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author jpayne
date Mon, 08 Dec 2025 20:28:57 +0000
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1 <tool id="refchooser" name="Refchooser" version="0.2.1" python_template_version="3.5" profile="21.05">
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2 <description>Select centroidal assembly from a collection of closely-related assemblies, for reference purposes</description>
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3 <requirements>
1
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4 <container type="docker">quay.io/galaxytrakr/refchooser:0.2.3</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 mkdir ./assemblies &&
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8 #for assembly in $assemblies
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9 ln -sf '$assembly' ./assemblies/${assembly.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta &&
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10 #end for
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11 refchooser sketch ./assemblies ./sketches &&
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12 refchooser matrix ./assemblies ./sketches ${matrix} &&
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13 export BEST=\$(refchooser metrics --sort Mean_Distance --top 1 ./assemblies ./sketches | tail -n 1 | cut -f 1) &&
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14 echo "*** best accession \$BEST ***" >&2 &&
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15 mkdir output &&
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16 cp ./assemblies/\$BEST.fasta output/\$BEST.fasta &&
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17 ls -l output/
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18 ]]></command>
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19 <inputs>
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20 <param type="data_collection" collection_type="list" name="assemblies" format="fasta" />
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21 </inputs>
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22 <outputs>
1
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23 <data name="matrix" label="Refchooser distance matrix for $on_string" format="tsv" hidden="false" />
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24 <data name="best" format="txt" label="Centroidal_assembly" >
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25 <discover_datasets directory="output" pattern="__designation_and_ext__" ext="fasta" assign_primary_output="true" visible="true" />
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26 </data>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="assemblies">
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31 <collection type="list">
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32 <element name="SRR498285" value="test/reference_selection/assemblies/SRR498285_contigs.fasta" />
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33 <element name="SRR498286" value="test/reference_selection/assemblies/SRR498286_contigs.fasta" />
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34 <element name="SRR498361" value="test/reference_selection/assemblies/SRR498361_contigs.fasta" />
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35 <element name="SRR498363" value="test/reference_selection/assemblies/SRR498363_contigs.fasta" />
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36 <element name="SRR498372" value="test/reference_selection/assemblies/SRR498372_contigs.fasta" />
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37 <element name="SRR498379" value="test/reference_selection/assemblies/SRR498379_contigs.fasta" />
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38 <element name="SRR498381" value="test/reference_selection/assemblies/SRR498381_contigs.fasta" />
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39 <element name="SRR498384" value="test/reference_selection/assemblies/SRR498384_contigs.fasta" />
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40 <element name="SRR498386" value="test/reference_selection/assemblies/SRR498386_contigs.fasta" />
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41 <element name="SRR498387" value="test/reference_selection/assemblies/SRR498387_contigs.fasta" />
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42 </collection>
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43 </param>
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44 <output name="best" >
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45 <discovered_dataset designation="SRR498286" ftype="fasta">
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46 <assert_contents>
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47 <has_text text="SRR498286" />
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48 </assert_contents>
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49 </discovered_dataset>
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50 </output>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54 Some important help text.
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55 ]]></help>
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56 <citations>
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57 <citation type="bibtex">
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58 @misc{githubrefchooser,
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59 author = {Davis, Steven},
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60 year = {2019},
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61 title = {Refchooser},
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62 publisher = {GitHub},
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63 journal = {GitHub repository},
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64 url = {https://refchooser.readthedocs.io/en/latest/},
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65 }</citation>
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66 </citations>
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67 </tool>