Mercurial > repos > petr-novak > get_organelle
diff get_organelle.xml @ 0:0ff5b94932fe draft
"planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
author | petr-novak |
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date | Tue, 31 May 2022 10:56:52 +0000 |
parents | |
children | a388d670fd54 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_organelle.xml Tue May 31 10:56:52 2022 +0000 @@ -0,0 +1,43 @@ +<tool id="get_organelle" name="Assemble organelle genome from genomic skimming data" version="0.1.0" python_template_version="3.5"> + <requirements> + <requirement type="package" version="1.7.6.1">getOrganelle</requirement> + <requirement type="package" version="0.0.1">getorganelledb</requirement> + <requirement type="set_environment">GETORGANELLEDB</requirement> + + </requirements> + <command detect_errors="exit_code"><![CDATA[ + get_organelle_from_reads.py -1 '$fastq1' -2 '$fastq2' -t 10 -o assembly_dir --config-dir \${GETORGANELLEDB} -F ${ref_db} && + cat assembly_dir/*.fasta > ${assembly_contigs} && + zip -r assembly.zip assembly_dir && + mv assembly.zip ${assembly_zip} + + + ]]></command> + <inputs> + <param type="data" name="fastq1" format="fastq" help="FASTQ forward reads"/> + <param type="data" name="fastq2" format="fastq" help="FASTQ reverse reads" /> + <param type="select" label="Assembly type" name="ref_db" > + <option value="embplant_pt" selected="true" > Embryophyta plant plastome </option> + <option value="embplant_mt">Embryophyta plant mitogenome </option> + <option value="embplant_nr">Embryophyta plant ribosomal RNA </option> + <option value="other_pt">Non-embryophyta plant plastome </option> + <option value="animal_mt">Animal mitogenome </option> + <option value="fungus_mt">Fungus mitogenome </option> + <option value="fungus_nr">Fungus ribosomal RNA </option> + </param> + </inputs> + <outputs> + <data name="assembly_contigs" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (contigs)" /> + <data name="assembly_zip" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (full results as archive)" /> + </outputs> + <help><![CDATA[ + This toolkit assemblies organelle genome from genomic skimming data. + + Citation: Jian-Jun Jin*, Wen-Bin Yu*, Jun-Bo Yang, Yu Song, Claude W. dePamphilis, Ting-Shuang Yi, De-Zhu Li. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 21, 241 (2020). https://doi.org/10.1186/s13059-020-02154-5 + + Source code - https://github.com/Kinggerm/GetOrganelle + + Organelle Database - https://github.com/Kinggerm/GetOrganelleDB + + ]]></help> +</tool> \ No newline at end of file