Mercurial > repos > petr-novak > dante_ltr

comparison clean_dante_ltr.xml @ 3:6ae4a341d1f3 draft

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"planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
author petr-novak
date Tue, 03 May 2022 12:38:12 +0000
parents f131886ea194
children b91ca438a1cb
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2:f131886ea194 3:6ae4a341d1f3
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