| Previous changeset 13:2ae2d26e3270 (2018-12-12) |
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Commit message:
"planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e" |
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modified:
LICENSE README w4mcorcov.xml w4mcorcov_calc.R w4mcorcov_input.R w4mcorcov_lib.R w4mcorcov_output.R w4mcorcov_salience.R w4mcorcov_util.R w4mcorcov_wrapper.R |
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| diff -r 2ae2d26e3270 -r 90708fdbc22d w4mcorcov.xml --- a/w4mcorcov.xml Wed Dec 12 09:20:02 2018 -0500 +++ b/w4mcorcov.xml Wed Nov 18 18:53:37 2020 +0000 |
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| b'@@ -1,4 +1,4 @@\n-\xef\xbb\xbf<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.17">\n+\xef\xbb\xbf<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.18">\n <description>OPLS-DA Contrasts of Univariate Results</description>\n <macros>\n <xml name="paramPairSigFeatOnly">\n@@ -25,7 +25,7 @@\n <requirements>\n <requirement type="package">r-base</requirement>\n <requirement type="package">r-batch</requirement>\n- <requirement type="package" version="1.10.0">bioconductor-ropls</requirement>\n+ <requirement type="package" version="1.22.0">bioconductor-ropls</requirement>\n </requirements>\n <command detect_errors="aggressive"><![CDATA[\n Rscript \'$__tool_directory__/w4mcorcov_wrapper.R\'\n@@ -57,6 +57,7 @@\n contrast_detail \'$contrast_detail\'\n contrast_corcov \'$contrast_corcov\'\n contrast_salience \'$contrast_salience\'\n+ min_crossval_i \'$min_crossval_i\'\n ]]></command>\n <inputs>\n <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"\n@@ -135,6 +136,9 @@\n <param name="labelFeatures" type="text" value="3"\n label="How many features having extreme loadings should be labelled on cov-vs.-cor plot?"\n help="Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify \'ALL\' to label all features or \'0\' to label no features; this choice has no effect on the OPLS-DA loadings plot."/>\n+ <param name="min_crossval_i" type="text" value="7"\n+ label="Minumum number of samples for OPLS-DA cross-validation."\n+ help="What is the minimum number of samples to be used by the ropls package for cross-validation of OPLS-DA predictions? This should be not more than half the number of your samples."/>\n <conditional name="advanced">\n <param name="advancedFeatures" type="select" \n label="Advanced (C-plots and customized p-value adjustment)"\n@@ -179,7 +183,121 @@\n <data name="contrast_salience" format="tabular" label="${tool.name}_${variableMetadata_in.name}_salience" />\n </outputs>\n <tests>\n- <!-- test #1 -->\n+ <!-- test #1 - issue 14 -->\n+ <test>\n+ <param name="dataMatrix_in" value="issue14_input_dataMatrix.tsv"/>\n+ <param name="sampleMetadata_in" value="issue14_input_sampleMetadata.tsv"/>\n+ <param name="variableMetadata_in" value="issue14_input_variableMetadata.tsv"/>\n+ <param name="tesC" value="none"/>\n+ <param name="facC" value="tissue_flowering"/>\n+ <param name="labelFeatures" value="3"/>\n+ <param name="min_crossval_i" value="4"/>\n+ <param name="fdr_features" value="ALL"/>\n+ <param name="levCSV" value="*"/>\n+ <param name="matchingC" value="wildcard"/>\n+ <output name="contrast_corcov">\n+ <assert_contents>\n+ <!-- column-labels line -->\n+ <has_text text="featureID" />\n+ <has_text text="factorLevel1" />\n+ <has_text text="factorLevel2" />\n+ <has_text text="correlation" />\n+ <has_text text="covariance" />\n+ <has_text text="vip4p" />\n+ <has_text text="vip4o" />\n+ <!-- a matched line -->\n+ <has_text text="NM516T283_1" />\n+ <has_text text="flower_yes" />\n+ <has_text text="leaf_no" />\n+ <has_text text="-0.98475578586" />\n+ <has_text text="-58.1219648" />\n+ <has_text text="2.0103501" />\n+ <has_text text="2.872672881" />\n+ <has_text text="-0.1208407903" />\n+ <has_text text="-0.2032249" />\n+ <has_text text="-0.9857575" />\n+ <has_text text="-0.983684189899" />\n+ <has_text text="516.080116" />\n+ <has_text text="282.50076" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- test #2 - issue 6 -->\n+ <test>\n+ <param name="dataMatrix_in" value="input_dataMatrix.ts'..b'eatures" value="3"/>\n+ <param name="min_crossval_i" value="7"/>\n <param name="fdr_features" value="ALL"/>\n <param name="levCSV" value="*"/>\n <param name="matchingC" value="wildcard"/>\n@@ -386,7 +508,7 @@\n </assert_contents>\n </output>\n </test>\n- <!-- test #5 -->\n+ <!-- test #8 -->\n <test>\n <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>\n <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>\n@@ -394,6 +516,7 @@\n <param name="tesC" value="none"/>\n <param name="facC" value="k._10"/>\n <param name="labelFeatures" value="3"/>\n+ <param name="min_crossval_i" value="7"/>\n <param name="fdr_features" value="ALL"/>\n <param name="levCSV" value="k1,k.2"/>\n <param name="matchingC" value="none"/>\n@@ -422,79 +545,6 @@\n </assert_contents>\n </output>\n </test>\n- <!-- test #6 - issue 6 -->\n- <test>\n- <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>\n- <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>\n- <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>\n- <param name="tesC" value="none"/>\n- <param name="facC" value="k._10"/>\n- <param name="labelFeatures" value="3"/>\n- <param name="fdr_features" value="ALL"/>\n- <param name="levCSV" value="k_3,k-4"/>\n- <param name="matchingC" value="none"/>\n- <output name="contrast_corcov">\n- <assert_contents>\n- <!-- column-labels line -->\n- <has_text text="featureID" />\n- <has_text text="factorLevel1" />\n- <has_text text="factorLevel2" />\n- <has_text text="correlation" />\n- <has_text text="covariance" />\n- <has_text text="vip4p" />\n- <has_text text="vip4o" />\n- <!-- first matched line -->\n- <has_text text="M349.2383T700" />\n- <has_text text="-0.1221966" />\n- <has_text text="-917311734" />\n- <has_text text="0.0304592" />\n- <has_text text="0.104748883" />\n- <has_text text="-0.002736415" />\n- <has_text text="-0.0113968" />\n- <has_text text="0.387723" />\n- <has_text text="-0.3812168081" />\n- <has_text text="0.154611878" />\n- </assert_contents>\n- </output>\n- </test>\n- <!-- test #7 - issue 8 -->\n- <test>\n- <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>\n- <param name="sampleMetadata_in" value="issue8_input_sampleMetadata.tsv"/>\n- <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>\n- <param name="tesC" value="none"/>\n- <param name="facC" value="k._10"/>\n- <param name="labelFeatures" value="3"/>\n- <param name="fdr_features" value="ALL"/>\n- <param name="levCSV" value="k_3,k-4"/>\n- <param name="matchingC" value="none"/>\n- <output name="contrast_corcov">\n- <assert_contents>\n- <!-- column-labels line -->\n- <has_text text="featureID" />\n- <has_text text="factorLevel1" />\n- <has_text text="factorLevel2" />\n- <has_text text="correlation" />\n- <has_text text="covariance" />\n- <has_text text="vip4p" />\n- <has_text text="vip4o" />\n- <!-- k1 rejected by levCSV, leaving only k_3 and k-4 -->\n- <not_has_text text="k1" />\n- <not_has_text text="other" />\n- <!-- first matched line -->\n- <has_text text="M200.005T296" />\n- <has_text text="-0.1829149760" />\n- <has_text text="-115723402" />\n- <has_text text="0.0892595" />\n- <has_text text="0.00492288" />\n- <has_text text="-0.00801895" />\n- <has_text text="0.0005356178" />\n- <has_text text="0.1848186" />\n- <has_text text="-0.428802311" />\n- <has_text text="0.0882045811" />\n- </assert_contents>\n- </output>\n- </test>\n </tests>\n <help><![CDATA[\n \n' |
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| diff -r 2ae2d26e3270 -r 90708fdbc22d w4mcorcov_calc.R --- a/w4mcorcov_calc.R Wed Dec 12 09:20:02 2018 -0500 +++ b/w4mcorcov_calc.R Wed Nov 18 18:53:37 2020 +0000 |
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| @@ -22,8 +22,8 @@ , algoC = x_algorithm , predI = 1 , orthoI = if (ncol(x_dataMatrix) > 1) 1 else 0 - , printL = FALSE - , plotL = FALSE + , fig.pdfC = 'none' + , info.txtC = 'none' , crossvalI = x_crossval_i , scaleC = "pareto" # data centered and pareto scaled here only. This line fixes issue #2. ) @@ -443,6 +443,7 @@ # matchingC is one of { "none", "wildcard", "regex" } matchingC <- calc_env$matchingC labelFeatures <- calc_env$labelFeatures + minCrossvalI <- as.integer(calc_env$min_crossval_i) # arg/env checking if (!(facC %in% names(smpl_metadata))) { @@ -600,7 +601,7 @@ } , x_show_labels = labelFeatures , x_progress = progress_action - , x_crossval_i = min(7, length(chosen_samples)) + , x_crossval_i = min(minCrossvalI, length(chosen_samples)) , x_env = calc_env ) if ( is.null(my_cor_cov) ) { @@ -674,7 +675,7 @@ } , x_show_labels = labelFeatures , x_progress = progress_action - , x_crossval_i = min(7, length(chosen_samples)) + , x_crossval_i = min(minCrossvalI, length(chosen_samples)) , x_env = calc_env ) if ( is.null(my_cor_cov) ) { @@ -753,7 +754,7 @@ , x_prefix = "Features" , x_show_labels = labelFeatures , x_progress = progress_action - , x_crossval_i = min(7, length(chosen_samples)) + , x_crossval_i = min(minCrossvalI, length(chosen_samples)) , x_env = calc_env ) if ( is.null(my_cor_cov) ) { @@ -806,7 +807,7 @@ , x_prefix = "Features" , x_show_labels = labelFeatures , x_progress = progress_action - , x_crossval_i = min(7, length(chosen_samples)) + , x_crossval_i = min(minCrossvalI, length(chosen_samples)) , x_env = calc_env ) if ( is.null(my_cor_cov) ) { |
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| diff -r 2ae2d26e3270 -r 90708fdbc22d w4mcorcov_wrapper.R --- a/w4mcorcov_wrapper.R Wed Dec 12 09:20:02 2018 -0500 +++ b/w4mcorcov_wrapper.R Wed Nov 18 18:53:37 2020 +0000 |
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| @@ -4,7 +4,7 @@ # - w4mcorcov_lib.R # - w4mcorcov_input.R # - w4mcorcov_calc.R - +options(warn=1) ## constants ##---------- @@ -108,6 +108,7 @@ my_env$levCSV <- as.character(argVc["levCSV"]) my_env$matchingC <- as.character(argVc["matchingC"]) my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL' +my_env$min_crossval_i <- as.character(argVc["min_crossval_i"]) # Minumum number of samples for OPLS-DA cross-validation my_env$fdr_features <- as.character(argVc["fdr_features"]) # number of features to consider when adjusting p-value, or 'ALL' my_env$cplot_o <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested my_env$cplot_p <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested @@ -131,6 +132,24 @@ quit(save = "no", status = 10, runLast = TRUE) } +min_crossval_i <- my_env$min_crossval_i +crossval_check <- TRUE +if ( is.na(min_crossval_i) ) { + crossval_check <- FALSE +} else if ( is.null(min_crossval_i) ) { + crossval_check <- FALSE +} else { + if ( is.na(as.numeric(min_crossval_i)) ) + crossval_check <- FALSE + else if ( as.numeric(min_crossval_i) < 0 ) + crossval_check <- FALSE +} +if ( !crossval_check ) { + my_log("invalid argument: min_crossval_i") + print(min_crossval_i) + quit(save = "no", status = 10, runLast = TRUE) +} + corcov_tsv_colnames <- TRUE corcov_tsv_append <- FALSE corcov_tsv_action <- function(tsv) { |