Mercurial > repos > petr-novak > get_organelle

comparison get_organelle.xml @ 0:0ff5b94932fe draft

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"planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
author petr-novak
date Tue, 31 May 2022 10:56:52 +0000
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1 <tool id="get_organelle" name="Assemble organelle genome from genomic skimming data" version="0.1.0" python_template_version="3.5">
2 <requirements>
3 <requirement type="package" version="1.7.6.1">getOrganelle</requirement>
4 <requirement type="package" version="0.0.1">getorganelledb</requirement>
5 <requirement type="set_environment">GETORGANELLEDB</requirement>
6
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 get_organelle_from_reads.py -1 '$fastq1' -2 '$fastq2' -t 10 -o assembly_dir --config-dir \${GETORGANELLEDB} -F ${ref_db} &&
10 cat assembly_dir/*.fasta > ${assembly_contigs} &&
11 zip -r assembly.zip assembly_dir &&
12 mv assembly.zip ${assembly_zip}
13
14
15 ]]></command>
16 <inputs>
17 <param type="data" name="fastq1" format="fastq" help="FASTQ forward reads"/>
18 <param type="data" name="fastq2" format="fastq" help="FASTQ reverse reads" />
19 <param type="select" label="Assembly type" name="ref_db" >
20 <option value="embplant_pt" selected="true" > Embryophyta plant plastome </option>
21 <option value="embplant_mt">Embryophyta plant mitogenome </option>
22 <option value="embplant_nr">Embryophyta plant ribosomal RNA </option>
23 <option value="other_pt">Non-embryophyta plant plastome </option>
24 <option value="animal_mt">Animal mitogenome </option>
25 <option value="fungus_mt">Fungus mitogenome </option>
26 <option value="fungus_nr">Fungus ribosomal RNA </option>
27 </param>
28 </inputs>
29 <outputs>
30 <data name="assembly_contigs" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (contigs)" />
31 <data name="assembly_zip" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (full results as archive)" />
32 </outputs>
33 <help><![CDATA[
34 This toolkit assemblies organelle genome from genomic skimming data.
35
36 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
37
38 Source code - https://github.com/Kinggerm/GetOrganelle
39
40 Organelle Database - https://github.com/Kinggerm/GetOrganelleDB
41
42 ]]></help>
43 </tool>