Mercurial > repos > petr-novak > dante_ltr
comparison clean_dante_ltr.xml @ 14:3b3a87915ef6 draft
"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
author | petr-novak |
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date | Mon, 30 Jan 2023 10:05:47 +0000 |
parents | 559940c04c44 |
children | 0ea5d893a057 |
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13:559940c04c44 | 14:3b3a87915ef6 |
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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" /> |