Mercurial > repos > petr-novak > dante_ltr
comparison clean_dante_ltr.xml @ 3:6ae4a341d1f3 draft
"planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
author | petr-novak |
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date | Tue, 03 May 2022 12:38:12 +0000 |
parents | f131886ea194 |
children | b91ca438a1cb |
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2:f131886ea194 | 3:6ae4a341d1f3 |
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1 <tool id="clean_dante_ltr" name="DANTE_LTR transposamble elements filtering" version="0.1.4" python_template_version="3.5"> | 1 <tool id="clean_dante_ltr" name="DANTE_LTR transposamble elements 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> |
10 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
11 Rscript ${__tool_directory__}/clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu 32 | 11 Rscript ${__tool_directory__}/clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu 32 |
12 && | 12 && |
13 mv output_clean.gff3 $dante_ltr_clean | 13 mv output_clean.gff3 $dante_ltr_clean |
14 && | 14 && |
15 mv output_RM_lib.fasta $rm_lib | 15 mv output_RM_lib_non_redundant.fasta $rm_lib |
16 && | |
17 mv output_RM_lib_full_TE.fasta $te_full | |
18 && | |
19 mv output_RM_lib_5LTR.fasta $ltr5 | |
20 && | |
21 mv output_RM_lib_3LTR.fasta $ltr3 | |
22 && | |
23 mv output_summary.pdf $summary | |
24 | |
16 ]]></command> | 25 ]]></command> |
17 <inputs> | 26 <inputs> |
18 <param type="data" name="dante_ltr" format="gff3" /> | 27 <param type="data" name="dante_ltr" format="gff3" /> |
19 <param type="data" name="reference" format="fasta" /> | 28 <param type="data" name="reference" format="fasta" /> |
20 </inputs> | 29 </inputs> |
21 <outputs> | 30 <outputs> |
22 <data name="dante_ltr_clean" format="gff3" label="Annotation of validated LTR transposable | 31 <data name="dante_ltr_clean" format="gff3" label="Annotation of validated LTR transposable |
23 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> | 32 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> |
24 <data name="rm_lib" format="fasta" label="Non-redundant library of LTR transposable | 33 <data name="rm_lib" format="fasta" label="Non-redundant library of LTR transposable |
25 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> | 34 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> |
35 | |
36 <data name="te_full" format="fasta" label="Full length LTR transposable | |
37 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> | |
38 | |
39 <data name="ltr5" format="fasta" label="5'LTR of transposable | |
40 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> | |
41 | |
42 <data name="ltr3" format="fasta" label="3'LTR of transposable | |
43 elements based on annotation $dante_ltr.hid and reference $reference.hid"/> | |
44 | |
45 <data name="summary" format="pdf" label="Summary of TE and LTR lenghts based on | |
46 $dante_ltr.hid and reference $reference.hid"/> | |
47 | |
26 </outputs> | 48 </outputs> |
27 <help><![CDATA[ | 49 <help><![CDATA[ |
28 This tool takes output from DANTE_LTR search identifies good quality transposable elements. | 50 This tool takes output from DANTE_LTR search identifies good quality transposable elements. |
29 Good quality TE are considered those which does not have any cross-similarity between distinct lineages. | 51 Good quality TE are considered those which does not have any cross-similarity between distinct lineages. |
30 Output from this tool is a annotation in GFF3 format and | 52 Output from this tool is a annotation in GFF3 format and |