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1 <tool id="lissero" name="lissero" version="1.0.0+galaxy0" python_template_version="3.5" profile="21.05">
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2 <requirements>
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3 <requirement type="package">lissero</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 lissero
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7 #if $settings.advanced == "advanced"
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8 --min_id $settings.min_id
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9 --min_cov $settings.min_cov
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10 #end if
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11 '$input1' > output1;
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11
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12 python $__tool_directory__/variant4b.py output1 output2.txt ${input1.name};
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10
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13 ]]></command>
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14 <inputs>
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15 <param type="data" name="input1" format="fasta" />
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16 <conditional name="settings">
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17 <param name="advanced" type="select" label="Specify advanced parameters">
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18 <option value="simple" selected="true">No, use program defaults.</option>
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19 <option value="advanced">Yes, see full parameter list.</option>
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20 </param>
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21 <when value="simple">
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22 </when>
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23 <when value="advanced">
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24 <param name="min_id" type="float" label="Minimum percent identity to accept a match" value="95.0" min="0" max="100" />
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25 <param name="min_cov" type="float" label="Minimum coverage of a gene to accept a match" value="95.0" min="0" max="100" />
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26 </when>
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27 </conditional>
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28 </inputs>
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29 <outputs>
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30 <data format="tabular" name="lissero.tsv" label="${tool.name} on ${on_string}: LisSero" from_work_dir="*.txt"/>
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31 </outputs>
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32 <help><![CDATA[
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33 Usage: lissero [OPTIONS] FASTA...
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34
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35 In silico serogroup prediction for L. monocytogenes. Alleles: lmo1118,
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36 lmo0737, ORF2819, ORF2110, Prs
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37
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38 References:
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39
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40 Doumith et al. Differentiation of the major Listeria monocytogenes
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41 serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22
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42
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43 Options:
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44 -h, --help Show this message and exit.
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45 --min_id FLOAT Minimum percent identity to accept a match. [0-100][default=95.0]
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46 --min_cov FLOAT Minimum coverage of the gene to accept a match. [0-100][default=95.0]
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47
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48 ]]></help>
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49 <citations>
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50 <citation type="doi">10.1128/JCM.42.8.3819-3822.2004</citation>
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51 </citations>
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52 </tool>
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