Mercurial > repos > greg > multilocus_genotype

comparison multilocus_genotype.xml @ 7:18001e7cb199 draft

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author greg
date Wed, 28 Nov 2018 13:49:18 -0500
parents a71901fd5325
children 8f2f346a5e1c
comparison
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6:a71901fd5325 7:18001e7cb199
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="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>
7 <requirement type="package" version="0.7.6">r-dplyr</requirement>
6 <requirement type="package" version="3.0.0">r-ggplot2</requirement> 8 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
7 <requirement type="package" version="1.20">r-knitr</requirement> 9 <requirement type="package" version="1.20">r-knitr</requirement>
8 <requirement type="package" version="1.6.0">r-optparse</requirement> 10 <requirement type="package" version="1.6.0">r-optparse</requirement>
9 <requirement type="package" version="2.8.1">r-poppr</requirement> 11 <requirement type="package" version="2.8.1">r-poppr</requirement>
10 <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement> 12 <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement>
13 <requirement type="package" version="1.1.1">r-rpostgres</requirement>
11 <requirement type="package" version="2.5_3">r-vegan</requirement> 14 <requirement type="package" version="2.5_3">r-vegan</requirement>
12 <requirement type="package" version="1.8.0">r-vcfr</requirement> 15 <requirement type="package" version="1.8.0">r-vcfr</requirement>
13 </requirements> 16 </requirements>
14 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
15 #set output_plots_dir = 'output_plots_dir' 18 #set output_plots_dir = 'output_plots_dir'
16 mkdir $output_plots_dir && 19 mkdir $output_plots_dir &&
17 Rscript '$__tool_directory__/multilocus_genotype.R' 20 Rscript '$__tool_directory__/multilocus_genotype.R'
21 --database_connection_string '$__app__.config.corals_database_connection'
22 --input_affy_metadata '$input_affy_metadata'
23 --input_pop_info '$input_pop_info'
18 --input_vcf '$input_vcf' 24 --input_vcf '$input_vcf'
19 --input_pop_info '$input_pop_info' 25 --output_stag_db_report '$output_stag_db_report'
20 --output_missing_data '$output_missing_data'
21 --output_mlg_id '$output_mlg_id']]></command> 26 --output_mlg_id '$output_mlg_id']]></command>
22 <inputs> 27 <inputs>
23 <param name="input_vcf" type="data" format="vcf" label="VCF file" /> 28 <param name="input_vcf" type="data" format="vcf" label="VCF file" />
29 <param name="input_affy_metadata" type="data" format="csv" label="Affymetrix 96 well plate file" />
24 <param name="input_pop_info" type="data" format="txt" label="Population information file" /> 30 <param name="input_pop_info" type="data" format="txt" label="Population information file" />
25 </inputs> 31 </inputs>
26 <outputs> 32 <outputs>
33 <data name="output_stag_db_report" format="csv" label="${tool.name} (stag db report) on ${on_string}"/>
27 <data name="output_mlg_id" format="txt" label="${tool.name} (MLGs) on ${on_string}"/> 34 <data name="output_mlg_id" format="txt" label="${tool.name} (MLGs) on ${on_string}"/>
28 <data name="output_missing_data" format="txt" label="${tool.name} (missing GT) on ${on_string}"/>
29 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}"> 35 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
30 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/> 36 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
31 </collection> 37 </collection>
32 </outputs> 38 </outputs>
33 <tests> 39 <tests>
54 **Required options** 60 **Required options**
55 </help> 61 </help>
56 <citations> 62 <citations>
57 </citations> 63 </citations>
58 </tool> 64 </tool>
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