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comparison dante_ltr_search.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="dante_ltr_search" name="DANTE_LTR transposable element identification" version="0.1.5" python_template_version="3.5"> 1 <tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.1.5" python_template_version="3.5">
2 <requirements> 2 <requirements>
3 <requirement type="package">blast</requirement> 3 <requirement type="package">blast</requirement>
4 <requirement type="package">r-optparse</requirement> 4 <requirement type="package">r-optparse</requirement>
5 <requirement type="package">bioconductor-bsgenome</requirement> 5 <requirement type="package">bioconductor-bsgenome</requirement>
6 <requirement type="package">bioconductor-biostrings</requirement> 6 <requirement type="package">bioconductor-biostrings</requirement>
11 Rscript ${__tool_directory__}/extract_putative_ltr.R --gff3 '$dante' --reference_sequence '$reference' --output output --cpu 32 11 Rscript ${__tool_directory__}/extract_putative_ltr.R --gff3 '$dante' --reference_sequence '$reference' --output output --cpu 32
12 && 12 &&
13 mv output.gff3 $te_ltr_gff 13 mv output.gff3 $te_ltr_gff
14 ]]></command> 14 ]]></command>
15 <inputs> 15 <inputs>
16 <param type="data" name="dante" format="gff3" label="Filtered gff3 output from DANTE pipeline"/> 16 <param type="data" name="dante" format="gff3" label="Filtered GFF3 output from DANTE pipeline"/>
17 <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" /> 17 <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" />
18 </inputs> 18 </inputs>
19 <outputs> 19 <outputs>
20 <data name="te_ltr_gff" format="gff3" label="Annotation of detected LTR transposable elements 20 <data name="te_ltr_gff" format="gff3" label="LTR retrotransposons annotation (GFF3)
21 based on the annotation $dante.hid and reference $reference.hid" /> 21 based on DANTE annotation $dante.hid and reference $reference.hid" />
22 </outputs> 22 </outputs>
23 <help><![CDATA[ 23 <help><![CDATA[
24 This tool uses output from DANTE annotation pipeline to identify full length LTR 24 This tool uses output from DANTE annotation pipeline to identify full length LTR
25 transposable elements. Output is in the GFF3 format and include annotation of 25 transposable elements. Output is in the GFF3 format and include annotation of
26 5' and 3' Longe Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS). 26 5' and 3' Longe Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS).