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annotate mob_typer.xml @ 5:09424ec94e80 draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit e3f242a0dbf429ac0394b6962441aaef367645a8"
author nml
date Wed, 13 Nov 2019 14:09:11 -0500
parents 2c7f721a4905
children 9424de64bfa8
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1 <tool id="mob_typer" name="MOB-Typer" version="1.4.9.1+galaxy0">
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2 <description>Get the plasmid type and mobility given its sequence</description>
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3 <requirements>
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4 <requirement type="package" version="1.4.9.1">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 mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}"
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10 --min_rep_evalue '$adv_param.min_rep_evalue_value'
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11 --min_mob_evalue '$adv_param.min_mob_evalue_value'
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12 --min_con_evalue '$adv_param.min_con_evalue_value'
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13 --min_ori_evalue '$adv_param.min_ori_evalue_value'
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14 --min_mpf_evalue '$adv_param.min_mpf_evalue'
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15 --min_rep_ident '$adv_param.min_rep_ident'
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16 --min_mob_ident '$adv_param.min_mob_ident'
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17 --min_ori_ident '$adv_param.min_ori_ident'
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18 --min_mpf_ident '$adv_param.min_mpf_ident'
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19 --outdir '.';
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
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24 <section name="adv_param" title="Advanced parameters" expanded="False">
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25 <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/>
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26 <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/>
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27 <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/>
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28 <param name="min_ori_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for oriT elements blastn"/>
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29 <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/>
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30 <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>
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31 <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>
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32 <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer" min="0" max="100" value="90"/>
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33 <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer" min="0" max="100" value="80"/>
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34 </section>
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35 </inputs>
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36 <outputs>
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37 <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
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38 <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
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39 </data>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
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44 <assert_stdout>
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45 <has_text text="JN253636"/>
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46 </assert_stdout>
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47 </test>
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48 </tests>
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49 <help>
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50
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51 **Syntax**
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52
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53 This tool provides *in-silico* predictions on plasmid typing including identification of replicon, relaxase and mate-pair formation protein types. MOB-typer also predicts mobility of a plasmid (Conjugative, Mobilizable, Non-mobilizable). Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single plasmid.
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54
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55 For more information please visit https://github.com/phac-nml/mob-suite/.
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57 -----
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58
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59 **Input:**
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60
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61 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
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62
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63
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64 **Output:**
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65
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66 Tab-delimited report listing identified plasmid(s) and their predicted mobility. Refer to https://github.com/phac-nml/mob-suite#mob-typer-report-file-format for the description of each column.
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67
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68
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69 </help>
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70 <citations>
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71 <citation type="bibtex">
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72 @misc{githubmob-suite,
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73 author = {Robertson J, Nash J},
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74 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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75 publisher = {GitHub},
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76 journal = {GitHub repository},
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77 doi = {10.1099/mgen.0.000206},
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78 url = {https://github.com/phac-nml/mob-suite}
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79 }</citation>
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80 </citations>
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81 </tool>