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annotate mob_typer.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_typer" name="MOB-Typer" version="1.4.1">
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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="1.4.1">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_typer --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" --evalue '${adv_param.evalue}' --min_ident '${adv_param.min_ident}' --min_cov '${adv_param.min_cov}' --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="min_ident" label="Minimum sequence identity for BLAST" type="float" min="1" max="100" value="80"/>
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15 <param name="min_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="float" min="1" max="100" value="65"/>
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16 </section>
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17 </inputs>
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18 <outputs>
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19 <data name="outfile1" label="${tool.name}: Report from ${input.name}" format="tabular" hidden="false">
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20 <discover_datasets pattern=".+_report\.txt" visible="true" ext="tabular" assign_primary_output="true"/>
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21 </data>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
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26 <assert_stdout>
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27 <has_text text="JN253636"/>
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28 </assert_stdout>
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29 </test>
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30 </tests>
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31 <help>
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32
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33 **Syntax**
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34
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35 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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36
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37 For more information please visit https://github.com/phac-nml/mob-suite/.
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38
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39 -----
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41 **Input:**
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42
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43 A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
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44
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46 **Output:**
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47
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48 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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49
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50
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51 </help>
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52 <citations>
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53 <citation type="bibtex">
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54 @misc{githubmob-suite,
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55 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
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56 publisher = {GitHub},
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57 journal = {GitHub repository},
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58 url = {https://github.com/phac-nml/mob-suite},
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59 }</citation>
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60 </citations>
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61 </tool>