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author | estrain |
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date | Thu, 08 Feb 2024 21:07:43 +0000 |
parents | 92600b70b259 |
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<tool id="lissero" name="lissero" version="1.0.1+galaxy0" python_template_version="3.5" profile="21.05"> <requirements> <requirement type="package">lissero</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ lissero #if $settings.advanced == "advanced" --min_id $settings.min_id --min_cov $settings.min_cov #end if '$input1' > output1; python $__tool_directory__/variant4b.py output1 output2.txt ${input1.element_identifier}; ]]></command> <inputs> <param type="data" name="input1" format="fasta" /> <conditional name="settings"> <param name="advanced" type="select" label="Specify advanced parameters"> <option value="simple" selected="true">No, use program defaults.</option> <option value="advanced">Yes, see full parameter list.</option> </param> <when value="simple"> </when> <when value="advanced"> <param name="min_id" type="float" label="Minimum percent identity to accept a match" value="95.0" min="0" max="100" /> <param name="min_cov" type="float" label="Minimum coverage of a gene to accept a match" value="95.0" min="0" max="100" /> </when> </conditional> </inputs> <outputs> <data format="tabular" name="lissero.tsv" label="${tool.name} on ${on_string}: LisSero" from_work_dir="*.txt"/> </outputs> <help><![CDATA[ Usage: lissero [OPTIONS] FASTA... In silico serogroup prediction for L. monocytogenes. Alleles: lmo1118, lmo0737, ORF2819, ORF2110, Prs References: Doumith et al. Differentiation of the major Listeria monocytogenes serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22 Options: -h, --help Show this message and exit. --min_id FLOAT Minimum percent identity to accept a match. [0-100][default=95.0] --min_cov FLOAT Minimum coverage of the gene to accept a match. [0-100][default=95.0] ]]></help> <citations> <citation type="doi">10.1128/JCM.42.8.3819-3822.2004</citation> </citations> </tool>