Mercurial > repos > petr-novak > repeat_annotation_pipeline3

annotate repeat_annotate_custom.xml @ 11:5366d5ea04bc draft

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author petr-novak
date Fri, 04 Aug 2023 12:35:32 +0000
parents 276efc4cb17f
children 755a4d643184
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1 <tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.6" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="4.1.2.p1">repeatmasker</requirement>
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4 <requirement type="package">bioconductor-rtracklayer</requirement>
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5 </requirements>
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6 <required_files>
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7 <include type="literal" path="clean_rm_output.R"/>
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8 </required_files>
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9 <command detect_errors="exit_code"><![CDATA[
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11 #if $sensitivity.value == 'default':
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12 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi
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13 #else:
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14 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi $sensitivity
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15 #end if
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16 &&
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17 ls -l * >&2 &&
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18 cp `basename $input`.out $output2
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19 &&
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20 Rscript ${__tool_directory__}/clean_rm_output.R $output2 $output1
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21
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22 ]]></command>
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23 <inputs>
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24 <param type="data" name="input" format="fasta" label="Genome assembly to annotate" />
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25 <param type="data" name="repeat_library" format="fasta" label="RepeatExplorer based Library of Repetitive Sequences"
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26 help="custom database of repetitive sequences should be provided in fasta format. Sequence header should specify repeat class:
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27 >sequence_id#classification_level1/classification_level2/..." />
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28 <param type="select" label="sensitivity" name="sensitivity" >
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29 <option value="default" selected="true" >Default sensitivity </option>
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30 <option value="-s">Slow search, more sensitive </option>
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31 <option value="-q">Quick search, less sensitive </option>
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32 </param>
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33 <param argument="-nolow" type="boolean" truevalue="" falsevalue="-nolow" checked="false" label="Perform masking of low complexity and simple repeats" />
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34 </inputs>
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35 <outputs>
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36 <data name="output1" format="gff3" label="Repeat Annotation (GFF3) on ${on_string}"/>
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37 <data name="output2" format="tabular" label="Raw output from RepeatMasker on ${on_string}" />
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38 </outputs>
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39 <help><![CDATA[
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40 This tools uses RepeatMasker to annotate repetitive sequences in the genome assemblies using custom library of repeats created either from RepeatExplorer output or from DANTE_LTR transposable element library.
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41 Library of repeats can be created from RepeatExplorer output from contigs and TAREAN consensus sequences.
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42 Fasta formatted library of repeats must contain header containing information about classification of repeats as **>sequence_id#classification_level1/classification_level2/...**
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43
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44 Classification in RepeatExplorer based library follows predetermined classification levels. User can however specify additional classification levels or custom classifications.
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45 Conflicts in annotations are resolved based on classification hierarchy.
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46 ]]></help>
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47 </tool>
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