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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="3.0.0">r-ggplot2</requirement>
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7 <requirement type="package" version="1.20">r-knitr</requirement>
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8 <requirement type="package" version="1.6.0">r-optparse</requirement>
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9 <requirement type="package" version="2.8.1">r-poppr</requirement>
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10 <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement>
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11 <requirement type="package" version="2.5_3">r-vegan</requirement>
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12 <requirement type="package" version="1.8.0">r-vcfr</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code"><![CDATA[
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15 #set output_plots_dir = 'output_plots_dir'
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16 mkdir $output_plots_dir &&
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17 Rscript '$__tool_directory__/multilocus_genotype.R'
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18 --input_vcf '$input_vcf'
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19 --input_pop_info '$input_pop_info'
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20 --output_missing_data '$output_missing_data'
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21 --output_mlg_id '$output_mlg_id']]></command>
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22 <inputs>
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23 <param name="input_vcf" type="data" format="vcf" label="VCF file" />
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24 <param name="input_pop_info" type="data" format="txt" label="Population information file" />
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25 </inputs>
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26 <outputs>
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27 <data name="output_mlg_id" format="txt" label="${tool.name} (MLGs) on ${on_string}"/>
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28 <data name="output_missing_data" format="txt" label="${tool.name} (missing GT) on ${on_string}"/>
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29 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
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30 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
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31 </collection>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/>
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36 <param name="input_pop_info" value="pop_info.txt" ftype="txt"/>
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37 <output_collection name="output_plot_collection" type="list">
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38 <element name="phylogeny_tree.pdf" file="phylogeny_tree.pdf" ftype="pdf" compare="contains"/>
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39 <element name="dissimiliarity_distance_matrix.pdf" file="dissimiliarity_distance_matrix.pdf" ftype="pdf" compare="contains"/>
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40 <element name="filter_stats.pdf" file="filter_stats.pdf" ftype="pdf" compare="contains"/>
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41 <element name="genotype_accumulation_curve.pdf" file="genotype_accumulation_curve.pdf" ftype="pdf" compare="contains"/>
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42 <element name="genotype_accumulation_curve_for_gind.pdf" file="genotype_accumulation_curve_for_gind.pdf" ftype="pdf" compare="contains"/>
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43 </output_collection>
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44 </test>
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45 </tests>
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46 <help>
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47 **What it does**
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48
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49 Renders the unique combination of the alleles for two or more loci for each individual. The multilocus genotypes
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50 are critically important for tracking dispersal and population structure of organisms, especially those that
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51 reproduce clonally (plants, sponges, cnidarians, flatworms, annelids, sea stars, and many more).
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52 -----
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53
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54 **Required options**
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55 </help>
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56 <citations>
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57 </citations>
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58 </tool>
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