Mercurial > repos > iuc > compleasm
diff compleasm.xml @ 5:7109a27a11db draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 0db08b58079fe83ce390bac19bcb056ed44932d3
author | iuc |
---|---|
date | Mon, 20 Jan 2025 09:55:04 +0000 |
parents | 8f20a5b9b282 |
children |
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--- a/compleasm.xml Wed Jul 24 17:43:14 2024 +0000 +++ b/compleasm.xml Mon Jan 20 09:55:04 2025 +0000 @@ -11,9 +11,10 @@ </requirements> <version_command>compleasm --version</version_command> <command><![CDATA[ - - mkdir -p galaxy_db && - cp -r '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/' && + mkdir -p 'galaxy_db/' && + ln -s '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/${lineage_dataset}' && + ## Create a compleasm-specific empty file to avoid redownloading the lineage data (https://github.com/huangnengCSU/compleasm/blob/0.2.6/compleasm.py#L165) + touch 'galaxy_db/${lineage_dataset}.done' && compleasm run -a '$input' @@ -21,7 +22,7 @@ --mode $mode -L 'galaxy_db' -l '$lineage_dataset' - -t "\${GALAXY_SLOTS:-1}" + -t "\${GALAXY_SLOTS:-1}" #if str($specified_contigs) != '': --specified_contigs '$specified_contigs' @@ -43,7 +44,7 @@ </sanitizer> <validator type="regex">[0-9a-zA-Z_ ]+</validator> </param> - + <param name="outputs" type="select" multiple="true" label="Which outputs should be generated"> <option value="full_table_busco" selected="true">full busco table</option> <option value="full_table">full table</option> @@ -72,7 +73,7 @@ </data> <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta"> <filter>outputs and 'translated_protein' in outputs</filter> - </data> + </data> </outputs> <tests> @@ -80,18 +81,24 @@ <param name="input" value="small_genome.fasta"/> <param name="mode" value="busco"/> <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/> - <param name="busco_database" value="eukaryota_odb10"/> - <param name="lineage_dataset" value="eukaryota_odb10"/> + <param name="busco_database" value="entomoplasmatales_odb10"/> + <param name="lineage_dataset" value="entomoplasmatales_odb10"/> <output name="full_table_busco"> <assert_contents> <has_text text="Busco id"/> - <has_text text="Missing"/> + <has_text text="496at186328	Missing"/> + <has_text text="165at186328	Complete"/> + <has_text text="421at186328	Complete"/> + <has_text text="90at186328	Complete"/> </assert_contents> </output> <output name="full_table"> <assert_contents> - <has_text text="Gene"/> - <has_text text="Missing"/> + <has_text text="Gene	Status"/> + <has_text text="496at186328	Missing"/> + <has_text text="165at186328	Single"/> + <has_text text="421at186328	Single"/> + <has_text text="90at186328	Single"/> </assert_contents> </output> <output name="miniprot"> @@ -101,19 +108,22 @@ </output> <output name="translated_protein"> <assert_contents> - <has_text text="GGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGG"/> - <has_text text="AAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAHVTLQQLDLCSLDSVRAAADALRTAYPRIDVLINNAGVMW"/> + <has_text text="EKDFYQELGVSSDASPEEIKRAYRKLARDLHPDANPGNPAA"/> + <has_text text="AASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVD"/> </assert_contents> </output> + <assert_stdout> + <has_text text="S:1.20%, 4"/> + </assert_stdout> </test> </tests> <help><![CDATA[ - compleasm_ assesses genome completeness based on genome assembly. + compleasm_ assesses genome completeness based on genome assembly. .. _compleasm: https://github.com/huangnengCSU/compleasm - ]]> + ]]> </help> <expand macro="citation"/> </tool>