comparison repeat_annotate_custom.xml @ 2:3f8ae272f4f3 draft

Uploaded

1:a084343c7cc1

    <requirements>
        <requirement type="package">repeatmasker</requirement>
        <requirement type="package">bioconductor-rtracklayer</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        RepeatMasker -dir \$(pwd) '$input' -pa 12 -lib '$repeat_library' -xsmall -nolow -no_is -e ncbi -s
        &&
        ls -l * >&2 &&
        cp `basename $input`.out  $output2
        &&
        Rscript ${__tool_directory__}/clean_rm_output.R $output2 $output1

    <help><![CDATA[
        This tools uses RepeatMasker to annotate repetitive sequences in the genome assemblie using custom library of repeats created from RepeatExplorer output.
        Library of repeats created from RepeatExplorer ouput are contigs and TAREAN consensus sequences in fasta format where sequence header containg information about classification of repeats as **>sequence_id#classification_level1/classification_level2/...**

        Classification in RepeatExplorer based library follows predetermined classification levels. User can however specify additional classification levels or ciompletelly custom classifications. Conflicts in annotations are resolved based on classification hierarchy.
        

 
    ]]></help>
</tool>

2:3f8ae272f4f3

    <requirements>
        <requirement type="package">repeatmasker</requirement>
        <requirement type="package">bioconductor-rtracklayer</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall -nolow -no_is -e ncbi -s
        &&
        ls -l * >&2 &&
        cp `basename $input`.out  $output2
        &&
        Rscript ${__tool_directory__}/clean_rm_output.R $output2 $output1

    <help><![CDATA[
        This tools uses RepeatMasker to annotate repetitive sequences in the genome assemblie using custom library of repeats created from RepeatExplorer output.
        Library of repeats created from RepeatExplorer ouput are contigs and TAREAN consensus sequences in fasta format where sequence header containg information about classification of repeats as **>sequence_id#classification_level1/classification_level2/...**

        Classification in RepeatExplorer based library follows predetermined classification levels. User can however specify additional classification levels or ciompletelly custom classifications. Conflicts in annotations are resolved based on classification hierarchy.
    ]]></help>
</tool>