Mercurial > repos > petr-novak > dante_ltr

comparison clean_dante_ltr.xml @ 14:3b3a87915ef6 draft

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"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
author petr-novak
date Mon, 30 Jan 2023 10:05:47 +0000
parents 559940c04c44
children 0ea5d893a057
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13:559940c04c44 14:3b3a87915ef6
1 <tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="0.1.8.0" python_template_version="3.5"> 1 <tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="0.2.2.0" python_template_version="3.5">
2 <requirements> 2 <requirements>
3 3 <requirement type="package">dante_ltr=0.2.2.0</requirement>
4 <requirement type="package">r-optparse</requirement>
5 <requirement type="package">blast</requirement>
6 <requirement type="package">bioconductor-bsgenome</requirement>
7 <requirement type="package">bioconductor-biostrings</requirement>
8 <requirement type="package">bioconductor-rtracklayer</requirement>
9 </requirements> 4 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
11 Rscript ${__tool_directory__}/clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu 32 6 clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1}
12 && 7 &&
13 mv output_clean.gff3 $dante_ltr_clean 8 mv output_clean.gff3 $dante_ltr_clean
14 && 9 &&
15 mv output_RM_lib_non_redundant.fasta $rm_lib 10 mv output_RM_lib_non_redundant.fasta $rm_lib
16 && 11 &&
19 mv output_RM_lib_5LTR.fasta $ltr5 14 mv output_RM_lib_5LTR.fasta $ltr5
20 && 15 &&
21 mv output_RM_lib_3LTR.fasta $ltr3 16 mv output_RM_lib_3LTR.fasta $ltr3
22 && 17 &&
23 mv output_summary.pdf $summary 18 mv output_summary.pdf $summary
24
25 ]]></command> 19 ]]></command>
26 <inputs> 20 <inputs>
27 <param type="data" name="dante_ltr" format="gff3" 21 <param type="data" name="dante_ltr" format="gff3"
28 label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/> 22 label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/>
29 <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" /> 23 <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" />