| Previous changeset 0:bea08702ed51 (2019-05-17) Next changeset 2:655d1fbcd3e6 (2019-06-12) |
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Commit message:
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty |
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modified:
mixomics_blocksplsda.xml mixomics_blocksplsda_script.R mixomics_plotvar.xml mixomics_plotvar_script.R |
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| diff -r bea08702ed51 -r 6595c17673cb mixomics_blocksplsda.xml --- a/mixomics_blocksplsda.xml Fri May 17 05:00:22 2019 -0400 +++ b/mixomics_blocksplsda.xml Wed Jun 12 11:22:33 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.1.0" profile="16.04" workflow_compatible="true"> +<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.2.0" 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> @@ -79,9 +79,9 @@ </inputs> <outputs> - <data name="rdata_out" format="rdata" label="${tool.id}_output.rdata" /> - <data name="sample_metadata_out" format="tabular" label="${tool.id}_${sample_metadata_in.name}" /> - <collection name="blocks_output" type="list" label="${tool.id}_blocks_output"> + <data name="rdata_out" format="rdata" label="${tool.name}_output.rdata" /> + <data name="sample_metadata_out" format="tabular" label="${tool.name}_${sample_metadata_in.name}" /> + <collection name="blocks_output" type="list" label="${tool.name}_blocks_output"> <discover_datasets pattern="(?P<designation>.+)\.tsv" directory="outdir" format="tabular" /> </collection> </outputs> @@ -148,6 +148,16 @@ Variables metadata files are optional. If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created. +1. Data matrix format + * Rows = variables, Columns = samples + * First row = samples name. MUST be the same and in the same order in every block as well as in the sample metadata file (transposed) + * First column = variables name + +2. Variables metadata format + * Rows = variables, Columns = metadata + * First row = metadata column names + * First column = variables names. MUST be the same and in the same order than in the associated data matrix + Global input files: =================== @@ -160,6 +170,11 @@ By default, the last column of the samples metadata matrix will be used as samples description factors. If it's not the case, the column number can be inputed in the `Sample description column number` parameter. +1. Samples metadata format + * Rows = samples, Columns = metadata + * First row = metadata column names + * First column = sample names. These names must be identical (transposed) and in the same order than for the blocks data matrices + ---------- Parameters ---------- |
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| diff -r bea08702ed51 -r 6595c17673cb mixomics_blocksplsda_script.R --- a/mixomics_blocksplsda_script.R Fri May 17 05:00:22 2019 -0400 +++ b/mixomics_blocksplsda_script.R Wed Jun 12 11:22:33 2019 -0400 |
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| @@ -164,17 +164,17 @@ # print("Block.splsda variates:") # print(mixomics_result$variates) -for(bname in names(mixomics_result$variates)) +for(block_name in names(mixomics_result$variates)) { - # print(bname) - # print(mixomics_result$variates[[bname]]) + # print(block_name) + # print(mixomics_result$variates[[block_name]]) # Format the column names to add the block name and replace spaces - colnames(mixomics_result$variates[[bname]]) <- paste("block.splsda", bname, gsub(" ", "_", colnames(mixomics_result$variates[[bname]])), sep = "_") - # print(mixomics_result$variates[[bname]]) + colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_") + # print(mixomics_result$variates[[block_name]]) # Append the new columns to the sample metadata matrix - sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[bname]]) + sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]]) } # print(sample_metadata) @@ -196,6 +196,9 @@ meta_variable <- mixomics_result$loadings[[block_name]] # print(head(meta_variable)) + # Format the column names to add the block name and replace spaces + colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_") + # Read input block variable metadata files if provided (optional) if(block_meta_var != "None") { |
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| diff -r bea08702ed51 -r 6595c17673cb mixomics_plotvar.xml --- a/mixomics_plotvar.xml Fri May 17 05:00:22 2019 -0400 +++ b/mixomics_plotvar.xml Wed Jun 12 11:22:33 2019 -0400 |
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| @@ -26,7 +26,7 @@ <param name="input_rdata" type="data" format="rdata" label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)"/> <section name="adv" title="Advanced Options" expanded="false"> <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue="" label="Plot legend"/> - <param name="cutoff" type="float" value="0.85" min="0" max="1" label="Cut-off" /> + <param name="cutoff" type="float" value="0" min="0" max="1" label="Cut-off" /> </section> </inputs> |
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| diff -r bea08702ed51 -r 6595c17673cb mixomics_plotvar_script.R --- a/mixomics_plotvar_script.R Fri May 17 05:00:22 2019 -0400 +++ b/mixomics_plotvar_script.R Wed Jun 12 11:22:33 2019 -0400 |
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| @@ -36,9 +36,9 @@ pdf(args$output_pdf) -plotVar(mixomics_result, - legend = args$legend, - cutoff = args$cutoff) +# plotVar(mixomics_result, +# legend = args$legend, +# cutoff = args$cutoff) for(k in 1:(length(mixomics_result$names[[3]])-1)) { |