Mercurial > repos > petr-novak > dante_ltr
comparison dante_ltr_search.xml @ 12:ff01d4263391 draft
"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
author | petr-novak |
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date | Thu, 21 Jul 2022 08:23:15 +0000 |
parents | 9de392f2fc02 |
children | 559940c04c44 |
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11:54bd36973253 | 12:ff01d4263391 |
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1 <tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.1.6.1" python_template_version="3.5"> | 1 <tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.1.7.0" python_template_version="3.5"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package">blast</requirement> | 3 <requirement type="package">blast</requirement> |
4 <requirement type="package">r-optparse</requirement> | 4 <requirement type="package">r-optparse</requirement> |
5 <requirement type="package">bioconductor-bsgenome</requirement> | 5 <requirement type="package">bioconductor-bsgenome</requirement> |
6 <requirement type="package">bioconductor-biostrings</requirement> | 6 <requirement type="package">bioconductor-biostrings</requirement> |
7 <requirement type="package">bioconductor-rtracklayer</requirement> | 7 <requirement type="package">bioconductor-rtracklayer</requirement> |
8 <requirement type="package" version="3.7.12">python</requirement> | |
8 | 9 |
9 </requirements> | 10 </requirements> |
10 <command detect_errors="exit_code"><![CDATA[ | 11 <command detect_errors="exit_code"><![CDATA[ |
11 Rscript ${__tool_directory__}/extract_putative_ltr.R --gff3 '$dante' --reference_sequence '$reference' -M $max_missing --output output --cpu 32 | 12 python ${__tool_directory__}/detect_putative_ltr_wrapper.py --gff3 '$dante' |
13 --reference_sequence '$reference' -M $max_missing --output output --cpu 32 | |
12 && | 14 && |
13 mv output.gff3 $te_ltr_gff | 15 mv output.gff3 $te_ltr_gff |
14 && | 16 && |
15 mv output_statistics.csv $statistics | 17 mv output_statistics.csv $statistics |
16 ]]></command> | 18 ]]></command> |
29 This tool uses output from DANTE annotation pipeline to identify full length LTR | 31 This tool uses output from DANTE annotation pipeline to identify full length LTR |
30 transposable elements. Output is in the GFF3 format and include annotation of | 32 transposable elements. Output is in the GFF3 format and include annotation of |
31 5' and 3' Long Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS). | 33 5' and 3' Long Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS). |
32 | 34 |
33 All identified elements contains set of protein domains as defined in | 35 All identified elements contains set of protein domains as defined in |
34 REXdb_.Based on the results of detection of structural features, | 36 REXdb_. Based on the results of detection of structural features, |
35 elements falls into five categories: | 37 elements falls into five categories: |
36 | 38 |
37 - elements with domains, 5'LTR, 3'LTR, TSD and PBS - rank DLTP | 39 - elements with domains, 5'LTR, 3'LTR, TSD and PBS - rank DLTP |
38 - elements with domains, 5'LTR, 3'LTR and PBS (TSD was not found) rank DLP | 40 - elements with domains, 5'LTR, 3'LTR and PBS (TSD was not found) rank DLP |
39 - elements with domains, 5' LTR, 3'LTR, TSD (PBS was not found) - rank DTL | 41 - elements with domains, 5' LTR, 3'LTR, TSD (PBS was not found) - rank DTL |
40 - elements with protein domains, 5'LTR and 3'LTR (PBS and LDS were not found) - rank DL | 42 - elements with protein domains, 5'LTR and 3'LTR (PBS and LDS were not found) - rank DL |
41 - elements as cluster of proteins domains with same classification, no LTRs - rank D | 43 - elements as cluster of proteins domains with same classification, no LTRs - rank D |
42 | 44 |
43 .. _REXdb: https://doi.org/10.1186/s13100-018-0144-1 | 45 .. _REXdb: https://doi.org/10.1186/s13100-018-0144-1 |
44 | 46 |
47 Principles of detection of LTR retrotransposons is describet in github_ repository of this tool. | |
48 | |
49 .. _github: https://github.com/kavonrtep/dante_ltr | |
50 | |
51 | |
45 ]]></help> | 52 ]]></help> |
46 </tool> | 53 </tool> |