Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison repeat_annotate_custom.xml @ 3:4ea506b39297 draft
"planemo upload"
author | petr-novak |
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date | Tue, 08 Mar 2022 13:58:51 +0000 |
parents | 7f1032da7a0a |
children | d7bb42f254a2 |
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2:7f1032da7a0a | 3:4ea506b39297 |
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1 <tool id="repeat_annotate" name="RepeatExplorer Based Assembly Annotation" version="0.1.2" python_template_version="3.5"> | 1 <tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.2" 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[ |
7 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall -nolow -no_is -e ncbi -s | 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 | |
8 && | 13 && |
9 ls -l * >&2 && | 14 ls -l * >&2 && |
10 cp `basename $input`.out $output2 | 15 cp `basename $input`.out $output2 |
11 && | 16 && |
12 Rscript ${__tool_directory__}/clean_rm_output.R $output2 $output1 | 17 Rscript ${__tool_directory__}/clean_rm_output.R $output2 $output1 |
15 <inputs> | 20 <inputs> |
16 <param type="data" name="input" format="fasta" label="Genome/ Assembly to annotate" /> | 21 <param type="data" name="input" format="fasta" label="Genome/ Assembly to annotate" /> |
17 <param type="data" name="repeat_library" format="fasta" label="RepeatExplorer based Library of Repetitive Sequences" | 22 <param type="data" name="repeat_library" format="fasta" label="RepeatExplorer based Library of Repetitive Sequences" |
18 help="custom database of repetitive sequences should be provided in fasta format. Sequence header should specify repeat class: | 23 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/..." /> | 24 >sequence_id#classification_level1/classification_level2/..." /> |
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> | |
20 </inputs> | 30 </inputs> |
21 <outputs> | 31 <outputs> |
22 <data name="output1" format="gff3" label="Repeat Annotation on ${on_string}, cleaned gff"/> | 32 <data name="output1" format="gff3" label="Repeat Annotation on ${on_string}, cleaned gff"/> |
23 <data name="output2" format="tabular" label="Raw output from RepeatMasker on ${on_string}" /> | 33 <data name="output2" format="tabular" label="Raw output from RepeatMasker on ${on_string}" /> |
24 </outputs> | 34 </outputs> |
25 <help><![CDATA[ | 35 <help><![CDATA[ |
26 This tools uses RepeatMasker to annotate repetitive sequences in the genome assemblie using custom library of repeats created from RepeatExplorer output. | 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. |
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/...** | 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/...** | |
28 | 39 |
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. | 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. | |
30 ]]></help> | 42 ]]></help> |
31 </tool> | 43 </tool> |
32 | 44 |