Mercurial > repos > petr-novak > repeat_annotation_pipeline
changeset 2:be93d5b35ab6 draft default tip
Uploaded
author | petr-novak |
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date | Wed, 06 Oct 2021 12:12:11 +0000 |
parents | d557f5422e92 |
children | |
files | repeat_annotate_custom.xml |
diffstat | 1 files changed, 35 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repeat_annotate_custom.xml Wed Oct 06 12:12:11 2021 +0000 @@ -0,0 +1,35 @@ +<tool id="repeat_annotate" name="RepeatExplorer Based Assembly Annotation" version="0.1.0" python_template_version="3.5"> + <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 + + ]]></command> + <inputs> + <param type="data" name="input" format="fasta" label="Genome/ Assembly to annotate" /> + <param type="data" name="repeat_library" format="fasta" label="RepeatExplorer based Library of Repetitive Sequences" + help="custom database of repetitive sequences should be provided in fasta format. Sequence header should specify repeat class: + >sequence_id#classification_level1/classification_level2/..." /> + </inputs> + <outputs> + <data name="output1" format="gff3" label="Repeat Annotation on ${on_string}, cleaned gff"/> + <data name="output2" format="tabular" label="RepeatMasker on ${on_string}, original output" /> + </outputs> + <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> +