Mercurial > repos > greg > multilocus_genotype

comparison multilocus_genotype.xml @ 4:a7cce4091e80 draft

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author greg
date Wed, 21 Nov 2018 09:14:09 -0500
parents ba2df0561b12
children 73cfe1260e98
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3:1bc815d9c8c5 4:a7cce4091e80
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="1.6.0">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> 4 <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> 5 <requirement type="package" version="5.1">r-ape</requirement>
10 <requirement type="package" version="3.0.0">r-ggplot2</requirement> 6 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
11 <requirement type="package" version="1.20">r-knitr</requirement> 7 <requirement type="package" version="1.20">r-knitr</requirement>
8 <requirement type="package" version="1.6.0">r-optparse</requirement>
9 <requirement type="package" version="2.8.1">r-poppr</requirement>
10 <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement>
11 <requirement type="package" version="2.5_3">r-vegan</requirement>
12 <requirement type="package" version="1.8.0">r-vcfr</requirement>
12 </requirements> 13 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
14 #set output_plots_dir = 'output_plots_dir' 15 #set output_plots_dir = 'output_plots_dir'
15 mkdir $output_plots_dir && 16 mkdir $output_plots_dir &&
16 Rscript '$__tool_directory__/multilocus_genotype.R' 17 Rscript '$__tool_directory__/multilocus_genotype.R'
17 --input_vcf '$input_vcf' 18 --input_vcf '$input_vcf'
18 --input_pop_info '$input_pop_info']]></command> 19 --input_pop_info '$input_pop_info'
20 --output_missing_data '$output_missing_data'
21 --output_mlg_id '$output_mlg_id']]></command>
19 <inputs> 22 <inputs>
20 <param name="input_vcf" type="data" format="vcf" label="VCF file" /> 23 <param name="input_vcf" type="data" format="vcf" label="VCF file" />
21 <param name="input_pop_info" type="data" format="txt" label="Population information file" /> 24 <param name="input_pop_info" type="data" format="txt" label="Population information file" />
22 </inputs> 25 </inputs>
23 <outputs> 26 <outputs>
27 <data name="output_mlg_id" format="txt"/>
28 <data name="output_missing_data" format="txt"/>
24 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}"> 29 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
25 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/> 30 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
26 </collection> 31 </collection>
27 </outputs> 32 </outputs>
28 <tests> 33 <tests>