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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="2.1.1">r-adegenet</requirement>
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5 <requirement type="package" version="5.1">r-ape</requirement>
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6 <requirement type="package" version="1.11.6">r-data.table</requirement>
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7 <requirement type="package" version="1.2.2">r-dbplyr</requirement>
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8 <requirement type="package" version="0.7.6">r-dplyr</requirement>
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9 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
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10 <requirement type="package" version="1.20">r-knitr</requirement>
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11 <requirement type="package" version="1.6.0">r-optparse</requirement>
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12 <requirement type="package" version="2.8.1">r-poppr</requirement>
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13 <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement>
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14 <requirement type="package" version="1.1.1">r-rpostgres</requirement>
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15 <requirement type="package" version="0.8.1">r-tidyr</requirement>
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16 <requirement type="package" version="2.5_3">r-vegan</requirement>
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17 <requirement type="package" version="1.8.0">r-vcfr</requirement>
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18 </requirements>
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19 <command detect_errors="exit_code"><![CDATA[
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20 #set output_plots_dir = 'output_plots_dir'
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21 mkdir $output_plots_dir &&
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22 Rscript '$__tool_directory__/multilocus_genotype.R'
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23 --database_connection_string '$__app__.config.corals_database_connection'
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24 --input_affy_metadata '$input_affy_metadata'
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25 --input_pop_info '$input_pop_info'
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26 --input_vcf '$input_vcf'
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27 --output_stag_db_report '$output_stag_db_report'
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28 &> multilocus_genotype.log;
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29 if [[ $? -ne 0 ]]; then
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30 cp multilocus_genotype.log '$output_stag_db_report';
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31 exit 1;
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32 fi]]></command>
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33 <inputs>
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34 <param name="input_vcf" type="data" format="vcf" label="VCF file" />
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35 <param name="input_affy_metadata" type="data" format="tabular" label="Affymetrix 96 well plate file" />
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36 <param name="input_pop_info" type="data" format="txt" label="Genotype population information file" />
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37 </inputs>
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38 <outputs>
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39 <data name="output_stag_db_report" format="csv" label="${tool.name} (stag db report) on ${on_string}"/>
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40 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
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41 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
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42 </collection>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/>
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47 <param name="input_affy_metadata" value="affy_metadata.tabular" ftype="tabular"/>
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48 <param name="input_pop_info" value="pop_info.txt" ftype="txt"/>
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49 <output name="output_stag_db_report" file="output_stag_db_report.csv" ftype="csv"/>
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50 <output_collection name="output_plot_collection" type="list">
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51 <element name="nj_phylogeny.pdf" file="nj_phylogeny.pdf" ftype="pdf" compare="contains"/>
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52 <element name="missing_data.pdf" file="missing_data.pdf" ftype="pdf" compare="contains"/>
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53 <element name="percent_breakdown.pdf" file="percent_breakdown.pdf" ftype="pdf" compare="contains"/>
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54 </output_collection>
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55 </test>
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56 </tests>
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57 <help>
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58 **What it does**
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59
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60 Renders the unique combination of the alleles for two or more loci for each individual. The multilocus genotypes
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61 are critically important for tracking dispersal and population structure of organisms, especially those that
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62 reproduce clonally (plants, sponges, cnidarians, flatworms, annelids, sea stars, and many more).
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63 -----
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64
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65 **Required options**
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66 </help>
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67 <citations>
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68 </citations>
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69 </tool>
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