58 "All" "Other" ""
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40 9 8 53 53 "All" "Other" ""
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41 10 9 53 53 "All" "Other" ""
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42 11 10 51 51 "All" "Other" ""
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43 12 11 45 45 "All" "Other" ""
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44 13 12 44 44 "All" "Other" ""
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45 14 13 44 44 "All" "Other" ""
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46 15 14 39 39 "All" "Other" ""
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47 16 15 37 37 "All" "Other" ""
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48 17 16 30 30 "All/repeat/satellite" "Putative satellites (low confidence)" ""
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49 18 17 28 28 "All/repeat/satellite" "Putative satellites (low confidence)" ""
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50 19 18 26 26 "All/repeat/satellite" "Putative satellites (high confidence)" ""
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51 20 19 23 23 "All/repeat/../CRM" "Other" ""
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52 21 20 21 21 "All" "Other" ""
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53 22 21 21 21 "All" "Other" ""
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54 23 22 21 21 "All" "Other" ""
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55 24 23 21 21 "All" "Other" ""
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56 25 24 20 20 "All/repeat/../Ogre" "Other" ""
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57
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58
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59 Only Cluster, Automatic_annotation/Final_annnotation are mandatory"
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60
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61 Clusters with higher number than those in CLUSTER_TABLE are removed from Repeat library
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62
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63 Contigs are provided in followinf format::
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64
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65
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66 >CL25Contig1
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67 AGATCAAGATGGCGCCGGAGGACATGGAGAAAACGACGTTTATCACTCCCTGGGGAACATTTTGCTACAAGGTAATGCCT
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68 TTCGGTCTGAAGAACGCAGGGGCCACTTACCAACGAGCAATGGTAACTT
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69 >CL1Contig4#All/repeat/satellite
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70 ACCCGAAGGCCGGCTCAACCCGAAGTTGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGA
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71 A
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72 >CL1Contig5
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73 TGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACCCGAAGT
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74 TGATAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACACGAAGT
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75 TGAGAGGAACATCTGACCTCGCCGTCAGGCATCTGTTAAA
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76
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77
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78 Resulting repeat library will have following format::
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79
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80 >CL25Contig1#All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre
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81 AGATCAAGATGGCGCCGGAGGACATGGAGAAAACGACGTTTATCACTCCCTGGGGAACATTTTGCTACAAGGTAATGCCT
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82 TTCGGTCTGAAGAACGCAGGGGCCACTTACCAACGAGCAATGGTAACTT
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83 >CL1Contig4#All/repeat/satellite
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84 ACCCGAAGGCCGGCTCAACCCGAAGTTGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGA
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85 A
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86 >CL1Contig5#All/repeat/satellite
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87 TGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACCCGAAGT
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88 TGATAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACACGAAGT
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89 TGAGAGGAACATCTGACCTCGCCGTCAGGCATCTGTTAAA
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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 </tool>
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