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planemo upload commit c5b9a5678302366ab392fc9b24104509beb07c38-dirty
author jpayne
date Mon, 11 Aug 2025 15:37:26 +0000
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1 <tool id="refchooser" name="Refchooser" version="0.2.1" python_template_version="3.5" profile="21.05">
2 <description>Select centroidal assembly from a collection of closely-related assemblies, for reference purposes</description>
3 <requirements>
4 <container type="docker">cfsanbiostatistics/refchooser:0.2.1</container>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 mkdir ./assemblies &&
8 #for assembly in $assemblies
9 ln -sf '$assembly' ./assemblies/${assembly.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta &&
10 #end for
11 refchooser sketch ./assemblies ./sketches &&
12 refchooser matrix ./assemblies ./sketches ${matrix} &&
13 export BEST=\$(refchooser metrics --sort Mean_Distance --top 1 ./assemblies ./sketches | tail -n 1 | cut -f 1) &&
14 echo "*** best accession \$BEST ***" >&2 &&
15 cat ./assemblies/\$BEST.fasta > $output
16 ]]></command>
17 <inputs>
18 <param type="data_collection" collection_type="list" name="assemblies" format="fasta" />
19 </inputs>
20 <outputs>
21 <data name="matrix" label="Distance matrix" format="tsv" visible="false" />
22 <data name="output" label="Centroidal assembly" format="fasta" />
23 </outputs>
24 <tests>
25 <test>
26 <param name="assemblies">
27 <collection type="list">
28 <element name="SRR498285" value="test/reference_selection/assemblies/SRR498285_contigs.fasta" />
29 <element name="SRR498286" value="test/reference_selection/assemblies/SRR498286_contigs.fasta" />
30 <element name="SRR498361" value="test/reference_selection/assemblies/SRR498361_contigs.fasta" />
31 <element name="SRR498363" value="test/reference_selection/assemblies/SRR498363_contigs.fasta" />
32 <element name="SRR498372" value="test/reference_selection/assemblies/SRR498372_contigs.fasta" />
33 <element name="SRR498379" value="test/reference_selection/assemblies/SRR498379_contigs.fasta" />
34 <element name="SRR498381" value="test/reference_selection/assemblies/SRR498381_contigs.fasta" />
35 <element name="SRR498384" value="test/reference_selection/assemblies/SRR498384_contigs.fasta" />
36 <element name="SRR498386" value="test/reference_selection/assemblies/SRR498386_contigs.fasta" />
37 <element name="SRR498387" value="test/reference_selection/assemblies/SRR498387_contigs.fasta" />
38 </collection>
39 </param>
40 <output name="output" value="test/reference_selection/assemblies/SRR498286_contigs.fasta" />
41 </test>
42 </tests>
43 <help><![CDATA[
44 Some important help text.
45 ]]></help>
46 <citations>
47 <citation type="bibtex">
48 @misc{githubrefchooser,
49 author = {Davis, Steven},
50 year = {2019},
51 title = {Refchooser},
52 publisher = {GitHub},
53 journal = {GitHub repository},
54 url = {https://refchooser.readthedocs.io/en/latest/},
55 }</citation>
56 </citations>
57 </tool>