Mercurial > repos > greg > multilocus_genotype

comparison multilocus_genotype.xml @ 9:8f2f346a5e1c draft

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author greg
date Tue, 04 Dec 2018 13:44:12 -0500
parents 18001e7cb199
children c755744296ca
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8:d2057e183772 9:8f2f346a5e1c
20 Rscript '$__tool_directory__/multilocus_genotype.R' 20 Rscript '$__tool_directory__/multilocus_genotype.R'
21 --database_connection_string '$__app__.config.corals_database_connection' 21 --database_connection_string '$__app__.config.corals_database_connection'
22 --input_affy_metadata '$input_affy_metadata' 22 --input_affy_metadata '$input_affy_metadata'
23 --input_pop_info '$input_pop_info' 23 --input_pop_info '$input_pop_info'
24 --input_vcf '$input_vcf' 24 --input_vcf '$input_vcf'
25 --output_stag_db_report '$output_stag_db_report' 25 --output_stag_db_report '$output_stag_db_report']]></command>
26 --output_mlg_id '$output_mlg_id']]></command>
27 <inputs> 26 <inputs>
28 <param name="input_vcf" type="data" format="vcf" label="VCF file" /> 27 <param name="input_vcf" type="data" format="vcf" label="VCF file" />
29 <param name="input_affy_metadata" type="data" format="csv" label="Affymetrix 96 well plate file" /> 28 <param name="input_affy_metadata" type="data" format="tabular" label="Affymetrix 96 well plate file" />
30 <param name="input_pop_info" type="data" format="txt" label="Population information file" /> 29 <param name="input_pop_info" type="data" format="txt" label="Population information file" />
31 </inputs> 30 </inputs>
32 <outputs> 31 <outputs>
33 <data name="output_stag_db_report" format="csv" label="${tool.name} (stag db report) on ${on_string}"/> 32 <data name="output_stag_db_report" format="csv" label="${tool.name} (stag db report) on ${on_string}"/>
34 <data name="output_mlg_id" format="txt" label="${tool.name} (MLGs) on ${on_string}"/>
35 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}"> 33 <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
36 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/> 34 <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
37 </collection> 35 </collection>
38 </outputs> 36 </outputs>
39 <tests> 37 <tests>
40 <test> 38 <test>
41 <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/> 39 <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/>
40 <param name="input_affy_metadata" value="affy_metadata.tabular" ftype="tabular"/>
42 <param name="input_pop_info" value="pop_info.txt" ftype="txt"/> 41 <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"/>
43 <output_collection name="output_plot_collection" type="list"> 43 <output_collection name="output_plot_collection" type="list">
44 <element name="phylogeny_tree.pdf" file="phylogeny_tree.pdf" ftype="pdf" compare="contains"/> 44 <element name="geno_accumulation_curve.pdf" file="geno_accumulation_curve.pdf" ftype="pdf" compare="contains"/>
45 <element name="dissimiliarity_distance_matrix.pdf" file="dissimiliarity_distance_matrix.pdf" ftype="pdf" compare="contains"/> 45 <element name="geno_rarifaction_curve.pdf" file="geno_rarifaction_curve.pdf" ftype="pdf" compare="contains"/>
46 <element name="filter_stats.pdf" file="filter_stats.pdf" ftype="pdf" compare="contains"/> 46 <element name="nj_phylogeny.pdf" file="nj_phylogeny.pdf" ftype="pdf" compare="contains"/>
47 <element name="genotype_accumulation_curve.pdf" file="genotype_accumulation_curve.pdf" ftype="pdf" compare="contains"/>
48 <element name="genotype_accumulation_curve_for_gind.pdf" file="genotype_accumulation_curve_for_gind.pdf" ftype="pdf" compare="contains"/>
49 </output_collection> 47 </output_collection>
50 </test> 48 </test>
51 </tests> 49 </tests>
52 <help> 50 <help>
53 **What it does** 51 **What it does**