Mercurial > repos > estrain > lissero
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author | estrain |
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date | Tue, 13 Dec 2022 18:24:57 +0000 |
parents | 6690f5040e05 |
children | d1e5ac182915 |
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<tool id="lissero" name="lissero" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05"> <requirements> <requirement type="package">lissero</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ lissero #if $advanced --min_id $advanced.min_id --min_cov $advanced.min_cov #end if '$input1' > '$output1'; ]]></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 name="output1" format="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>