Mercurial > repos > greg > multilocus_genotype
comparison multilocus_genotype.xml @ 0:725b160c91f0 draft
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| author | greg |
|---|---|
| date | Thu, 25 Oct 2018 10:50:53 -0400 |
| parents | |
| children | ba2df0561b12 |
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| -1:000000000000 | 0:725b160c91f0 |
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| 1 <tool id="multilocus_genotype" name="Multilocus genotype" version="1.0.0"> | |
| 2 <description>unique combination of alleles for loci</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.6.0">r-optparse</requirement> | |
| 5 <requirement type="package" version="1.8.0">r-vcfr</requirement> | |
| 6 <requirement type="package" version="2.8.1">r-poppr</requirement> | |
| 7 <requirement type="package" version="2.1.1">r-adegenet</requirement> | |
| 8 <requirement type="package" version="5.1">r-ape</requirement> | |
| 9 <requirement type="package" version="5.1">r-ape</requirement> | |
| 10 <requirement type="package" version="3.0.0">r-ggplot2</requirement> | |
| 11 <requirement type="package" version="1.20">r-knitr</requirement> | |
| 12 </requirements> | |
| 13 <command detect_errors="exit_code"><![CDATA[ | |
| 14 #set output_plots_dir = 'output_plots_dir' | |
| 15 mkdir $output_plots_dir && | |
| 16 Rscript '$__tool_directory__/multilocus_genotype.R' | |
| 17 --input_vcf '$input_vcf' | |
| 18 --input_pop_info 'input_pop_info']]></command> | |
| 19 <inputs> | |
| 20 <param name="input_vcf" type="data" format="vcf" label="VCF file" /> | |
| 21 <param name="input_pop_info" type="data" format="txt" label="Population information file" /> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}"> | |
| 25 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/> | |
| 26 </collection> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/> | |
| 31 <param name="input_pop_info" value="pop_info.txt" ftype="txt"/> | |
| 32 <output_collection name="output_plot_collection" type="list"> | |
| 33 <element name="phylogeny_tree.pdf" file="phylogeny_tree.pdf" ftype="pdf" compare="contains"/> | |
| 34 <element name="dissimiliarity_distance_matrix.pdf" file="dissimiliarity_distance_matrix.pdf" ftype="pdf" compare="contains"/> | |
| 35 <element name="filter_stats.pdf" file="filter_stats.pdf" ftype="pdf" compare="contains"/> | |
| 36 <element name="genotype_accumulation_curve.pdf" file="genotype_accumulation_curve.pdf" ftype="pdf" compare="contains"/> | |
| 37 <element name="genotype_accumulation_curve_for_gind.pdf" file="genotype_accumulation_curve_for_gind.pdf" ftype="pdf" compare="contains"/> | |
| 38 </output_collection> | |
| 39 </test> | |
| 40 </tests> | |
| 41 <help> | |
| 42 **What it does** | |
| 43 | |
| 44 Renders the unique combination of the alleles for two or more loci for each individual. The multilocus genotypes | |
| 45 are critically important for tracking dispersal and population structure of organisms, especially those that | |
| 46 reproduce clonally (plants, sponges, cnidarians, flatworms, annelids, sea stars, and many more). | |
| 47 ----- | |
| 48 | |
| 49 **Required options** | |
| 50 </help> | |
| 51 <citations> | |
| 52 </citations> | |
| 53 </tool> |