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planemo upload commit 0afa3db59f582bebcb1aed2cc0f3dc2ade807d86-dirty
author jpayne
date Mon, 08 Dec 2025 20:28:57 +0000
parents 91bc7378c1c5
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0:91bc7378c1c5 1:dcf6c2409ebb
1 <tool id="refchooser" name="Refchooser" version="0.2.1" python_template_version="3.5" profile="21.05"> 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> 2 <description>Select centroidal assembly from a collection of closely-related assemblies, for reference purposes</description>
3 <requirements> 3 <requirements>
4 <container type="docker">cfsanbiostatistics/refchooser:0.2.1</container> 4 <container type="docker">quay.io/galaxytrakr/refchooser:0.2.3</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 mkdir ./assemblies && 7 mkdir ./assemblies &&
8 #for assembly in $assemblies 8 #for assembly in $assemblies
9 ln -sf '$assembly' ./assemblies/${assembly.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta && 9 ln -sf '$assembly' ./assemblies/${assembly.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta &&
10 #end for 10 #end for
11 refchooser sketch ./assemblies ./sketches && 11 refchooser sketch ./assemblies ./sketches &&
12 refchooser matrix ./assemblies ./sketches ${matrix} && 12 refchooser matrix ./assemblies ./sketches ${matrix} &&
13 export BEST=\$(refchooser metrics --sort Mean_Distance --top 1 ./assemblies ./sketches | tail -n 1 | cut -f 1) && 13 export BEST=\$(refchooser metrics --sort Mean_Distance --top 1 ./assemblies ./sketches | tail -n 1 | cut -f 1) &&
14 echo "*** best accession \$BEST ***" >&2 && 14 echo "*** best accession \$BEST ***" >&2 &&
15 cat ./assemblies/\$BEST.fasta > $output 15 mkdir output &&
16 cp ./assemblies/\$BEST.fasta output/\$BEST.fasta &&
17 ls -l output/
16 ]]></command> 18 ]]></command>
17 <inputs> 19 <inputs>
18 <param type="data_collection" collection_type="list" name="assemblies" format="fasta" /> 20 <param type="data_collection" collection_type="list" name="assemblies" format="fasta" />
19 </inputs> 21 </inputs>
20 <outputs> 22 <outputs>
21 <data name="matrix" label="Distance matrix" format="tsv" visible="false" /> 23 <data name="matrix" label="Refchooser distance matrix for $on_string" format="tsv" hidden="false" />
22 <data name="output" label="Centroidal assembly" format="fasta" /> 24 <data name="best" format="txt" label="Centroidal_assembly" >
25 <discover_datasets directory="output" pattern="__designation_and_ext__" ext="fasta" assign_primary_output="true" visible="true" />
26 </data>
23 </outputs> 27 </outputs>
24 <tests> 28 <tests>
25 <test> 29 <test>
26 <param name="assemblies"> 30 <param name="assemblies">
27 <collection type="list"> 31 <collection type="list">
35 <element name="SRR498384" value="test/reference_selection/assemblies/SRR498384_contigs.fasta" /> 39 <element name="SRR498384" value="test/reference_selection/assemblies/SRR498384_contigs.fasta" />
36 <element name="SRR498386" value="test/reference_selection/assemblies/SRR498386_contigs.fasta" /> 40 <element name="SRR498386" value="test/reference_selection/assemblies/SRR498386_contigs.fasta" />
37 <element name="SRR498387" value="test/reference_selection/assemblies/SRR498387_contigs.fasta" /> 41 <element name="SRR498387" value="test/reference_selection/assemblies/SRR498387_contigs.fasta" />
38 </collection> 42 </collection>
39 </param> 43 </param>
40 <output name="output" value="test/reference_selection/assemblies/SRR498286_contigs.fasta" /> 44 <output name="best" >
45 <discovered_dataset designation="SRR498286" ftype="fasta">
46 <assert_contents>
47 <has_text text="SRR498286" />
48 </assert_contents>
49 </discovered_dataset>
50 </output>
41 </test> 51 </test>
42 </tests> 52 </tests>
43 <help><![CDATA[ 53 <help><![CDATA[
44 Some important help text. 54 Some important help text.
45 ]]></help> 55 ]]></help>