Mercurial > repos > greg > multilocus_genotype

comparison multilocus_genotype.xml @ 18:1190ee1456f6 draft default tip

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author greg
date Mon, 13 May 2019 08:37:37 -0400
parents 6b8061a95c04
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17:85f8fc57eee4 18:1190ee1456f6
1 <tool id="multilocus_genotype" name="Multilocus genotype" version="1.0.0"> 1 <tool id="multilocus_genotype" name="Multilocus genotype" version="1.0.0">
2 <description>unique combination of alleles for loci</description> 2 <description>unique combination of alleles for loci</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.16.0">bioconductor-snprelate</requirement>
4 <requirement type="package" version="2.1.1">r-adegenet</requirement> 5 <requirement type="package" version="2.1.1">r-adegenet</requirement>
5 <requirement type="package" version="5.1">r-ape</requirement> 6 <requirement type="package" version="5.1">r-ape</requirement>
6 <requirement type="package" version="1.11.6">r-data.table</requirement> 7 <requirement type="package" version="1.11.6">r-data.table</requirement>
7 <requirement type="package" version="1.2.2">r-dbplyr</requirement> 8 <requirement type="package" version="1.2.2">r-dbplyr</requirement>
8 <requirement type="package" version="0.7.6">r-dplyr</requirement> 9 <requirement type="package" version="0.7.6">r-dplyr</requirement>
9 <requirement type="package" version="3.0.0">r-ggplot2</requirement> 10 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
10 <requirement type="package" version="1.20">r-knitr</requirement> 11 <requirement type="package" version="1.20">r-knitr</requirement>
12 <requirement type="package" version="3.3.0">r-maps</requirement>
13 <requirement type="package" version="1.2.6">r-mapproj</requirement>
11 <requirement type="package" version="1.6.0">r-optparse</requirement> 14 <requirement type="package" version="1.6.0">r-optparse</requirement>
12 <requirement type="package" version="2.8.1">r-poppr</requirement> 15 <requirement type="package" version="2.8.1">r-poppr</requirement>
13 <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement> 16 <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement>
14 <requirement type="package" version="1.1.1">r-rpostgres</requirement> 17 <requirement type="package" version="1.1.1">r-rpostgres</requirement>
15 <requirement type="package" version="0.8.1">r-tidyr</requirement> 18 <requirement type="package" version="0.8.1">r-tidyr</requirement>
19 <requirement type="package" version="1.8.0">r-vcfr</requirement>
16 <requirement type="package" version="2.5_3">r-vegan</requirement> 20 <requirement type="package" version="2.5_3">r-vegan</requirement>
17 <requirement type="package" version="1.8.0">r-vcfr</requirement> 21 <requirement type="package" version="0.1.5">r-yarrr</requirement>
18 </requirements> 22 </requirements>
19 <command detect_errors="exit_code"><![CDATA[ 23 <command detect_errors="exit_code"><![CDATA[
20 #set output_plots_dir = 'output_plots_dir' 24 #set output_plots_dir = 'output_plots_dir'
21 mkdir $output_plots_dir && 25 mkdir $output_plots_dir &&
22 Rscript '$__tool_directory__/multilocus_genotype.R' 26 Rscript '$__tool_directory__/multilocus_genotype.R'
23 --database_connection_string '$__app__.config.corals_database_connection' 27 --database_connection_string '$__app__.config.corals_database_connection'
24 --input_affy_metadata '$input_affy_metadata' 28 --input_affy_metadata '$input_affy_metadata'
25 --input_pop_info '$input_pop_info' 29 --input_pop_info '$input_pop_info'
26 --input_vcf '$input_vcf' 30 --input_vcf '$input_vcf'
31 #if str($output_nj_phylogeny_tree) == "yes":
32 --output_nj_phylogeny_tree '$output_nj_phylogeny_tree'
33 #end if
27 --output_stag_db_report '$output_stag_db_report' 34 --output_stag_db_report '$output_stag_db_report'
28 &> multilocus_genotype.log; 35 &> '$output_log']]></command>
29 if [[ $? -ne 0 ]]; then
30 cp multilocus_genotype.log '$output_stag_db_report';
31 exit 1;
32 fi]]></command>
33 <inputs> 36 <inputs>
34 <param name="input_vcf" type="data" format="vcf" label="VCF file" /> 37 <param name="input_vcf" type="data" format="vcf" label="VCF file" />
35 <param name="input_affy_metadata" type="data" format="tabular" label="Affymetrix 96 well plate file" /> 38 <param name="input_affy_metadata" type="data" format="tabular" label="Affymetrix 96 well plate file" />
36 <param name="input_pop_info" type="data" format="txt" label="Genotype population information file" /> 39 <param name="input_pop_info" type="data" format="txt" label="Genotype population information file" />
40 <param name="output_nj_phylogeny_tree" type="select" display="radio" label="Plot neighbor-joining phylogeny tree?">
41 <option value="yes">Yes</option>
42 <option value="no" selected="true">No</option>
43 </param>
37 </inputs> 44 </inputs>
38 <outputs> 45 <outputs>
39 <data name="output_stag_db_report" format="csv" label="${tool.name} (stag db report) on ${on_string}"/>
40 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}"> 46 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
41 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/> 47 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
42 </collection> 48 </collection>
49 <data name="output_stag_db_report" format="csv" label="${tool.name} (stag db report) on ${on_string}"/>
50 <data name="output_log" format="txt" label="${tool.name} (process log) on ${on_string}"/>
43 </outputs> 51 </outputs>
44 <tests> 52 <tests>
45 <test> 53 <test>
46 <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/> 54 <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/>
47 <param name="input_affy_metadata" value="affy_metadata.tabular" ftype="tabular"/> 55 <param name="input_affy_metadata" value="affy_metadata.tabular" ftype="tabular"/>
58 **What it does** 66 **What it does**
59 67
60 Renders the unique combination of the alleles for two or more loci for each individual. The multilocus genotypes 68 Renders the unique combination of the alleles for two or more loci for each individual. The multilocus genotypes
61 are critically important for tracking dispersal and population structure of organisms, especially those that 69 are critically important for tracking dispersal and population structure of organisms, especially those that
62 reproduce clonally (plants, sponges, cnidarians, flatworms, annelids, sea stars, and many more). 70 reproduce clonally (plants, sponges, cnidarians, flatworms, annelids, sea stars, and many more).
71
63 ----- 72 -----
64 73
65 **Required options** 74 **Required options**
66 </help> 75 </help>
67 <citations> 76 <citations>