Mercurial > repos > iuc > compleasm
diff compleasm.xml @ 0:07a74537acd5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 89b9cc3af83916f8d14911ac3484ad2e35ded0a4
author | iuc |
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date | Wed, 14 Feb 2024 14:31:44 +0000 |
parents | |
children | 79413aecc398 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/compleasm.xml Wed Feb 14 14:31:44 2024 +0000 @@ -0,0 +1,104 @@ +<tool id="compleasm" name="compleasm" version="@TOOL_VERSION@+galaxy0" profile="20.01"> + <description>completeness of genome assemblies</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">compleasm</requirement> + </requirements> + <command><![CDATA[ + compleasm run + -a '$input' + -o galaxy + --mode $mode + -l '$busco_database' + + #if str($specified_contigs) != '': + --specified_contigs '$specified_contigs' + #end if + + ]]></command> + <inputs> + <param argument="-a" name="input" type="data" format="fasta" label="Input genome file"/> + <param name="mode" type="select" label="The mode of evaluation" help="If you want to use hmmsearch, select BUSCO mode. Otherwise, select lite mode"> + <option value="busco" selected="true">BUSCO</option> + <option value="lite">Lite</option> + </param> + + <param argument="--specified_contigs" type="text" label="Specify the contigs to be evaluated" optional="true" help="e.g. chr1 chr2 chr3. If not specified, all contigs will be evaluated"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </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> + <option value="miniprot">miniprot</option> + <option value="translated_protein">translated proteins</option> + </param> + + <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false"> + <options from_data_table="busco_database"/> + </param> + </inputs> + + <outputs> + <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy/*_odb10/full_table_busco_format.tsv"> + <filter>outputs and 'full_table_busco' in outputs</filter> + </data> + <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy/*_odb10/full_table.tsv"> + <filter>outputs and 'full_table' in outputs</filter> + </data> + <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy/*_odb10/miniprot_output.gff"> + <filter>outputs and 'miniprot' in outputs</filter> + </data> + <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy/*_odb10/translated_protein.fasta"> + <filter>outputs and 'translated_protein' in outputs</filter> + </data> + </outputs> + + <tests> + <test expect_num_outputs="4"> + <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"/> + <output name="full_table_busco"> + <assert_contents> + <has_text text="Busco id"/> + <has_text text="Missing"/> + </assert_contents> + </output> + <output name="full_table"> + <assert_contents> + <has_text text="Gene"/> + <has_text text="Missing"/> + </assert_contents> + </output> + <output name="miniprot"> + <assert_contents> + <has_text text="##gff-version 3"/> + </assert_contents> + </output> + <output name="translated_protein"> + <assert_contents> + <has_text text="GGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGG"/> + <has_text text="AAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAHVTLQQLDLCSLDSVRAAADALRTAYPRIDVLINNAGVMW"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + + compleasm_ assesses genome completeness based on genome assembly. + + .. _compleasm: https://github.com/huangnengCSU/compleasm + + ]]> + </help> + <expand macro="citation"/> +</tool>