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> |