comparison dante_ltr_search.xml @ 12:ff01d4263391 draft

"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"

11:54bd36973253

<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.1.6.1" 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>

    </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
        &&
        mv output.gff3 $te_ltr_gff
        &&
        mv output_statistics.csv $statistics
    ]]></command>

        This tool uses output from DANTE annotation pipeline to identify full length LTR
        transposable elements. Output is in the GFF3 format and include annotation of
        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,
        elements falls into five categories:

        - elements with domains, 5'LTR, 3'LTR, TSD and PBS - rank DLTP
        - elements with domains, 5'LTR, 3'LTR and PBS (TSD was not found) rank DLP
        - elements with domains, 5' LTR, 3'LTR, TSD (PBS was not found) - rank DTL
        - elements with protein domains, 5'LTR and 3'LTR (PBS and LDS were not found)  - rank DL
        - elements as cluster of proteins domains with same classification, no LTRs - rank D

       .. _REXdb: https://doi.org/10.1186/s13100-018-0144-1

    ]]></help>
</tool>

12:ff01d4263391

<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[
        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
        &&
        mv output_statistics.csv $statistics
    ]]></command>

        This tool uses output from DANTE annotation pipeline to identify full length LTR
        transposable elements. Output is in the GFF3 format and include annotation of
        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,
        elements falls into five categories:

        - elements with domains, 5'LTR, 3'LTR, TSD and PBS - rank DLTP
        - elements with domains, 5'LTR, 3'LTR and PBS (TSD was not found) rank DLP
        - elements with domains, 5' LTR, 3'LTR, TSD (PBS was not found) - rank DTL
        - elements with protein domains, 5'LTR and 3'LTR (PBS and LDS were not found)  - rank DL
        - elements as cluster of proteins domains with same classification, no LTRs - rank D

       .. _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>