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1 <tool id="multilocus_genotype" name="Multilocus genotype" version="1.0.0">
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2 <description>unique combination of alleles for loci</description>
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3 <requirements>
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4 <requirement type="package" version="1.16.0">bioconductor-snprelate</requirement>
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5 <requirement type="package" version="2.1.1">r-adegenet</requirement>
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6 <requirement type="package" version="5.1">r-ape</requirement>
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7 <requirement type="package" version="1.11.6">r-data.table</requirement>
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8 <requirement type="package" version="1.2.2">r-dbplyr</requirement>
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9 <requirement type="package" version="0.7.6">r-dplyr</requirement>
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10 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
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11 <requirement type="package" version="1.20">r-knitr</requirement>
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12 <requirement type="package" version="3.3.0">r-maps</requirement>
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13 <requirement type="package" version="1.2.6">r-mapproj</requirement>
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14 <requirement type="package" version="1.6.0">r-optparse</requirement>
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15 <requirement type="package" version="2.8.1">r-poppr</requirement>
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16 <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement>
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17 <requirement type="package" version="1.1.1">r-rpostgres</requirement>
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18 <requirement type="package" version="0.8.1">r-tidyr</requirement>
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19 <requirement type="package" version="1.8.0">r-vcfr</requirement>
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20 <requirement type="package" version="2.5_3">r-vegan</requirement>
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21 <requirement type="package" version="0.1.5">r-yarrr</requirement>
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22 </requirements>
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23 <command detect_errors="exit_code"><![CDATA[
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24 #set output_plots_dir = 'output_plots_dir'
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25 mkdir $output_plots_dir &&
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26 Rscript '$__tool_directory__/multilocus_genotype.R'
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27 --database_connection_string '$__app__.config.corals_database_connection'
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28 --input_affy_metadata '$input_affy_metadata'
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29 --input_pop_info '$input_pop_info'
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30 --input_vcf '$input_vcf'
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31 #if str($output_nj_phylogeny_tree) == "yes":
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32 --output_nj_phylogeny_tree '$output_nj_phylogeny_tree'
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33 #end if
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34 --output_stag_db_report '$output_stag_db_report'
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35 &> '$output_log']]></command>
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36 <inputs>
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37 <param name="input_vcf" type="data" format="vcf" label="VCF file" />
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38 <param name="input_affy_metadata" type="data" format="tabular" label="Affymetrix 96 well plate file" />
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39 <param name="input_pop_info" type="data" format="txt" label="Genotype population information file" />
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40 <param name="output_nj_phylogeny_tree" type="select" display="radio" label="Plot neighbor-joining phylogeny tree?">
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41 <option value="yes">Yes</option>
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42 <option value="no" selected="true">No</option>
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43 </param>
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44 </inputs>
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45 <outputs>
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46 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
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47 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
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48 </collection>
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49 <data name="output_stag_db_report" format="csv" label="${tool.name} (stag db report) on ${on_string}"/>
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50 <data name="output_log" format="txt" label="${tool.name} (process log) on ${on_string}"/>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/>
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55 <param name="input_affy_metadata" value="affy_metadata.tabular" ftype="tabular"/>
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56 <param name="input_pop_info" value="pop_info.txt" ftype="txt"/>
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57 <output name="output_stag_db_report" file="output_stag_db_report.csv" ftype="csv"/>
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58 <output_collection name="output_plot_collection" type="list">
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59 <element name="nj_phylogeny.pdf" file="nj_phylogeny.pdf" ftype="pdf" compare="contains"/>
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60 <element name="missing_data.pdf" file="missing_data.pdf" ftype="pdf" compare="contains"/>
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61 <element name="percent_breakdown.pdf" file="percent_breakdown.pdf" ftype="pdf" compare="contains"/>
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62 </output_collection>
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63 </test>
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64 </tests>
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65 <help>
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66 **What it does**
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67
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68 Renders the unique combination of the alleles for two or more loci for each individual. The multilocus genotypes
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69 are critically important for tracking dispersal and population structure of organisms, especially those that
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70 reproduce clonally (plants, sponges, cnidarians, flatworms, annelids, sea stars, and many more).
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71
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72 -----
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73
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74 **Required options**
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75 </help>
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76 <citations>
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77 </citations>
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78 </tool>
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