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annotate mob_recon.xml @ 0:820eec3fa31f draft

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planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
author nml
date Thu, 24 May 2018 12:17:20 -0400
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820eec3fa31f planemo upload for repository https://github.com/phac-nml/mob-suite commit 8c045f39dc0cdaa69876714f74f0470de6ce3c6c-dirty
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1 <tool id="mob_recon" name="MOB-Recon" version="1.4.1">
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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="1.4.1">mob_suite</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 ln -s "${input}" "${input.name}";
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8 mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" --evalue '${adv_param.evalue}' --unicycler_contigs '${adv_param.unicycler_contigs}' --run_circlator '${adv_param.run_circlator}' --run_typer --outdir '.';
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9 </command>
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10 <inputs>
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11 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
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12 <section name="adv_param" title="Advanced parameters" expanded="False">
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13 <param name="evalue" label="Minimum e-value threshold for BLAST" type="float" min="0.000000000000000000001" max="1" value="0.00001"/>
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14 <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True">
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15 <option value="True">Yes</option>
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16 <option value="False">No</option>
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17 </param>
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18 <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
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19 <option value="True">Yes</option>
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20 <option value="False">No</option>
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21 </param>
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22
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23 </section>
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24 </inputs>
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25 <outputs>
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26 <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name}: Overall contig MOB-recon report from ${input.name}"/>
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27 <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name}: Repetitive elements BLAST report from ${input.name}"/>
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28 <data name="outfile3" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name}: Chromosomal sequences (if any) from ${input.name}"/>
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29 <data name="outfile4" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name}: Aggregate MOB-typer report for all contigs from ${input.name}"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
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34 <section name="adv_param">
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35 <param name="evalue" value="0.00001"/>
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36 <param name="unicycler_contigs" value="True"/>
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37 <param name="run_circlator" value="True"/>
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38 </section>
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39 <output name="outfile1">
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40 <assert_contents>
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41 <has_text text="NC_019097"/>
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42 </assert_contents>
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43 </output>
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44 </test>
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45 </tests>
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46 <help>
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47
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48 **Syntax**
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49
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50 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
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51
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52 For more information please visit https://github.com/phac-nml/mob-suite/.
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53
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54 -----
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55
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56 **Input:**
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57
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58 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
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59
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60
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61 **Output:**
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62
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63 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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64
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65
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66 </help>
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67 <citations>
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68 <citation type="bibtex">
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69 @misc{githubmob-suite,
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70 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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71 publisher = {GitHub},
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72 journal = {GitHub repository},
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73 url = {https://github.com/phac-nml/mob-suite},
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74 }</citation>
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75 </citations>
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76 </tool>