| Previous changeset 4:b0ab97ffc2a1 (2020-03-09) Next changeset 6:bc28839b17fb (2020-03-10) |
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Commit message:
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252 |
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modified:
mixomics_blocksplsda.xml mixomics_blocksplsda_script.R |
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| diff -r b0ab97ffc2a1 -r 1ee8d2c20c0a mixomics_blocksplsda.xml --- a/mixomics_blocksplsda.xml Mon Mar 09 11:53:32 2020 -0400 +++ b/mixomics_blocksplsda.xml Tue Mar 10 06:27:02 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.3.0" profile="16.04" workflow_compatible="true"> +<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.4.0" profile="16.04" workflow_compatible="true"> <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description> @@ -31,13 +31,14 @@ --sample_description_col ${sample_description_col} --ncomp ${ncomp} ${correlation} - --scheme ${adv.scheme} - --mode ${adv.mode} + ##--scheme ${adv.scheme} + ##--mode ${adv.mode} --maxiter ${adv.maxiter} - ${adv.scale} - --init ${adv.init} - --tol ${adv.tol} - ${adv.nearzerovar} + ##${adv.scale} + --scale ## always activated hidden param + ##--init ${adv.init} + ##--tol ${adv.tol} + ##${adv.nearzerovar} --rdata_out ${rdata_out} --sample_metadata_out ${sample_metadata_out} --variable_metadata_outdir outdir @@ -95,7 +96,7 @@ <param name="tol" type="float" value="1e-06" min="0" label="Convergence stopping value" help="[tol]" /> - <param name="nearzerovar" type="boolean" truevalue="-\-nearzerovar" falsevalue="" checked="false" + <param name="nearzerovar" type="boolean" truevalue="-\-nearzerovar" falsevalue="" checked="true" label="Should be set to TRUE in particular for data with many zero values" /> --> </section> </inputs> |
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| diff -r b0ab97ffc2a1 -r 1ee8d2c20c0a mixomics_blocksplsda_script.R --- a/mixomics_blocksplsda_script.R Mon Mar 09 11:53:32 2020 -0400 +++ b/mixomics_blocksplsda_script.R Tue Mar 10 06:27:02 2020 -0400 |
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| @@ -11,18 +11,28 @@ parser <- ArgumentParser(description='Run the mixOmics block.splsda function') -parser$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") -parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE, help="Samples metadata file") -parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer', required=TRUE, help="Sample description column number") -parser$add_argument('--ncomp', dest='ncomp', type='integer', required=TRUE, help="Number of components to include in the model") -parser$add_argument('--correlation', dest='correlation', action="store_true", help="Add correlation between all blocks") -parser$add_argument('--scheme', dest='scheme', required=TRUE, help="Scheme") -parser$add_argument('--mode', dest='mode', required=TRUE, help="Mode") -parser$add_argument('--maxiter', dest='maxiter', type='integer', required=TRUE, help="Maximum number of iterations") -parser$add_argument('--scale', dest='scale', action="store_true", help="Each block is standardized to zero means and unit variances") -parser$add_argument('--init', dest='init', required=TRUE, help="Init (svd or svd.single)") -parser$add_argument('--tol', dest='tol', type='double', required=TRUE, help="Convergence stopping value") -parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", help="Should be set in particular for data with many zero values") +parser$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") +parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE, + help="Samples metadata file") +parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer', + default=0, help="Sample description column number") +parser$add_argument('--ncomp', dest='ncomp', type='integer', default=2, + help="Number of components to include in the model") +parser$add_argument('--correlation', dest='correlation', action="store_true", + help="Add correlation between all blocks") +parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme") +parser$add_argument('--mode', dest='mode', default="regression", help="Mode") +parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100, + help="Maximum number of iterations") +parser$add_argument('--scale', dest='scale', action="store_true", + help="Each block is standardized to zero means and unit variances") +parser$add_argument('--init', dest='init', default="svd", + help="Init (svd or svd.single)") +parser$add_argument('--tol', dest='tol', type='double', default=1e-06, + help="Convergence stopping value") +parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", + help="Should be set in particular for data with many zero values") parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file") parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file") parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory") |