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5
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1 <tool id="cpo_tree_drawer" name="cpo_tree_drawer" version="0.1.0">
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2 <description>This tool makes a phylogenetic tree using data from snippy alignments, clustalw NJ tree and metadat from cpo_prediction workflow using ETE3</description>
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1
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3 <requirements>
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7
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4 <requirement type="package" version="3.6">python</requirement>
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5 <requirement type="package" version="0.23.4">pandas</requirement>
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5
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6 <requirement type="package" version="3.1.1">ete3</requirement>
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7
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7 <requirement type="package" version="5.6.0">pyqt</requirement>
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9
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8 <requirement type="package" version="5.6.2">qt</requirement>
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5
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9 </requirements>
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1
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12 python '$__tool_directory__/cpo_galaxy_tree.py'
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13 '-t $tree'
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14 '-d $distance'
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15 '-m $metadata'
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param type="data" name="tree" format="txt"/>
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20 <param type="data" name="distance" format="tabular" />
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21 <param type="data" name="metadata" format="tabular" />
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22 </inputs>
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23 <outputs>
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8
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24 <data name="tsvSummary" format="pdf" from_work_dir="tree.pdf"/>
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1
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="ID" value="BC11-Kpn005_S2"/>
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29 <param name="mlst" value="BC11-Kpn005_S2.mlst"/>
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30 <param name="mobsuitecontig" value="contig_report"/>
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31 <param name="mobsuiteaggregate" value="mobtyper_aggregate_report"/>
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32 <param name="abricate" value="BC11-Kpn005_S2.cp"/>
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33 <param name="rgi" value="BC11-Kpn005_S2.rgi.txt"/>
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34 <param name="plasmidfinder" value="BC11-Kpn005_S2.origins"/>
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35 <param name="expected" value="Klebsiella pneumoniae"/>
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36 <output name="tsvSummary" file="summary.tsv"/>
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37 <output name="txtSummary" file="summary.txt"/>
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38 </test>
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39 </tests>
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40 <help>
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41 This tool parses stuff.
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42 </help>
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43 <citations>
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44 <citation type="bibtex">
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45 @misc{cpo,
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46 author = {j, j},
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47 year = {2018},
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48 title = {cpo_prediction},
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49 publisher = {j},
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50 journal = {j of j},
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51 url = {https://bfjia.net,
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52 }</citation>
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53 </citations>
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9
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54 </tool>
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