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