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1 <tool id="pmlst" name="pmlst" version="2.0+galaxy1">
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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 <requirement type="package" version="2.7.1">blastn</requirement>
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12 </requirements>
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13
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14
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15 <!--<command> python3 $__tool_directory__/pmlst/pmlst.py -i $input -s $s -p $__tool_directory__/pmlst/pmlst_db/ > $output </command>-->
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16
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17 <!--<command> perl $__tool_directory__/pmlst.pl $__tool_directory__ $input $s > $output </command>-->
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18
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19 <command detect_errors="aggressive"><![CDATA[
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20
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21 #import re
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22 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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23 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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24
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25 ## Add single quotes around each input file identifier
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26 #set $_input_file = "'{}'".format($input.element_identifier)
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27 ln -s '${input}' ${_input_file} &&
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28
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29
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30 perl $__tool_directory__/pmlst.pl $__tool_directory__ $_input_file $s > $output
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31
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32
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33
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34 ]]></command>
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35
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36 <inputs>
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37 <param format="fasta" name="input" type="data" label="Select FASTA files: " />
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38
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39
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40 <param name="s" type="select" label="Scheme database used for pMLST prediction:">
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41
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42 <option value="incac">incac</option>
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43 <option value="incf">incf</option>
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44 <option value="inchi1">inchi1</option>
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45 <option value="inchi2">inchi2</option>
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46 <option value="inci1">inci1</option>
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47 <option value="incn">incn</option>
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48 <option value="pbssb1-family">pbssb1-family</option>
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49
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50 </param>
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51
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52
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53 </inputs>
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54
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55 <outputs>
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56 <data format="tabular" name="output" />
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57 </outputs>
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58
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59 <help>
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60
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61 </help>
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62 <citations>
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63 <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
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64 </citations>
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65 </tool>
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66
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