Mercurial > repos > petr-novak > repeat_annotation_pipeline2
comparison repeat_annotate_custom.xml @ 3:e955b40ad3a4 draft default tip
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| author | petr-novak |
|---|---|
| date | Tue, 12 Oct 2021 07:43:54 +0000 |
| parents | 3f8ae272f4f3 |
| children |
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| 2:3f8ae272f4f3 | 3:e955b40ad3a4 |
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| 1 <tool id="repeat_annotate" name="RepeatExplorer Based Assembly Annotation" version="0.1.0" python_template_version="3.5"> | 1 <tool id="repeat_annotate" name="RepeatExplorer Based Assembly Annotation" version="0.1.1" python_template_version="3.5"> |
| 2 <requirements> | 2 <requirements> |
| 3 <requirement type="package">repeatmasker</requirement> | 3 <requirement type="package">repeatmasker</requirement> |
| 4 <requirement type="package">bioconductor-rtracklayer</requirement> | 4 <requirement type="package">bioconductor-rtracklayer</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
| 18 help="custom database of repetitive sequences should be provided in fasta format. Sequence header should specify repeat class: | 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/..." /> | 19 >sequence_id#classification_level1/classification_level2/..." /> |
| 20 </inputs> | 20 </inputs> |
| 21 <outputs> | 21 <outputs> |
| 22 <data name="output1" format="gff3" label="Repeat Annotation on ${on_string}, cleaned gff"/> | 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" /> | 23 <data name="output2" format="tabular" label="Raw output from RepeatMasker on ${on_string}" /> |
| 24 </outputs> | 24 </outputs> |
| 25 <help><![CDATA[ | 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. | 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/...** | 27 Library of repeats can be created from RepeatExplorer ouputt from contigs and TAREAN consensus sequences. Fasta formated library of repeats must contain header containg information about classification of repeats as **>sequence_id#classification_level1/classification_level2/...** |
| 28 | 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. | 29 Classification in RepeatExplorer based library follows predetermined classification levels. User can however specify additional classification levels or completelly custom classifications. Conflicts in annotations are resolved based on classification hierarchy. |
| 30 ]]></help> | 30 ]]></help> |
| 31 </tool> | 31 </tool> |
| 32 | 32 |