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1
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1 <tool id="cpo_clustalw" name="cpo_clustalw" version="2.1">
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5
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2 <description>Modified version of clustalw2 v2.1 to produce NJ trees from an SNIPPY produced alignment</description>
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1
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3 <requirements>
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4 <requirement type="package" version="2.1">clustalw</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 clustalw2 -tree -infile=$input -outputtree=nj
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9 ]]>
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10 </command>
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11 <inputs>
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12 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
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13 </inputs>
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14 <outputs>
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15 <data name="phylip" format="txt" from_work_dir="*.ph"/>
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16 <data name="njtree" format="txt" from_work_dir="*.nj*"/>
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17 </outputs>
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18 <help>
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19
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20 **Syntax**
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21
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22 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
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23
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24 For more information please visit https://github.com/phac-nml/mob-suite/.
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25
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26 -----
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27
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28 **Input:**
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29
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30 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
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31
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32
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33 **Output:**
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34
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35 Tab-delimited report listing information for each input contig on its cluster number, possible replicon, relaxase, and repetitive elements types, etc. Refer to https://github.com/phac-nml/mob-suite#mob-recon-contig-report-format for the description of each column.
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36
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37 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
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38
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39
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40 </help>
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41 <citations>
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42 <citation type="bibtex">
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43 @misc{githubmob-suite,
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44 author = {Robertson J, Nash J},
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45 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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46 publisher = {GitHub},
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47 journal = {GitHub repository},
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48 doi = {10.1099/mgen.0.000206},
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49 url = {https://github.com/phac-nml/mob-suite}
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50 }</citation>
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51 </citations>
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5
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52 </tool>
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