Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison repeat_annotate_custom.xml @ 6:b53f5a456d01 draft
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
author | petr-novak |
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date | Thu, 19 May 2022 08:23:55 +0000 |
parents | d7bb42f254a2 |
children | acf12f2e8355 |
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5:eca9213923b1 | 6:b53f5a456d01 |
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16 && | 16 && |
17 Rscript ${__tool_directory__}/clean_rm_output.R $output2 $output1 | 17 Rscript ${__tool_directory__}/clean_rm_output.R $output2 $output1 |
18 | 18 |
19 ]]></command> | 19 ]]></command> |
20 <inputs> | 20 <inputs> |
21 <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" /> |
22 <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" |
23 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: |
24 >sequence_id#classification_level1/classification_level2/..." /> | 24 >sequence_id#classification_level1/classification_level2/..." /> |
25 <param type="select" label="sensitivity" name="sensitivity" > | 25 <param type="select" label="sensitivity" name="sensitivity" > |
26 <option value="default" selected="true" >Default sensitivity </option> | 26 <option value="default" selected="true" >Default sensitivity </option> |
27 <option value="-s">Slow search, more sensitive </option> | 27 <option value="-s">Slow search, more sensitive </option> |
28 <option value="-q">Quick search, more sensitive </option> | 28 <option value="-q">Quick search, less sensitive </option> |
29 </param> | 29 </param> |
30 </inputs> | 30 </inputs> |
31 <outputs> | 31 <outputs> |
32 <data name="output1" format="gff3" label="Repeat Annotation on ${on_string}, cleaned gff"/> | 32 <data name="output1" format="gff3" label="Repeat Annotation (GFF3) on ${on_string}"/> |
33 <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}" /> |
34 </outputs> | 34 </outputs> |
35 <help><![CDATA[ | 35 <help><![CDATA[ |
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. | 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. | 37 Library of repeats can be created from RepeatExplorer output from contigs and TAREAN consensus sequences. |