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comparison refchooser.xml @ 2:719889ec4e14 draft

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planemo upload commit 92689f52a93241194941ecf374629245c8fb9093
author galaxytrakr
date Mon, 16 Mar 2026 15:02:07 +0000
parents dcf6c2409ebb
children 806262ab8081
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1:dcf6c2409ebb 2:719889ec4e14
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+galaxy0.1" 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">quay.io/galaxytrakr/refchooser:0.2.3</container> 4 <container type="docker">cfsanbiostatistics/refchooser:0.2.1</container>
5
5 </requirements> 6 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
7 mkdir ./assemblies && 8 mkdir ./assemblies &&
8 #for assembly in $assemblies 9 #for assembly in $assemblies
9 ln -sf '$assembly' ./assemblies/${assembly.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta && 10 ln -sf '$assembly' ./assemblies/${assembly.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta &&
11 refchooser sketch ./assemblies ./sketches && 12 refchooser sketch ./assemblies ./sketches &&
12 refchooser matrix ./assemblies ./sketches ${matrix} && 13 refchooser matrix ./assemblies ./sketches ${matrix} &&
13 export BEST=\$(refchooser metrics --sort Mean_Distance --top 1 ./assemblies ./sketches | tail -n 1 | cut -f 1) && 14 export BEST=\$(refchooser metrics --sort Mean_Distance --top 1 ./assemblies ./sketches | tail -n 1 | cut -f 1) &&
14 echo "*** best accession \$BEST ***" >&2 && 15 echo "*** best accession \$BEST ***" >&2 &&
15 mkdir output && 16 mkdir output &&
16 cp ./assemblies/\$BEST.fasta output/\$BEST.fasta && 17 cp ./assemblies/\$BEST.fasta output/\$BEST.fasta
17 ls -l output/
18 ]]></command> 18 ]]></command>
19 <inputs> 19 <inputs>
20 <param type="data_collection" collection_type="list" name="assemblies" format="fasta" /> 20 <param type="data_collection" collection_type="list" name="assemblies" format="fasta" />
21 </inputs> 21 </inputs>
22 <outputs> 22 <outputs>
23 <data name="matrix" label="Refchooser distance matrix for $on_string" format="tsv" hidden="false" /> 23 <data name="matrix" label="Refchooser distance matrix for $on_string" format="tsv" hidden="false" />
24 <data name="best" format="txt" label="Centroidal_assembly" > 24 <data name="best" format="txt" label="Best assembly" visible="false" >
25 <discover_datasets directory="output" pattern="__designation_and_ext__" ext="fasta" assign_primary_output="true" visible="true" /> 25 <discover_datasets directory="output" pattern="__designation_and_ext__" assign_primary_output="true" visible="true" />
26 </data> 26 </data>
27 </outputs> 27 </outputs>
28 <tests> 28 <tests>
29 <test> 29 <test>
30 <param name="assemblies"> 30 <param name="assemblies">