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"planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
author petrn
date Tue, 15 Feb 2022 16:44:31 +0000
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1 <tool id="annotate_contigs" name="Format Repeat Library" version="0.1.0" python_template_version="3.5">
2 <requirements>
3 <requirement type="package" version="2.60.0">bioconductor-biostrings</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 $__tool_directory__/annotate_contigs.R '$contigs' '$cluster_table' '$annotated_contigs'
7 ]]></command>
8 <inputs>
9 <param type="data" name="contigs" format="fasta" label="Contigs - Library of Repeats from TAREAN/RepeatExplorer pipeline" />
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"/>
11 </inputs>
12 <outputs>
13 <data name="annotated_contigs" format="fasta" label="Annotated Repeat Library based on ${contigs.hid} and ${cluster_table.hid}" />
14 </outputs>
15 <help><![CDATA[
16 **What this tool does**
17
18 Contigs from RepeatExplorer archive are annotated based on the classification of repeats from cluster_table.
19
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.
21
22 Example of tab delimited CLUSTER_TABLE::
23
24
25 "Number_of_reads_in_clusters" 3886
26 "Number_of_clusters" 822
27 "Number_of_superclusters" 821
28 "Number_of_singlets" 6114
29 "Number_of_analyzed_reads" 10000
30
31 "Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation" "TAREAN_annotation" "Final_annotation"
32 1 1 260 260 "All/repeat/satellite" "Putative satellites (low confidence)" ""
33 2 2 157 157 "All/repeat/satellite" "Putative satellites (low confidence)" ""
34 3 4 100 100 "All" "Other" ""
35 4 5 83 83 "All" "Other" ""
36 5 3 77 77 "All" "Other" ""
37 6 3 65 65 "All" "Other" ""
38 7 6 61 61 "All" "Other" ""
39 8 7 58 58 "All" "Other" ""
40 9 8 53 53 "All" "Other" ""
41 10 9 53 53 "All" "Other" ""
42 11 10 51 51 "All" "Other" ""
43 12 11 45 45 "All" "Other" ""
44 13 12 44 44 "All" "Other" ""
45 14 13 44 44 "All" "Other" ""
46 15 14 39 39 "All" "Other" ""
47 16 15 37 37 "All" "Other" ""
48 17 16 30 30 "All/repeat/satellite" "Putative satellites (low confidence)" ""
49 18 17 28 28 "All/repeat/satellite" "Putative satellites (low confidence)" ""
50 19 18 26 26 "All/repeat/satellite" "Putative satellites (high confidence)" ""
51 20 19 23 23 "All/repeat/../CRM" "Other" ""
52 21 20 21 21 "All" "Other" ""
53 22 21 21 21 "All" "Other" ""
54 23 22 21 21 "All" "Other" ""
55 24 23 21 21 "All" "Other" ""
56 25 24 20 20 "All/repeat/../Ogre" "Other" ""
57
58
59 Only Cluster, Automatic_annotation/Final_annnotation are mandatory"
60
61 Clusters with higher number than those in CLUSTER_TABLE are removed from Repeat library
62
63 Contigs are provided in followinf format::
64
65
66 >CL25Contig1
67 AGATCAAGATGGCGCCGGAGGACATGGAGAAAACGACGTTTATCACTCCCTGGGGAACATTTTGCTACAAGGTAATGCCT
68 TTCGGTCTGAAGAACGCAGGGGCCACTTACCAACGAGCAATGGTAACTT
69 >CL1Contig4#All/repeat/satellite
70 ACCCGAAGGCCGGCTCAACCCGAAGTTGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGA
71 A
72 >CL1Contig5
73 TGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACCCGAAGT
74 TGATAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACACGAAGT
75 TGAGAGGAACATCTGACCTCGCCGTCAGGCATCTGTTAAA
76
77
78 Resulting repeat library will have following format::
79
80 >CL25Contig1#All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre
81 AGATCAAGATGGCGCCGGAGGACATGGAGAAAACGACGTTTATCACTCCCTGGGGAACATTTTGCTACAAGGTAATGCCT
82 TTCGGTCTGAAGAACGCAGGGGCCACTTACCAACGAGCAATGGTAACTT
83 >CL1Contig4#All/repeat/satellite
84 ACCCGAAGGCCGGCTCAACCCGAAGTTGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGA
85 A
86 >CL1Contig5#All/repeat/satellite
87 TGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACCCGAAGT
88 TGATAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACACGAAGT
89 TGAGAGGAACATCTGACCTCGCCGTCAGGCATCTGTTAAA
90
91
92
93
94 ]]></help>
95 </tool>