1
+ − 1 <tool id="mlst" name="MLST" version="2.11">
+ − 2 <requirements>
+ − 3 <requirement type="package" version="2.11">mlst</requirement>
+ − 4 </requirements>
+ − 5
+ − 6 <version_command>mlst --version</version_command>
+ − 7
+ − 8 <command detect_errors="exit_code"><![CDATA[
+ − 9 mlst "$input_file" --nopath > "$report"
+ − 10 ]]></command>
+ − 11
+ − 12 <inputs>
+ − 13 <param type="data" name="input_file" format="fasta,genbank" />
+ − 14 <conditional name="settings">
+ − 15 <param name="advanced" type="select" label="Specify advanced parameters">
+ − 16 <option value="simple" selected="true">No, use program defaults.</option>
+ − 17 <option value="advanced">Yes, see full parameter list.</option>
+ − 18 </param>
+ − 19 <when value="simple">
+ − 20 </when>
+ − 21 <when value="advanced">
+ − 22 <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" />
+ − 23 <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" />
+ − 24 <param name="scheme" type="text" area="false" label="PubMLST Scheme" help="Turn off auto-detection and only use this scheme" optional="true" />
+ − 25 </when>
+ − 26 </conditional>
+ − 27 </inputs>
+ − 28
+ − 29 <outputs>
+ − 30 <data name="report" format="tabular" />
+ − 31 </outputs>
+ − 32
+ − 33 <tests>
+ − 34 <!-- Basic test - will produce no results. -->
+ − 35 <test>
+ − 36 <param name="input_file" value="Acetobacter.fna"/>
+ − 37 <param name="advanced" value="simple"/>
+ − 38 <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/>
+ − 39 </test>
+ − 40
+ − 41 <!-- Basic test - will produce results. -->
+ − 42 <test>
+ − 43 <param name="input_file" value="MRSA0252_trimmed.fna"/>
+ − 44 <param name="advanced" value="simple"/>
+ − 45 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
+ − 46 </test>
+ − 47
+ − 48 <!-- Advanced test - Min DNA Coverage 100 -->
+ − 49 <test>
+ − 50 <param name="input_file" value="MRSA0252_trimmed.fna"/>
+ − 51 <param name="advanced" value="advanced"/>
+ − 52 <param name="min_dna_cov" value="100"/>
+ − 53 <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
+ − 54 </test>
+ − 55
+ − 56 <!-- Advanced test - Min DNA ID 100 -->
+ − 57 <test>
+ − 58 <param name="input_file" value="MRSA0252_trimmed.fna"/>
+ − 59 <param name="advanced" value="advanced"/>
+ − 60 <param name="min_dna_id" value="100"/>
+ − 61 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
+ − 62 </test>
+ − 63 </tests>
+ − 64
+ − 65 <help>performs mlst</help>
+ − 66
+ − 67 <citations>
+ − 68 <citation type="bibtex">
+ − 69 @UNPUBLISHED{Seemann2016,
+ − 70 author = "Seemann T",
+ − 71 title = "MLST: Scan contig files against PubMLST typing schemes",
+ − 72 year = "2016",
+ − 73 note = "https://github.com/tseemann/mlst"}
+ − 74 </citation>
+ − 75 </citations>
+ − 76 </tool>