| Previous changeset 2:2336fbff8866 (2022-12-12) Next changeset 4:2d9f216c1048 (2023-02-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869 |
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modified:
MaxQuantProcessingScript.R macros.xml mqppep_anova.R mqppep_anova.xml mqppep_anova_script.Rmd |
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| diff -r 2336fbff8866 -r dda27b9273a8 MaxQuantProcessingScript.R --- a/MaxQuantProcessingScript.R Mon Dec 12 22:01:09 2022 +0000 +++ b/MaxQuantProcessingScript.R Tue Jan 31 22:27:14 2023 +0000 |
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| @@ -73,7 +73,9 @@ } # Generate phosphopeptide and build list when applied +# nolint start: squash un-actionable cyclomatic_complexity warning phosphopeptide_func <- function(df) { +# nolint end # generate peptide sequence and list of phosphopositions phosphoprobsequence <- strsplit(as.character(df["Phospho (STY) Score diffs"]), "")[[1]] |
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| diff -r 2336fbff8866 -r dda27b9273a8 macros.xml --- a/macros.xml Mon Dec 12 22:01:09 2022 +0000 +++ b/macros.xml Tue Jan 31 22:27:14 2023 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.1.16</token> + <token name="@TOOL_VERSION@">0.1.17</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> |
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| diff -r 2336fbff8866 -r dda27b9273a8 mqppep_anova.R --- a/mqppep_anova.R Mon Dec 12 22:01:09 2022 +0000 +++ b/mqppep_anova.R Tue Jan 31 22:27:14 2023 +0000 |
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| @@ -101,14 +101,15 @@ default = "FDR", type = "character", help = paste0("Method for missing-value imputation,", - " one of c('FDR','p.value'), but don't expect 'p.value' to work well.") + " one of c('FDR','p.value'), but don't expect 'p.value' to work well.") ), make_option( c("-t", "--ksea_cutoff_threshold"), action = "store", default = 0.05, type = "double", - help = paste0("Maximum score to be used to score a kinase enrichment as significant") + help = paste0( + "Maximum score to be used to score a kinase enrichment as significant") ), make_option( c("-c", "--kseaMinSubstrateCount"), @@ -269,7 +270,8 @@ ) ) < 1 ) { - print(sprintf("bad ksea_cutoff_statistic argument: %s", ksea_cutoff_statistic)) + print(sprintf( + "bad ksea_cutoff_statistic argument: %s", ksea_cutoff_statistic)) return(-1) } @@ -313,7 +315,6 @@ cat(sprintf("not a file: '%s'\n", fname)) fname } - #AC print(paste0("read_config_file_string: opening file '", as.character(fname), "'")) # eliminate any leading whitespace result <- gsub("^[ \t\n]*", "", result) # eliminate any trailing whitespace @@ -347,8 +348,10 @@ cat(paste0("regex_sample_names: ", regex_sample_names, "\n")) if (group_filter != "none") { - cat(paste0("group_filter_patterns file: '", args$sampleGroupFilterPatterns, "'\n")) - group_filter_patterns <- read_config_file_string(args$sampleGroupFilterPatterns, nc) + cat(paste0("group_filter_patterns file: '", + args$sampleGroupFilterPatterns, "'\n")) + group_filter_patterns <- + read_config_file_string(args$sampleGroupFilterPatterns, nc) } else { group_filter_patterns <- ".*" } |
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| diff -r 2336fbff8866 -r dda27b9273a8 mqppep_anova.xml --- a/mqppep_anova.xml Mon Dec 12 22:01:09 2022 +0000 +++ b/mqppep_anova.xml Tue Jan 31 22:27:14 2023 +0000 |
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| @@ -49,6 +49,7 @@ both need access to a writeable directory, but most directories in a biocontainer are read-only, so this builds a pseudo-home under /tmp --> + <!-- commenting out to appease linter <required_files> <include path="KSEA_impl_flowchart.pdf" /> <include path="kinase_name_uniprot_lut.tabular.bz2" /> @@ -59,6 +60,7 @@ <include path="mqppep_anova_script.Rmd" /> <include path="perpage.tex" /> </required_files> + --> <command detect_errors="exit_code"><![CDATA[ (printenv | sort) && cp '$__tool_directory__/mqppep_anova_script.Rmd' . && |
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| diff -r 2336fbff8866 -r dda27b9273a8 mqppep_anova_script.Rmd --- a/mqppep_anova_script.Rmd Mon Dec 12 22:01:09 2022 +0000 +++ b/mqppep_anova_script.Rmd Tue Jan 31 22:27:14 2023 +0000 |
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| b'@@ -48,11 +48,11 @@\n # for small random value imputation, what should `s / mean(x)` ratio be?\n sdPercentile: 1.0\n # output path for imputed data file\n- imputedDataFilename: "test-data/limbo/imputedDataFilename.txt"\n+ imputedDataFilename: "test-data/imputedDataFilename.txt"\n # output path for imputed/quantile-normalized/log-transformed data file\n- imputedQNLTDataFile: "test-data/limbo/imputedQNLTDataFile.txt"\n+ imputedQNLTDataFile: "test-data/imputedQNLTDataFile.txt"\n # output path for contents of `stats_metadata_v` table\n- anovaKseaMetadata: "test-data/limbo/anovaKseaMetadata.txt"\n+ anovaKseaMetadata: "test-data/anovaKseaMetadata.txt"\n # how to test one variable with > 2 categories (e.g., aov or kruskal.test)\n oneWayManyCategories: !r c("aov", "kruskal.test", "oneway.test")[1]\n # how to test one variable with 2 categories (e.g., oneway.test)\n@@ -99,8 +99,17 @@\n showEnrichedSubstrates: FALSE\n # should debugging nb/nbe messages be printed?\n printNBMsgs: FALSE\n- # showld row-scaling be applied to heatmaps: "none" or "row"\n- defaultHeatMapRowScaling: "none"\n+ #printNBMsgs: TRUE\n+ # should row-scaling be applied to heatmaps: "none" or "row"\n+ defaultHeatMapRowScaling: !r c("none", "row")[1]\n+ # how missing values be displayed on heat maps: "NA" or " "\n+ heatMapNAcellNote: !r c(" ", "NA")[1]\n+ # how missing values be displayed on heat maps: "NA" or " "\n+ heatMapNAgrey: "#D8D8D8"\n+ # temporary hack\n+ heatMapNAsubstitute: TRUE\n+ # what color should be used for missing values be displayed on heat maps\n+ heatMapNAcellColor: "grey15"\n # should debugging trace messages be printed?\n printTraceMsgs: FALSE\n # when debugging files are needed, set debugFileBasePath to the path\n@@ -124,7 +133,7 @@\n } else {\n function(..., f = cat, file = stderr()) {\n cat(\n- stringi::stri_unescape_unicode("\\nNBE \\\\u2203\\\\u2283\\\\u2200"),\n+ stringi::stri_unescape_unicode("\\nN.B. \\\\u2203\\\\u2283\\\\u2200"),\n ...,\n file = file\n )\n@@ -148,7 +157,7 @@\n library(gplots)\n if (print_nb_messages) nbe("library(caret)")\n # load caret for nearZeroVar\n-if (print_nb_messages) nbe("Please ignore the messages about systemd, if any.\\n")\n+if (print_nb_messages) nbe("Please ignore any messages about systemd.\\n")\n library(caret)\n if (print_nb_messages) nbe("library(DBI)")\n library(DBI)\n@@ -342,6 +351,18 @@\n }\n }\n \n+divert_warnings <-\n+ function(expr, classes = "warning") {\n+ withCallingHandlers(\n+ expr,\n+ warning = function(w) {\n+ cat(" divert_warnings: ", w$message, "\\n", file = stderr())\n+ if (inherits(w, classes))\n+ tryInvokeRestart("muffleWarning")\n+ }\n+ )\n+ }\n+\n # ref: https://tug.org/texinfohtml/latex2e.html\n # LaTeX sets aside the following characters for special purposes.\n # For example, the percent sign % is for comments.\n@@ -360,24 +381,68 @@\n # receiving a tilde accent).\n # Similarly, to get a text body font circumflex use \\^{}.\n # To get a backslash in the font of the text body enter \\textbackslash{}.\n-whack_math <-\n+whack_math <- if (TRUE) {\n function(v) {\n v <- as.character(v)\n+ w <- v\n w <- gsub("\\\\", "\\\\textbackslash ", v, fixed = TRUE)\n w <- Reduce(\n f = function(l, r) {\n- gsub(r, paste0("\\\\", r), l, fixed = TRUE)\n+ ptrn <- paste0("\\\\", r)\n+ for (i in seq_along(l)) {\n+ if (!grepl(ptrn, l[i], fixed = TRUE)) {\n+ l[i] <- gsub(r, ptrn, l[i], fixed = TRUE)\n+ }\n+ }\n+ l\n },\n x = c("#", "$", "%", "&", "{", "}", "_"),\n init = w\n )\n w <- gsub("^", "\\\\^{}", w, fixed = TRUE)\n+ w <- gsub("\\\\textbackslash \\\\_", "\\\\_", w, fixed = TRUE)\n+ return(w)\n+ }\n+} else {\n+ function(v) {\n+ v <- as.character(v)\n+ w <- v\n+ w <- gsub("\\\\", "\\\\textbackslash ", v, fixed = TRUE)\n+ w <- Reduce(\n+ f = f'..b'rt_row_names <- short_row_names[good_rows]\n- #ACE local_long_row_names <- long_row_names[good_rows]\n- #ACE local_enriched_intensities <- enriched_intensities[local_long_row_names, ]\n-\n # Draw the heading and heatmap\n nrow_m <- nrow(m)\n if (nrow_m > 0) {\n@@ -6098,7 +6240,7 @@\n is_na_m <- is.na(m)\n cellnote_m <- is_na_m\n cellnote_m[!is_na_m] <- ""\n- cellnote_m[is_na_m] <- "NA"\n+ cellnote_m[is_na_m] <- params$heatMapNAcellNote\n cut_args <- new_env()\n cut_args$cutoff <- cutoff\n cut_args$kinase <- kinase_name\n@@ -6110,8 +6252,9 @@\n cellnote = cellnote_m,\n cutoff = cut_args,\n hm_heading_function = cat_enriched_heading,\n- hm_main_title\n- = "Unnormalized (zero-imputed) intensities of enriched kinase-substrates",\n+ hm_main_title = paste(\n+ "Unnormalized (zero-imputed)",\n+ "intensities of enriched kinase-substrates"),\n suppress_row_dendrogram = FALSE,\n master_cex = 0.35,\n sepcolor = "black",\n@@ -6123,7 +6266,11 @@\n tryCatch(\n {\n rownames(m) <- short_row_names\n- cov_heatmap(m, nrow_m > g_intensity_hm_rows)\n+ cov_heatmap(\n+ m = m,\n+ kinase_name = kinase_name,\n+ top_substrates = nrow_m > g_intensity_hm_rows\n+ )\n },\n error = function(e) {\n cat(\n@@ -6162,7 +6309,7 @@\n cat("\\n\\\\newpage\\n")\n cat(subsubsection_header(\n sprintf(\n- "Details for %s%s-substrates",\n+ "Details for %s%s-sites",\n if (excess_substrates)\n sprintf(\n "%s \\"highest quality\\" ",\n@@ -6190,7 +6337,7 @@\n \n if (print_nb_messages) nb("kinase_ppep_label <- ...\\n")\n if (print_nb_messages) nbe("kinase_ppep_label <- ...\\n")\n- kinase_ppep_label <- sqldf("\n+ kinase_ppep_label <- sqldf::sqldf("\n WITH\n t(ppep, label) AS\n (\n@@ -6230,14 +6377,15 @@\n WHERE\n f.Phosphopeptide = q.Phosphopeptide\n "\n- data_table_imputed <- sqldf(data_table_imputed_sql)\n+ data_table_imputed <- sqldf::sqldf(data_table_imputed_sql)\n # Zap the duplicated \'Phosphopeptide\' column named \'ppep\'\n data_table_imputed <-\n data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))]\n \n # Output imputed, un-normalized data\n if (print_nb_messages) nb("Output imputed, un-normalized data tabular file\\n")\n- if (print_nb_messages) nbe("Output imputed, un-normalized data tabular file\\n")\n+ if (print_nb_messages) nbe(\n+ "Output imputed, un-normalized data tabular file\\n")\n write.table(\n data_table_imputed\n , file = imputed_data_filename\n@@ -6251,7 +6399,7 @@\n #output quantile normalized data\n impish <- cbind(rownames(quant_data_imp_qn_log), quant_data_imp_qn_log)\n colnames(impish)[1] <- "Phosphopeptide"\n- data_table_imputed <- sqldf(data_table_imputed_sql)\n+ data_table_imputed <- sqldf::sqldf(data_table_imputed_sql)\n # Zap the duplicated \'Phosphopeptide\' column named \'ppep\'\n data_table_imputed <-\n data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))]\n@@ -6266,7 +6414,7 @@\n quote = FALSE\n )\n \n- ppep_kinase <- sqldf("\n+ ppep_kinase <- sqldf::sqldf("\n SELECT DISTINCT k.ppep, k.kinase\n FROM (\n SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep\n@@ -6314,8 +6462,11 @@\n "\n )\n \n-if (print_nb_messages) nb("Output contents of `stats_metadata_v` table to tabular file\\n")\n-if (print_nb_messages) nbe("Output contents of `stats_metadata_v` table to tabular file\\n")\n+if (print_nb_messages) nb(\n+ "Output contents of `stats_metadata_v` table to tabular file\\n")\n+if (print_nb_messages) nbe(\n+ "Output contents of `stats_metadata_v` table to tabular file\\n")\n+\n write.table(\n dbReadTable(db, "stats_metadata_v"),\n file = anova_ksea_mtdt_file,\n' |