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1 <tool id="cpo_clustalw" name="cpo_clustalw" version="2.1">
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2 <description>makes tree from alignment</description>
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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 <tests>
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19 <test>
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20 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
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21 <section name="adv_param">
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22 <param name="evalue" value="0.00001"/>
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23 <param name="unicycler_contigs" value="True"/>
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24 <param name="run_circlator" value="True"/>
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25 </section>
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26 <output name="outfile1">
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27 <assert_contents>
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28 <has_text text="NC_019097"/>
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29 </assert_contents>
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30 </output>
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31 </test>
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32 </tests>
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33 <help>
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34
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35 **Syntax**
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36
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37 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
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38
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39 For more information please visit https://github.com/phac-nml/mob-suite/.
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40
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41 -----
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42
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43 **Input:**
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44
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45 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
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46
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47
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48 **Output:**
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49
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50 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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51
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52 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
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53
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54
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55 </help>
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56 <citations>
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57 <citation type="bibtex">
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58 @misc{githubmob-suite,
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59 author = {Robertson J, Nash J},
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60 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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61 publisher = {GitHub},
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62 journal = {GitHub repository},
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63 doi = {10.1099/mgen.0.000206},
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64 url = {https://github.com/phac-nml/mob-suite}
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65 }</citation>
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66 </citations>
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67 </tool> |
