Mercurial > repos > ppericard > mixomics_blocksplsda

comparison mixomics_blocksplsda_script.R @ 5:1ee8d2c20c0a draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
author ppericard
date Tue, 10 Mar 2020 06:27:02 -0400
parents b0ab97ffc2a1
children
comparison
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4:b0ab97ffc2a1 5:1ee8d2c20c0a
9 ## Get parameters ## 9 ## Get parameters ##
10 suppressPackageStartupMessages(require(argparse)) 10 suppressPackageStartupMessages(require(argparse))
11 11
12 parser <- ArgumentParser(description='Run the mixOmics block.splsda function') 12 parser <- ArgumentParser(description='Run the mixOmics block.splsda function')
13 13
14 parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE, help="Block name + nb variables to select + data matrix file + variables metadata file") 14 parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE,
15 parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE, help="Samples metadata file") 15 help="Block name + nb variables to select + data matrix file + variables metadata file")
16 parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer', required=TRUE, help="Sample description column number") 16 parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE,
17 parser$add_argument('--ncomp', dest='ncomp', type='integer', required=TRUE, help="Number of components to include in the model") 17 help="Samples metadata file")
18 parser$add_argument('--correlation', dest='correlation', action="store_true", help="Add correlation between all blocks") 18 parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer',
19 parser$add_argument('--scheme', dest='scheme', required=TRUE, help="Scheme") 19 default=0, help="Sample description column number")
20 parser$add_argument('--mode', dest='mode', required=TRUE, help="Mode") 20 parser$add_argument('--ncomp', dest='ncomp', type='integer', default=2,
21 parser$add_argument('--maxiter', dest='maxiter', type='integer', required=TRUE, help="Maximum number of iterations") 21 help="Number of components to include in the model")
22 parser$add_argument('--scale', dest='scale', action="store_true", help="Each block is standardized to zero means and unit variances") 22 parser$add_argument('--correlation', dest='correlation', action="store_true",
23 parser$add_argument('--init', dest='init', required=TRUE, help="Init (svd or svd.single)") 23 help="Add correlation between all blocks")
24 parser$add_argument('--tol', dest='tol', type='double', required=TRUE, help="Convergence stopping value") 24 parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme")
25 parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", help="Should be set in particular for data with many zero values") 25 parser$add_argument('--mode', dest='mode', default="regression", help="Mode")
26 parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100,
27 help="Maximum number of iterations")
28 parser$add_argument('--scale', dest='scale', action="store_true",
29 help="Each block is standardized to zero means and unit variances")
30 parser$add_argument('--init', dest='init', default="svd",
31 help="Init (svd or svd.single)")
32 parser$add_argument('--tol', dest='tol', type='double', default=1e-06,
33 help="Convergence stopping value")
34 parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true",
35 help="Should be set in particular for data with many zero values")
26 parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file") 36 parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file")
27 parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file") 37 parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file")
28 parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory") 38 parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory")
29 39
30 args <- parser$parse_args() 40 args <- parser$parse_args()