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comparison clean_dante_ltr.xml @ 6:b91ca438a1cb draft

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"planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
author petr-novak
date Thu, 19 May 2022 08:21:55 +0000
parents 6ae4a341d1f3
children c33d6583e548
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5:0c3111ab729b 6:b91ca438a1cb
1 <tool id="clean_dante_ltr" name="DANTE_LTR transposamble elements filtering" version="0.1.5" python_template_version="3.5"> 1 <tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="0.1.5" python_template_version="3.5">
2 <requirements> 2 <requirements>
3 3
4 <requirement type="package">r-optparse</requirement> 4 <requirement type="package">r-optparse</requirement>
5 <requirement type="package">blast</requirement> 5 <requirement type="package">blast</requirement>
6 <requirement type="package">bioconductor-bsgenome</requirement> 6 <requirement type="package">bioconductor-bsgenome</requirement>
22 && 22 &&
23 mv output_summary.pdf $summary 23 mv output_summary.pdf $summary
24 24
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <param type="data" name="dante_ltr" format="gff3" /> 27 <param type="data" name="dante_ltr" format="gff3"
28 <param type="data" name="reference" format="fasta" /> 28 label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/>
29 <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" />
29 </inputs> 30 </inputs>
30 <outputs> 31 <outputs>
31 <data name="dante_ltr_clean" format="gff3" label="Annotation of validated LTR transposable 32 <data name="dante_ltr_clean" format="gff3"
32 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> 33 label="Validated LTR retrotransposons annotation (GFF3) based on annotation
33 <data name="rm_lib" format="fasta" label="Non-redundant library of LTR transposable 34 $dante_ltr.hid and reference $reference.hid"/>
34 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> 35 <data name="rm_lib" format="fasta" label="Non-redundant library of LTR retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
35 36
36 <data name="te_full" format="fasta" label="Full length LTR transposable 37 <data name="te_full" format="fasta" label="Library of full length LTR retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
37 elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
38 38
39 <data name="ltr5" format="fasta" label="5'LTR of transposable 39 <data name="ltr5" format="fasta" label="Library of 5'LTR of retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
40 elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
41 40
42 <data name="ltr3" format="fasta" label="3'LTR of transposable 41 <data name="ltr3" format="fasta" label="Library of 3'LTR of retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
43 elements based on annotation $dante_ltr.hid and reference $reference.hid"/>
44 42
45 <data name="summary" format="pdf" label="Summary of TE and LTR lenghts based on 43 <data name="summary" format="pdf" label="LTR retrotransposons lengths summary based on $dante_ltr.hid and reference $reference.hid"/>
46 $dante_ltr.hid and reference $reference.hid"/>
47 44
48 </outputs> 45 </outputs>
49 <help><![CDATA[ 46 <help><![CDATA[
50 This tool takes output from DANTE_LTR search identifies good quality transposable elements. 47 This tool takes output from DANTE_LTR search identifies good quality retrotransposons.
51 Good quality TE are considered those which does not have any cross-similarity between distinct lineages. 48 Good quality retrotransposons are considered those which does not have any cross-similarity between distinct lineages.
52 Output from this tool is a annotation in GFF3 format and 49 Output from this tool is a annotation in GFF3 format and
53 non-redundant library of elements for custom RepeatMasker search. 50 libraries of elements for custom RepeatMasker search.
54 51
55 ]]></help> 52 ]]></help>
56 </tool> 53 </tool>