comparison dante_ltr_to_library.xml @ 17:d1c3b29b1478 draft

planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
author petr-novak
date Thu, 10 Aug 2023 12:22:28 +0000
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16:7ec262f92d89 17:d1c3b29b1478
1 <tool id="dante_ltr_to_library" name="Create representative library from DANTE_LTR output " version="@TOOL_VERSION@" python_template_version="3.5">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="requirements" />
6 <command detect_errors="exit_code"><![CDATA[
7 cp '$dante_ltr' dante_ltr.gff3 &&
8 dante_ltr_to_library --gff3 dante_ltr.gff3 --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1} --min_coverage 3
9 &&
10 ls -l output
11 &&
12 mv output/mmseqs2/mmseqs_representative_seq_clean.fasta $dante_ltr_library
13 ]]></command>
14 <inputs>
15 <param type="data" name="dante_ltr" format="gff3"
16 label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/>
17 <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" />
18 </inputs>
19 <outputs>
20 <data name="dante_ltr_library" format="fasta"
21 label="Representative library from DANTE_LTR $dante_ltr.hid on reference $reference.hid"/>
22 </outputs>
23 <help><![CDATA[
24 This tool extract representative sequences from LTR-RT library identified
25 by DANTE_LTR. Resulting library is suitable for RepeatMasker search.
26 ]]></help>
27 </tool>
28