Mercurial > repos > petr-novak > repeat_annotation_pipeline3

comparison repeat_annotate_custom.xml @ 6:b53f5a456d01 draft

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"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
author petr-novak
date Thu, 19 May 2022 08:23:55 +0000
parents d7bb42f254a2
children acf12f2e8355
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5:eca9213923b1 6:b53f5a456d01
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.