Mercurial > repos > petr-novak > get_organelle

annotate get_organelle.xml @ 5:513350816e4a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit a17736d0821e1f8366f416ea2cc6874851a74c26-dirty"
author petr-novak
date Wed, 01 Jun 2022 07:12:19 +0000
parents a388d670fd54
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
1 <tool id="get_organelle" name="Assemble organelle genome from genomic skimming data" version="0.1.0" python_template_version="3.5">
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
2 <requirements>
3
a388d670fd54 "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents: 0
diff changeset
3 <requirement type="package" version="1.7.6.1">getorganelle</requirement>
0
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
4 <requirement type="package" version="0.0.1">getorganelledb</requirement>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
5 <requirement type="set_environment">GETORGANELLEDB</requirement>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
6
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
7 </requirements>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
9 get_organelle_from_reads.py -1 '$fastq1' -2 '$fastq2' -t 10 -o assembly_dir --config-dir \${GETORGANELLEDB} -F ${ref_db} &&
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
10 cat assembly_dir/*.fasta > ${assembly_contigs} &&
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
11 zip -r assembly.zip assembly_dir &&
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
12 mv assembly.zip ${assembly_zip}
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
13
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
14
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
15 ]]></command>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
16 <inputs>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
17 <param type="data" name="fastq1" format="fastq" help="FASTQ forward reads"/>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
18 <param type="data" name="fastq2" format="fastq" help="FASTQ reverse reads" />
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
19 <param type="select" label="Assembly type" name="ref_db" >
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
20 <option value="embplant_pt" selected="true" > Embryophyta plant plastome </option>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
21 <option value="embplant_mt">Embryophyta plant mitogenome </option>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
22 <option value="embplant_nr">Embryophyta plant ribosomal RNA </option>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
23 <option value="other_pt">Non-embryophyta plant plastome </option>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
24 <option value="animal_mt">Animal mitogenome </option>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
25 <option value="fungus_mt">Fungus mitogenome </option>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
26 <option value="fungus_nr">Fungus ribosomal RNA </option>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
27 </param>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
28 </inputs>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
29 <outputs>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
30 <data name="assembly_contigs" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (contigs)" />
5
513350816e4a "planemo upload commit a17736d0821e1f8366f416ea2cc6874851a74c26-dirty"
petr-novak
parents: 3
diff changeset
31 <data name="assembly_zip" format="zip" label="Assembly from ${on_string} using ${ref_db} database (full results as archive)" />
0
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
32 </outputs>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
33 <help><![CDATA[
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
34 This toolkit assemblies organelle genome from genomic skimming data.
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
35
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
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
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
37
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
38 Source code - https://github.com/Kinggerm/GetOrganelle
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
39
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
40 Organelle Database - https://github.com/Kinggerm/GetOrganelleDB
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
41
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
42 ]]></help>
0ff5b94932fe "planemo upload commit 32e4182f0466ce67f42e288f4f35f4400703ea79-dirty"
petr-novak
parents:
diff changeset
43 </tool>