Mercurial > repos > petr-novak > get_organelle

annotate get_organelle.xml @ 4:b9297a39531a draft

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"planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
author petr-novak
date Wed, 01 Jun 2022 06:03:44 +0000
parents a388d670fd54
children 513350816e4a
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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">
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2 <requirements>
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3 <requirement type="package" version="1.7.6.1">getorganelle</requirement>
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4 <requirement type="package" version="0.0.1">getorganelledb</requirement>
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5 <requirement type="set_environment">GETORGANELLEDB</requirement>
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6
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 get_organelle_from_reads.py -1 '$fastq1' -2 '$fastq2' -t 10 -o assembly_dir --config-dir \${GETORGANELLEDB} -F ${ref_db} &&
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10 cat assembly_dir/*.fasta > ${assembly_contigs} &&
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11 zip -r assembly.zip assembly_dir &&
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12 mv assembly.zip ${assembly_zip}
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13
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14
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15 ]]></command>
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16 <inputs>
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17 <param type="data" name="fastq1" format="fastq" help="FASTQ forward reads"/>
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18 <param type="data" name="fastq2" format="fastq" help="FASTQ reverse reads" />
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19 <param type="select" label="Assembly type" name="ref_db" >
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20 <option value="embplant_pt" selected="true" > Embryophyta plant plastome </option>
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21 <option value="embplant_mt">Embryophyta plant mitogenome </option>
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22 <option value="embplant_nr">Embryophyta plant ribosomal RNA </option>
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23 <option value="other_pt">Non-embryophyta plant plastome </option>
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24 <option value="animal_mt">Animal mitogenome </option>
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25 <option value="fungus_mt">Fungus mitogenome </option>
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26 <option value="fungus_nr">Fungus ribosomal RNA </option>
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data name="assembly_contigs" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (contigs)" />
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31 <data name="assembly_zip" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (full results as archive)" />
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32 </outputs>
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33 <help><![CDATA[
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34 This toolkit assemblies organelle genome from genomic skimming data.
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35
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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
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37
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38 Source code - https://github.com/Kinggerm/GetOrganelle
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39
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40 Organelle Database - https://github.com/Kinggerm/GetOrganelleDB
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42 ]]></help>
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43 </tool>