Mercurial > repos > petr-novak > repeat_annotation_pipeline
comparison repeat_annotate_custom.xml @ 2:be93d5b35ab6 draft default tip
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| author | petr-novak |
|---|---|
| date | Wed, 06 Oct 2021 12:12:11 +0000 |
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| 1:d557f5422e92 | 2:be93d5b35ab6 |
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| 1 <tool id="repeat_annotate" name="RepeatExplorer Based Assembly Annotation" version="0.1.0" python_template_version="3.5"> | |
| 2 <requirements> | |
| 3 <requirement type="package">repeatmasker</requirement> | |
| 4 <requirement type="package">bioconductor-rtracklayer</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 RepeatMasker -dir \$(pwd) '$input' -pa 12 -lib '$repeat_library' -xsmall -nolow -no_is -e ncbi -s | |
| 8 && | |
| 9 ls -l * >&2 && | |
| 10 cp `basename $input`.out $output2 | |
| 11 && | |
| 12 Rscript ${__tool_directory__}/clean_rm_output.R $output2 $output1 | |
| 13 | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param type="data" name="input" format="fasta" label="Genome/ Assembly to annotate" /> | |
| 17 <param type="data" name="repeat_library" format="fasta" label="RepeatExplorer based Library of Repetitive Sequences" | |
| 18 help="custom database of repetitive sequences should be provided in fasta format. Sequence header should specify repeat class: | |
| 19 >sequence_id#classification_level1/classification_level2/..." /> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data name="output1" format="gff3" label="Repeat Annotation on ${on_string}, cleaned gff"/> | |
| 23 <data name="output2" format="tabular" label="RepeatMasker on ${on_string}, original output" /> | |
| 24 </outputs> | |
| 25 <help><![CDATA[ | |
| 26 This tools uses RepeatMasker to annotate repetitive sequences in the genome assemblie using custom library of repeats created from RepeatExplorer output. | |
| 27 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/...** | |
| 28 | |
| 29 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. | |
| 30 | |
| 31 | |
| 32 | |
| 33 ]]></help> | |
| 34 </tool> | |
| 35 |