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1 <tool id="pmlst" name="pmlst" version="2.0">
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2 <description>A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid categorization of IncN plasmids</description>
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3
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4
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5 <requirements>
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6 <requirement type="package" version="3.2.0">python3-openid</requirement>
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7 <requirement type="package" version="21.2.4">pip</requirement>
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8 <requirement type="package" version="1.79">biopython</requirement>
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9 <requirement type="package" version="1.5.6">cgecore</requirement>
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10 <requirement type="package" version="0.8.9">tabulate</requirement>
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11 </requirements>
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12
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13
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14 <!--<command> python3 $__tool_directory__/pmlst/pmlst.py -i $input -s $s -p $__tool_directory__/pmlst/pmlst_db/ > $output </command>-->
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15
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16 <command> perl $__tool_directory__/pmlst.pl $__tool_directory__ $input $s > $output </command>
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17
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18 <inputs>
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19 <param format="fasta" name="input" type="data" label="Select FASTA files: " />
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20
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21 <param name="s" type="select" label="Scheme database used for pMLST prediction:">
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22
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23 <option value="incac">incac</option>
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24 <option value="incf">incf</option>
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25 <option value="inchi1">inchi1</option>
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26 <option value="inchi2">inchi2</option>
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27 <option value="inci1">inci1</option>
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28 <option value="incn">incn</option>
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29 <option value="pbssb1-family">pbssb1-family</option>
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30
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31 </param>
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32
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33
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34 </inputs>
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35
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36 <outputs>
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37 <data format="tabular" name="output" />
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38 </outputs>
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39
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40 <help>
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41
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42 </help>
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43 <citations>
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44 <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
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45 </citations>
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46 </tool>
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47
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48
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49
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