Mercurial > repos > petr-novak > repeat_annotation_pipeline2
comparison format_repeat_library.xml @ 0:cf3cea0a3039 draft
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author | petr-novak |
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date | Thu, 07 Oct 2021 06:07:34 +0000 |
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-1:000000000000 | 0:cf3cea0a3039 |
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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> |