Mercurial > repos > petr-novak > repeat_annotation_pipeline3
annotate repeat_annotate_custom.xml @ 9:4a068d23fda6 draft
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| author | petr-novak |
|---|---|
| date | Wed, 03 May 2023 11:19:06 +0000 |
| parents | 2557cad81607 |
| children | 276efc4cb17f |
| rev | line source |
|---|---|
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"planemo upload commit fa6d4eb0c804e873b60bb2ba3d0e85646c9cd764"
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1 <tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.3" python_template_version="3.5"> |
| 0 | 2 <requirements> |
| 9 | 3 <requirement type="package" version="4.1.2.p1">repeatmasker</requirement> |
| 0 | 4 <requirement type="package">bioconductor-rtracklayer</requirement> |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 3 | 7 |
| 8 #if $sensitivity.value == 'default': | |
| 8 | 9 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi |
| 3 | 10 #else: |
| 8 | 11 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi $sensitivity |
| 3 | 12 #end if |
| 0 | 13 && |
| 14 ls -l * >&2 && | |
| 15 cp `basename $input`.out $output2 | |
| 16 && | |
| 17 Rscript ${__tool_directory__}/clean_rm_output.R $output2 $output1 | |
| 18 | |
| 19 ]]></command> | |
| 20 <inputs> | |
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21 <param type="data" name="input" format="fasta" label="Genome assembly to annotate" /> |
| 0 | 22 <param type="data" name="repeat_library" format="fasta" label="RepeatExplorer based Library of Repetitive Sequences" |
| 23 help="custom database of repetitive sequences should be provided in fasta format. Sequence header should specify repeat class: | |
| 24 >sequence_id#classification_level1/classification_level2/..." /> | |
| 3 | 25 <param type="select" label="sensitivity" name="sensitivity" > |
| 26 <option value="default" selected="true" >Default sensitivity </option> | |
| 27 <option value="-s">Slow search, more sensitive </option> | |
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28 <option value="-q">Quick search, less sensitive </option> |
| 3 | 29 </param> |
| 8 | 30 <param argument="-nolow" type="boolean" truevalue="-nolow" falsevalue="" checked="true" label="Perform masking of low complexity and simple repeats" /> |
| 0 | 31 </inputs> |
| 32 <outputs> | |
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"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
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33 <data name="output1" format="gff3" label="Repeat Annotation (GFF3) on ${on_string}"/> |
| 0 | 34 <data name="output2" format="tabular" label="Raw output from RepeatMasker on ${on_string}" /> |
| 35 </outputs> | |
| 36 <help><![CDATA[ | |
| 3 | 37 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. |
| 38 Library of repeats can be created from RepeatExplorer output from contigs and TAREAN consensus sequences. | |
| 39 Fasta formatted library of repeats must contain header containing information about classification of repeats as **>sequence_id#classification_level1/classification_level2/...** | |
| 0 | 40 |
| 3 | 41 Classification in RepeatExplorer based library follows predetermined classification levels. User can however specify additional classification levels or custom classifications. |
| 42 Conflicts in annotations are resolved based on classification hierarchy. | |
| 0 | 43 ]]></help> |
| 44 </tool> | |
| 45 |