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1 <tool id="cpo_mlst" name="cpo_mlst" version="2.11">
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2 <description>Modified MLST v2.11 to support for the cpo_prediction workflow</description>
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3 <requirements>
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1
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4 <requirement type="package" version="2.11">mlst</requirement>
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5 </requirements>
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6
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7 <version_command>mlst --version</version_command>
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8
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9 <command detect_errors="exit_code"><![CDATA[
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10 mlst "$input_file" --nopath > "$report"
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11 ]]></command>
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12
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13 <inputs>
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14 <param type="data" name="input_file" format="fasta,genbank" />
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15 <conditional name="settings">
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16 <param name="advanced" type="select" label="Specify advanced parameters">
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17 <option value="simple" selected="true">No, use program defaults.</option>
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18 <option value="advanced">Yes, see full parameter list.</option>
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19 </param>
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20 <when value="simple">
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21 </when>
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22 <when value="advanced">
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23 <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
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24 <param name="min_dna_cov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" />
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25 <param name="scheme" type="text" area="false" label="PubMLST Scheme" help="Turn off auto-detection and only use this scheme" optional="true" />
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26 </when>
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27 </conditional>
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28 </inputs>
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29
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30 <outputs>
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31 <data name="report" format="tabular" />
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32 </outputs>
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33
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34 <tests>
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35 <!-- Basic test - will produce no results. -->
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36 <test>
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37 <param name="input_file" value="Acetobacter.fna"/>
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38 <param name="advanced" value="simple"/>
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39 <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/>
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40 </test>
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41
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42 <!-- Basic test - will produce results. -->
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43 <test>
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44 <param name="input_file" value="MRSA0252_trimmed.fna"/>
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45 <param name="advanced" value="simple"/>
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46 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
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47 </test>
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48
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49 <!-- Advanced test - Min DNA Coverage 100 -->
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50 <test>
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51 <param name="input_file" value="MRSA0252_trimmed.fna"/>
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52 <param name="advanced" value="advanced"/>
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53 <param name="min_dna_cov" value="100"/>
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54 <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
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55 </test>
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56
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57 <!-- Advanced test - Min DNA ID 100 -->
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58 <test>
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59 <param name="input_file" value="MRSA0252_trimmed.fna"/>
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60 <param name="advanced" value="advanced"/>
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61 <param name="min_dna_id" value="100"/>
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62 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
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63 </test>
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64 </tests>
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65
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66 <help>performs mlst</help>
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67
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68 <citations>
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69 <citation type="bibtex">
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70 @UNPUBLISHED{Seemann2016,
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71 author = "Seemann T",
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72 title = "MLST: Scan contig files against PubMLST typing schemes",
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73 year = "2016",
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74 note = "https://github.com/tseemann/mlst"}
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75 </citation>
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76 </citations>
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77 </tool> |
