Mercurial > repos > petr-novak > dante_ltr
diff dante_ltr_search.xml @ 12:ff01d4263391 draft
"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
| author | petr-novak |
|---|---|
| date | Thu, 21 Jul 2022 08:23:15 +0000 |
| parents | 9de392f2fc02 |
| children | 559940c04c44 |
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--- a/dante_ltr_search.xml Wed Jul 13 11:02:55 2022 +0000 +++ b/dante_ltr_search.xml Thu Jul 21 08:23:15 2022 +0000 @@ -1,14 +1,16 @@ -<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.1.6.1" python_template_version="3.5"> +<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.1.7.0" python_template_version="3.5"> <requirements> <requirement type="package">blast</requirement> <requirement type="package">r-optparse</requirement> <requirement type="package">bioconductor-bsgenome</requirement> <requirement type="package">bioconductor-biostrings</requirement> <requirement type="package">bioconductor-rtracklayer</requirement> + <requirement type="package" version="3.7.12">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - Rscript ${__tool_directory__}/extract_putative_ltr.R --gff3 '$dante' --reference_sequence '$reference' -M $max_missing --output output --cpu 32 + python ${__tool_directory__}/detect_putative_ltr_wrapper.py --gff3 '$dante' + --reference_sequence '$reference' -M $max_missing --output output --cpu 32 && mv output.gff3 $te_ltr_gff && @@ -31,7 +33,7 @@ 5' and 3' Long Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS). All identified elements contains set of protein domains as defined in - REXdb_.Based on the results of detection of structural features, + REXdb_. Based on the results of detection of structural features, elements falls into five categories: - elements with domains, 5'LTR, 3'LTR, TSD and PBS - rank DLTP @@ -42,5 +44,10 @@ .. _REXdb: https://doi.org/10.1186/s13100-018-0144-1 + Principles of detection of LTR retrotransposons is describet in github_ repository of this tool. + + .. _github: https://github.com/kavonrtep/dante_ltr + + ]]></help> </tool> \ No newline at end of file