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1 <tool id="mob_recon" name="MOB-Recon" version="1.4.8">
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2 <description>Type contigs and extract plasmid sequences</description>
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3 <requirements>
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4 <requirement type="package" version="1.4.8">mob_suite</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 ln -s "${input}" "${input.name}";
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9
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10 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}"
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11 #if str($adv_param.unicycler_contigs) == "True":
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12 --unicycler_contigs
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13 #end if
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14 #if str($adv_param.run_circlator) == "True":
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15 --run_circlator
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16 #end if
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17 #if str($adv_param.min_length_condition.min_length_param) == "True":
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18 --min_length ${adv_param.min_length_condition.min_length_value}
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19 #end if
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20 --run_typer --outdir '.';
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
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25 <section name="adv_param" title="Advanced parameters" expanded="False">
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26 <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True">
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27 <option value="True">Yes</option>
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28 <option value="False">No</option>
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29 </param>
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30 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
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31 <option value="True">Yes</option>
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32 <option value="False">No</option>
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33 </param>
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34 <conditional name="min_length_condition">
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35 <param name="min_length_param" label="Minimum length of contigs to classify" type="select" value="False">
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36 <option value="False">No</option>
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37 <option value="True">Yes</option>
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38 </param>
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39 <when value="True">
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40 <param name="min_length_value" type="integer" value="500" min="50"/>
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41 </when>
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42 <when value="False"/>
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43 </conditional>
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44 </section>
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45 </inputs>
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46 <outputs>
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47 <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name}: Overall contig MOB-recon report"/>
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48 <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name}: Repetitive elements BLAST report"/>
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49 <data name="outfile3" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name}: Chromosomal sequences"/>
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50 <data name="outfile4" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name}: Aggregate MOB-typer report for all contigs"/>
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51 <data name="outfile5" format="fasta" label="${tool.name}: Plasmid sequence" hidden="true">
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52 <discover_datasets pattern="plasmid_.+\.(?P<ext>.+)" ext="fasta" visible="false" assign_primary_output="false"/>
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
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58 <section name="adv_param">
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59 <param name="evalue" value="0.00001"/>
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60 <param name="unicycler_contigs" value="True"/>
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61 <param name="run_circlator" value="True"/>
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62 </section>
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63 <output name="outfile1">
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64 <assert_contents>
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65 <has_text text="NC_019097"/>
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66 </assert_contents>
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67 </output>
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68 </test>
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69 </tests>
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70 <help>
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71
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72 **Syntax**
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73
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74 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
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75
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76 For more information please visit https://github.com/phac-nml/mob-suite/.
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77
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78 -----
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79
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80 **Input:**
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81
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82 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
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83
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84
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85 **Output:**
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86
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87 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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88
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89 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
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90
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91
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92 </help>
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93 <citations>
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94 <citation type="bibtex">
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95 @misc{githubmob-suite,
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96 author = {Robertson J, Nash J},
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97 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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98 publisher = {GitHub},
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99 journal = {GitHub repository},
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100 doi = {10.1099/mgen.0.000206},
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101 url = {https://github.com/phac-nml/mob-suite}
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102 }</citation>
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103 </citations>
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104 </tool> |
