Mercurial > repos > petr-novak > repeat_annotation_pipeline3
annotate repeat_annotate_custom.xml @ 4:d7bb42f254a2 draft
"planemo upload commit fa6d4eb0c804e873b60bb2ba3d0e85646c9cd764"
| author | petr-novak |
|---|---|
| date | Mon, 14 Mar 2022 10:16:07 +0000 |
| parents | 4ea506b39297 |
| children | b53f5a456d01 |
| rev | line source |
|---|---|
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4
d7bb42f254a2
"planemo upload commit fa6d4eb0c804e873b60bb2ba3d0e85646c9cd764"
petr-novak
parents:
3
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changeset
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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> |
| 3 <requirement type="package">repeatmasker</requirement> | |
| 4 <requirement type="package">bioconductor-rtracklayer</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 3 | 7 |
| 8 #if $sensitivity.value == 'default': | |
| 9 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall -nolow -no_is -e ncbi | |
| 10 #else: | |
| 11 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall -nolow -no_is -e ncbi $sensitivity | |
| 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> | |
| 21 <param type="data" name="input" format="fasta" label="Genome/ Assembly to annotate" /> | |
| 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> | |
| 28 <option value="-q">Quick search, more sensitive </option> | |
| 29 </param> | |
| 0 | 30 </inputs> |
| 31 <outputs> | |
| 32 <data name="output1" format="gff3" label="Repeat Annotation on ${on_string}, cleaned gff"/> | |
| 33 <data name="output2" format="tabular" label="Raw output from RepeatMasker on ${on_string}" /> | |
| 34 </outputs> | |
| 35 <help><![CDATA[ | |
| 3 | 36 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. |
| 37 Library of repeats can be created from RepeatExplorer output from contigs and TAREAN consensus sequences. | |
| 38 Fasta formatted library of repeats must contain header containing information about classification of repeats as **>sequence_id#classification_level1/classification_level2/...** | |
| 0 | 39 |
| 3 | 40 Classification in RepeatExplorer based library follows predetermined classification levels. User can however specify additional classification levels or custom classifications. |
| 41 Conflicts in annotations are resolved based on classification hierarchy. | |
| 0 | 42 ]]></help> |
| 43 </tool> | |
| 44 |