Mercurial > repos > greg > multilocus_genotype

comparison multilocus_genotype.xml @ 11:c755744296ca draft

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author greg
date Fri, 07 Dec 2018 09:12:54 -0500
parents 8f2f346a5e1c
children 6b8061a95c04
comparison
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10:6c93244a36e2 11:c755744296ca
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="2.1.1">r-adegenet</requirement> 4 <requirement type="package" version="2.1.1">r-adegenet</requirement>
5 <requirement type="package" version="5.1">r-ape</requirement> 5 <requirement type="package" version="5.1">r-ape</requirement>
6 <requirement type="package" version="1.11.6">r-data.table</requirement> 6 <requirement type="package" version="1.11.6">r-data.table</requirement>
7 <requirement type="package" version="1.2.2">r-dbplyr</requirement>
7 <requirement type="package" version="0.7.6">r-dplyr</requirement> 8 <requirement type="package" version="0.7.6">r-dplyr</requirement>
8 <requirement type="package" version="3.0.0">r-ggplot2</requirement> 9 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
9 <requirement type="package" version="1.20">r-knitr</requirement> 10 <requirement type="package" version="1.20">r-knitr</requirement>
10 <requirement type="package" version="1.6.0">r-optparse</requirement> 11 <requirement type="package" version="1.6.0">r-optparse</requirement>
11 <requirement type="package" version="2.8.1">r-poppr</requirement> 12 <requirement type="package" version="2.8.1">r-poppr</requirement>
12 <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement> 13 <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement>
13 <requirement type="package" version="1.1.1">r-rpostgres</requirement> 14 <requirement type="package" version="1.1.1">r-rpostgres</requirement>
15 <requirement type="package" version="0.8.1">r-tidyr</requirement>
14 <requirement type="package" version="2.5_3">r-vegan</requirement> 16 <requirement type="package" version="2.5_3">r-vegan</requirement>
15 <requirement type="package" version="1.8.0">r-vcfr</requirement> 17 <requirement type="package" version="1.8.0">r-vcfr</requirement>
16 </requirements> 18 </requirements>
17 <command detect_errors="exit_code"><![CDATA[ 19 <command detect_errors="exit_code"><![CDATA[
18 #set output_plots_dir = 'output_plots_dir' 20 #set output_plots_dir = 'output_plots_dir'
20 Rscript '$__tool_directory__/multilocus_genotype.R' 22 Rscript '$__tool_directory__/multilocus_genotype.R'
21 --database_connection_string '$__app__.config.corals_database_connection' 23 --database_connection_string '$__app__.config.corals_database_connection'
22 --input_affy_metadata '$input_affy_metadata' 24 --input_affy_metadata '$input_affy_metadata'
23 --input_pop_info '$input_pop_info' 25 --input_pop_info '$input_pop_info'
24 --input_vcf '$input_vcf' 26 --input_vcf '$input_vcf'
25 --output_stag_db_report '$output_stag_db_report']]></command> 27 --output_stag_db_report '$output_stag_db_report'
28 &> multilocus_genotype.log;
29 if [[ $? -ne 0 ]]; then
30 cp multilocus_genotype.log '$output_stag_db_report';
31 esit 1;
32 fi]]></command>
26 <inputs> 33 <inputs>
27 <param name="input_vcf" type="data" format="vcf" label="VCF file" /> 34 <param name="input_vcf" type="data" format="vcf" label="VCF file" />
28 <param name="input_affy_metadata" type="data" format="tabular" label="Affymetrix 96 well plate file" /> 35 <param name="input_affy_metadata" type="data" format="tabular" label="Affymetrix 96 well plate file" />
29 <param name="input_pop_info" type="data" format="txt" label="Population information file" /> 36 <param name="input_pop_info" type="data" format="txt" label="Genotype population information file" />
30 </inputs> 37 </inputs>
31 <outputs> 38 <outputs>
32 <data name="output_stag_db_report" format="csv" label="${tool.name} (stag db report) on ${on_string}"/> 39 <data name="output_stag_db_report" format="csv" label="${tool.name} (stag db report) on ${on_string}"/>
33 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}"> 40 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
34 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/> 41 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
39 <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/> 46 <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/>
40 <param name="input_affy_metadata" value="affy_metadata.tabular" ftype="tabular"/> 47 <param name="input_affy_metadata" value="affy_metadata.tabular" ftype="tabular"/>
41 <param name="input_pop_info" value="pop_info.txt" ftype="txt"/> 48 <param name="input_pop_info" value="pop_info.txt" ftype="txt"/>
42 <output name="output_stag_db_report" file="output_stag_db_report.csv" ftype="csv"/> 49 <output name="output_stag_db_report" file="output_stag_db_report.csv" ftype="csv"/>
43 <output_collection name="output_plot_collection" type="list"> 50 <output_collection name="output_plot_collection" type="list">
44 <element name="geno_accumulation_curve.pdf" file="geno_accumulation_curve.pdf" ftype="pdf" compare="contains"/>
45 <element name="geno_rarifaction_curve.pdf" file="geno_rarifaction_curve.pdf" ftype="pdf" compare="contains"/>
46 <element name="nj_phylogeny.pdf" file="nj_phylogeny.pdf" ftype="pdf" compare="contains"/> 51 <element name="nj_phylogeny.pdf" file="nj_phylogeny.pdf" ftype="pdf" compare="contains"/>
52 <element name="missing_data.pdf" file="missing_data.pdf" ftype="pdf" compare="contains"/>
53 <element name="percent_breakdown.pdf" file="percent_breakdown.pdf" ftype="pdf" compare="contains"/>
47 </output_collection> 54 </output_collection>
48 </test> 55 </test>
49 </tests> 56 </tests>
50 <help> 57 <help>
51 **What it does** 58 **What it does**