| Previous changeset 14:c0fd285eb553 (2022-11-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046 |
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modified:
Seurat.R seurat.xml |
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added:
citeseq_Seurat.R macros.xml test-data/adt.tab.gz test-data/markers.tsv test-data/protein_out.tsv test-data/rna.tab.gz test-data/rna_out.tsv |
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| diff -r c0fd285eb553 -r fab6ff46e019 Seurat.R --- a/Seurat.R Mon Nov 21 14:35:28 2022 +0000 +++ b/Seurat.R Fri Jul 07 01:43:02 2023 +0000 |
| b |
| b'@@ -8,19 +8,24 @@\n #\' low_thresholds: ""\n #\' high_thresholds: ""\n #\' numPCs: ""\n-#\' cells_use: ""\n #\' resolution: ""\n #\' perplexity: ""\n #\' min_pct: ""\n #\' logfc_threshold: ""\n+#\' end_step: ""\n #\' showcode: ""\n #\' warn: ""\n #\' varstate: ""\n #\' vlnfeat: ""\n #\' featplot: ""\n #\' PCplots: ""\n-#\' tsne: ""\n+#\' nmds: ""\n #\' heatmaps: ""\n+#\' norm_out: ""\n+#\' variable_out: ""\n+#\' pca_out : ""\n+#\' clusters_out: ""\n+#\' markers_out: ""\n #\' ---\n \n # nolint start\n@@ -34,87 +39,148 @@\n vlnfeat <- as.logical(params$vlnfeat)\n featplot <- as.logical(params$featplot)\n pc_plots <- as.logical(params$PCplots)\n-tsne <- as.logical(params$tsne)\n+nmds <- as.logical(params$nmds)\n heatmaps <- as.logical(params$heatmaps)\n-\n+end_step <- as.integer(params$end_step)\n+norm_out <- as.logical(params$norm_out)\n # we need that to not crash Galaxy with an UTF-8 error on German LC settings.\n loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n \n #+ echo = F, warning = `warn`, include =`varstate`\n min_cells <- as.integer(params$min_cells)\n min_genes <- as.integer(params$min_genes)\n-low_thresholds <- as.integer(params$low_thresholds)\n-high_thresholds <- as.integer(params$high_thresholds)\n-num_pcs <- as.integer(params$numPCs)\n-cells_use <- as.integer(params$cells_use)\n-resolution <- as.double(params$resolution)\n-perplexity <- as.integer(params$perplexity)\n-min_pct <- as.double(params$min_pct)\n-logfc_threshold <- as.double(params$logfc_thresh)\n print(paste0("Minimum cells: ", min_cells))\n print(paste0("Minimum features: ", min_genes))\n+low_thresholds <- as.integer(params$low_thresholds)\n+high_thresholds <- as.integer(params$high_thresholds)\n print(paste0("Umi low threshold: ", low_thresholds))\n print(paste0("Umi high threshold: ", high_thresholds))\n-print(paste0("Number of principal components: ", num_pcs))\n-print(paste0("Resolution: ", resolution))\n-print(paste0("Perplexity: ", perplexity))\n-print(paste0("Minimum percent of cells", min_pct))\n-print(paste0("Logfold change threshold", logfc_threshold))\n+\n+if (end_step >= 2) {\n+ variable_out <- as.logical(params$variable_out)\n+}\n+\n \n-#+ echo = FALSE\n+if (end_step >= 3) {\n+ num_pcs <- as.integer(params$numPCs)\n+ print(paste0("Number of principal components: ", num_pcs))\n+ pca_out <- as.logical(params$pca_out)\n+}\n+if (end_step >= 4) {\n+ if (params$perplexity == "") {\n+ perplexity <- -1\n+ print(paste0("Perplexity: ", perplexity))\n+ } else { \n+ perplexity <- as.integer(params$perplexity)\n+ print(paste0("Perplexity: ", perplexity))\n+ }\n+ resolution <- as.double(params$resolution)\n+ print(paste0("Resolution: ", resolution))\n+ clusters_out <- as.logical(params$clusters_out)\n+}\n+if (end_step >= 5) {\n+ min_pct <- as.double(params$min_pct)\n+ logfc_threshold <- as.double(params$logfc_thresh)\n+ print(paste0("Minimum percent of cells", min_pct))\n+ print(paste0("Logfold change threshold", logfc_threshold))\n+ markers_out <- as.logical(params$markers_out)\n+}\n+\n+\n if (showcode == TRUE) print("Read in data, generate inital Seurat object")\n #+ echo = `showcode`, warning = `warn`, message = F\n counts <- read.delim(params$counts, row.names = 1)\n seuset <- Seurat::CreateSeuratObject(counts = counts, min.cells = min_cells, min.features = min_genes)\n \n-#+ echo = FALSE\n if (showcode == TRUE && vlnfeat == TRUE) print("Raw data vizualization")\n #+ echo = `showcode`, warning = `warn`, include=`vlnfeat`\n-Seurat::VlnPlot(object = seuset, features = c("nFeature_RNA", "nCount_RNA"))\n-Seurat::FeatureScatter(object = seuset, feature1 = "nCount_RNA", feature2 = "nFeature_RNA")\n+if (vlnfeat == TRUE){\n+ print(Seurat::VlnPlot(object = seuset, features = c("nFeature_RNA", "nCount_RNA")))\n+ print(Seurat::FeatureScatter(object = seuset, feature1 = "nCount_RNA", feature2 = "nFeature_RNA"))\n+}\n \n-#+ echo = FALSE\n if (showcode == TRUE) print("Filter and normalize for UMI counts")\n #+ echo = `showco'..b't, npcs = num_pcs)\n-Seurat::VizDimLoadings(seuset, dims = 1:2)\n-Seurat::DimPlot(seuset, dims = c(1, 2), reduction = "pca")\n-Seurat::DimHeatmap(seuset, dims = 1:num_pcs, nfeatures = 30, reduction = "pca")\n-seuset <- Seurat::JackStraw(seuset, dims = num_pcs, reduction = "pca", num.replicate = 100)\n-seuset <- Seurat::ScoreJackStraw(seuset, dims = 1:num_pcs)\n-Seurat::JackStrawPlot(seuset, dims = 1:num_pcs)\n-Seurat::ElbowPlot(seuset, ndims = num_pcs, reduction = "pca")\n+if (end_step >= 3) {\n+ #+ echo = FALSE\n+ if (showcode == TRUE && pc_plots == TRUE) print("PCA Visualization")\n+ #+ echo = `showcode`, warning = `warn`, include = `pc_plots`\n+ seuset <- Seurat::RunPCA(seuset, npcs = num_pcs)\n+ seuset <- Seurat::JackStraw(seuset, dims = num_pcs, reduction = "pca", num.replicate = 100)\n+ seuset <- Seurat::ScoreJackStraw(seuset, dims = 1:num_pcs)\n+ if (pc_plots == TRUE) {\n+ print(Seurat::VizDimLoadings(seuset, dims = 1:2))\n+ print(Seurat::DimPlot(seuset, dims = c(1, 2), reduction = "pca"))\n+ print(Seurat::DimHeatmap(seuset, dims = 1:num_pcs, nfeatures = 30, reduction = "pca"))\n+ print(Seurat::JackStrawPlot(seuset, dims = 1:num_pcs))\n+ print(Seurat::ElbowPlot(seuset, ndims = num_pcs, reduction = "pca"))\n+ }\n+ if (pca_out == TRUE) {\n+ saveRDS(seuset, "pca_out.rds")\n+ }\n+}\n \n-#+ echo = FALSE\n-if (showcode == TRUE && tsne == TRUE) print("tSNE")\n-#+ echo = `showcode`, warning = `warn`, include = `tsne`\n-seuset <- Seurat::FindNeighbors(object = seuset)\n-seuset <- Seurat::FindClusters(object = seuset)\n-if (perplexity == -1) {\n- seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution);\n-} else {\n- seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution, perplexity = perplexity);\n+if (end_step >= 4) {\n+ #+ echo = FALSE\n+ if (showcode == TRUE && nmds == TRUE) print("tSNE and UMAP")\n+ #+ echo = `showcode`, warning = `warn`, include = `nmds`\n+ seuset <- Seurat::FindNeighbors(object = seuset)\n+ seuset <- Seurat::FindClusters(object = seuset)\n+ if (perplexity == -1) {\n+ seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution);\n+ } else {\n+ seuset <- Seurat::RunTSNE(seuset, dims = 1:num_pcs, resolution = resolution, perplexity = perplexity);\n+ }\n+ if (nmds == TRUE) {\n+ print(Seurat::DimPlot(seuset, reduction = "tsne"))\n+ }\n+ seuset <- Seurat::RunUMAP(seuset, dims = 1:num_pcs)\n+ if (nmds == TRUE) {\n+ print(Seurat::DimPlot(seuset, reduction = "umap"))\n+ }\n+ if (clusters_out == TRUE) {\n+ tsnedata <- Seurat::Embeddings(seuset, reduction="tsne")\n+ saveRDS(seuset, "tsne_out.rds")\n+ umapdata <- Seurat::Embeddings(seuset, reduction="umap")\n+ saveRDS(seuset, "umap_out.rds")\n+ }\n }\n-Seurat::DimPlot(seuset, reduction = "tsne")\n+\n \n-#+ echo = FALSE\n-if (showcode == TRUE && heatmaps == TRUE) print("Marker Genes")\n-#+ echo = `showcode`, warning = `warn`, include = `heatmaps`\n-markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold)\n-top10 <- dplyr::group_by(markers, cluster)\n-top10 <- dplyr::top_n(top10, 10, avg_log2FC)\n-Seurat::DoHeatmap(seuset, features = top10$gene)\n+if (end_step == 5) {\n+ #+ echo = FALSE\n+ if (showcode == TRUE && heatmaps == TRUE) print("Marker Genes")\n+ #+ echo = `showcode`, warning = `warn`, include = `heatmaps`\n+ markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold)\n+ top10 <- dplyr::group_by(markers, cluster)\n+ top10 <- dplyr::top_n(top10, n = 10, wt = avg_log2FC)\n+ print(top10)\n+ if (heatmaps == TRUE) {\n+ print(Seurat::DoHeatmap(seuset, features = top10$gene))\n+ }\n+ if (markers_out == TRUE) {\n+ saveRDS(seuset, "markers_out.rds")\n+ data.table::fwrite(x = markers, row.names=TRUE, sep="\\t", file = "markers_out.tsv")\n+ }\n+}\n # nolint end\n' |
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| diff -r c0fd285eb553 -r fab6ff46e019 citeseq_Seurat.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/citeseq_Seurat.R Fri Jul 07 01:43:02 2023 +0000 |
| [ |
| b'@@ -0,0 +1,260 @@\n+#\' ---\n+#\' title: "Seurat Cite-seq Analysis"\n+#\' author: "Performed using Galaxy"\n+#\' params:\n+#\' rna: ""\n+#\' prot: ""\n+#\' min_cells: ""\n+#\' min_genes: ""\n+#\' low_thresholds: ""\n+#\' high_thresholds: ""\n+#\' numPCs: ""\n+#\' resolution: ""\n+#\' perplexity: ""\n+#\' min_pct: ""\n+#\' logfc_threshold: ""\n+#\' showcode: ""\n+#\' warn: ""\n+#\' varstate: ""\n+#\' vlnfeat: ""\n+#\' featplot: ""\n+#\' PCplots: ""\n+#\' nmds: ""\n+#\' heatmaps: ""\n+#\' norm_out: ""\n+#\' variable_out: ""\n+#\' pca_out : ""\n+#\' clusters_out: ""\n+#\' markers_out: ""\n+#\' cite_markers: ""\n+#\' comparison: ""\n+#\' feat_comp: ""\n+#\' marker_compare: ""\n+#\' top_x: ""\n+#\' ---\n+\n+# nolint start\n+#+ echo=F, warning = F, message=F\n+options(show.error.messages = F, error = function() {\n+ cat(geterrmessage(), file = stderr()); q("no", 1, F)\n+})\n+\n+# we need that to not crash Galaxy with an UTF-8 error on German LC settings.\n+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n+\n+showcode <- as.logical(params$showcode)\n+warn <- as.logical(params$warn)\n+varstate <- as.logical(params$varstate)\n+vlnfeat <- as.logical(params$vlnfeat)\n+featplot <- as.logical(params$featplot)\n+pc_plots <- as.logical(params$PCplots)\n+nmds <- as.logical(params$nmds)\n+heatmaps <- as.logical(params$heatmaps)\n+end_step <- as.integer(params$end_step)\n+norm_out <- as.logical(params$norm_out)\n+comparison <- as.logical(params$comparison)\n+feature <- trimws(unlist(strsplit(as.character(params$feat_comp), ",")))\n+marker_compare <- as.logical(params$marker_compare)\n+top_x <- as.integer(params$top_x)\n+min_cells <- as.integer(params$min_cells)\n+min_genes <- as.integer(params$min_genes)\n+low_thresholds <- as.integer(params$low_thresholds)\n+high_thresholds <- as.integer(params$high_thresholds)\n+num_pcs <- as.integer(params$numPCs)\n+cells_use <- as.integer(params$cells_use)\n+resolution <- as.double(params$resolution)\n+min_pct <- as.double(params$min_pct)\n+logfc_threshold <- as.double(params$logfc_thresh)\n+variable_out <- as.logical(params$variable_out)\n+pca_out <- as.logical(params$pca_out)\n+clusters_out <- as.logical(params$clusters_out)\n+markers_out <- as.logical(params$markers_out)\n+\n+print(paste0("Minimum cells: ", min_cells))\n+print(paste0("Minimum features: ", min_genes))\n+print(paste0("Umi low threshold: ", low_thresholds))\n+print(paste0("Umi high threshold: ", high_thresholds))\n+print(paste0("Number of principal components: ", num_pcs))\n+print(paste0("Resolution: ", resolution))\n+print(paste0("Minimum percent of cells", min_pct))\n+print(paste0("Logfold change threshold", logfc_threshold))\n+if (params$perplexity == "") {\n+ perplexity <- -1\n+ print(paste0("Perplexity: ", perplexity))\n+} else { \n+ perplexity <- as.integer(params$perplexity)\n+ print(paste0("Perplexity: ", perplexity))\n+}\n+\n+#+ echo = FALSE\n+if (showcode == TRUE) print("Read in data, generate inital Seurat object")\n+#+ echo = `showcode`, warning = `warn`, message = F\n+rna <- read.delim(params$rna, row.names = 1)\n+rna <- Seurat::CollapseSpeciesExpressionMatrix(rna)\n+protein <- read.delim(params$prot, row.names = 1)\n+tryCatch(all.equal(colnames(rna), colnames(protein)), error = "Columns do not match in input files")\n+seuset <- Seurat::CreateSeuratObject(counts = rna, min.cells = min_cells, min.features = min_genes)\n+\n+if (showcode == TRUE) print("asdf")\n+#+ echo = `showcode`, warning = `warn`, message = F\n+prot_obj <- Seurat::CreateAssayObject(counts = protein)\n+\n+if (showcode == TRUE) print("qwer")\n+#+ echo = `showcode`, warning = `warn`, message = F\n+seuset[["ADT"]] <- prot_obj\n+\n+if (showcode == TRUE) print("zxcv")\n+#+ echo = `showcode`, warning = `warn`, message = F\n+Seurat::DefaultAssay(seuset) <- "RNA"\n+\n+if (showcode == TRUE && vlnfeat == TRUE) print("Raw data vizualization")\n+#+ echo = `showcode`, warning = `warn`, include=`vlnfeat`\n+if (vlnfeat == TRUE){\n+ print(Seurat::VlnPlot(object = seuset, features = c('..b' <- Seurat::Embeddings(seuset, reduction="tsne")\n+ saveRDS(seuset, "tsne_out.rds")\n+ umapdata <- Seurat::Embeddings(seuset, reduction="umap")\n+ saveRDS(seuset, "umap_out.rds")\n+}\n+\n+if (showcode == TRUE && heatmaps == TRUE) print("Marker Genes")\n+#+ echo = `showcode`, warning = `warn`, include = `heatmaps`\n+markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold)\n+top10 <- dplyr::group_by(markers, cluster)\n+top10 <- dplyr::top_n(top10, n = 10, wt = avg_log2FC)\n+print(top10)\n+if (heatmaps == TRUE) {\n+ print(Seurat::DoHeatmap(seuset, features = top10$gene))\n+}\n+if (markers_out == TRUE) {\n+ saveRDS(seuset, "markers_out.rds")\n+ data.table::fwrite(x = markers, row.names=TRUE, sep="\\t", file = "markers_out.tsv")\n+}\n+\n+#+ echo = FALSE\n+if (showcode == TRUE && comparison == TRUE) print("Compare")\n+#+ echo = `showcode`, warning = `warn`, include = `comparison`\n+ Seurat::DefaultAssay(seuset) <- "ADT"\n+ seuset <- Seurat::NormalizeData(seuset, normalization.method = "CLR", margin = 2)\n+ Seurat::DefaultAssay(seuset) <- "RNA"\n+ seuset <- Seurat::NormalizeData(seuset, normalization.method = "CLR", margin = 2, assay = "ADT")\n+if (comparison == TRUE) {\n+ for(x in feature) {\n+ Seurat::DefaultAssay(seuset) <- "ADT"\n+ p1 <- Seurat::FeaturePlot(seuset, x, cols = c("lightgrey", "red")) + ggplot2::ggtitle(paste0("Protein:", " ", x))\n+ Seurat::DefaultAssay(seuset) <- "RNA"\n+ p2 <- Seurat::FeaturePlot(seuset, x) + ggplot2::ggtitle(paste0("RNA:", " ", x))\n+ print(p1 | p2)\n+ label <- as.character(paste0(Seurat::Key(seuset[["ADT"]]), x))\n+ print(Seurat::VlnPlot(seuset, paste0("rna_", x)))\n+ print(Seurat::VlnPlot(seuset, paste0("adt_", x)))\n+ }\n+}\n+\n+#+ echo = FALSE\n+if (showcode == TRUE) print("Cite-seq")\n+#+ echo = `showcode`, warning = `warn`, include = `marker_compare`\n+rna_markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold, assay="RNA")\n+protein_markers <- Seurat::FindAllMarkers(seuset, only.pos = TRUE, min.pct = min_pct, logfc.threshold = logfc_threshold, assay="ADT")\n+if (marker_compare == TRUE) {\n+ data.table::fwrite(x = rna_markers, sep="\\t", file = "rna_out.tsv")\n+ data.table::fwrite(x = protein_markers, sep="\\t", file = "protein_out.tsv")\n+}\n+toprna <- dplyr::top_n(dplyr::group_by(rna_markers, cluster), n=5, avg_log2FC)\n+toprna <- head(as.list(unique(as.data.frame(toprna)$gene)), top_x)\n+topprot <- dplyr::top_n(dplyr::group_by(protein_markers, cluster), n=5, avg_log2FC)\n+topprot <- head(as.list(unique(as.data.frame(topprot)$gene)), top_x)\n+if(marker_compare == TRUE) {\n+ pdf(file="citeseq_out.pdf")\n+ rna_labels <- as.vector(toprna)\n+ rna_labels <- rna_labels[!duplicated(rna_labels)]\n+ prot_labels <- as.vector(topprot)\n+ prot_labels <- prot_labels[!duplicated(prot_labels)]\n+ for(rnamarker in rna_labels) {\n+ rnamarker <- paste("rna_", rnamarker, sep = "")\n+ for(protmarker in prot_labels) {\n+ protmarker <- paste("adt_", protmarker, sep="")\n+ plot <- Seurat::FeatureScatter(seuset, feature1 = rnamarker, feature2 = protmarker) + ggplot2::ggtitle(paste0(rnamarker, " vs ", protmarker))\n+ print(plot)\n+ }\n+ }\n+ for(rnamarker in rna_labels) {\n+ rnamarker <- paste("rna_", rnamarker, sep = "")\n+ for(rnamarker2 in rna_labels) {\n+ rnamarker2 <- paste("rna_", rnamarker2, sep="")\n+ plot <- Seurat::FeatureScatter(seuset, feature1 = rnamarker, feature2 = rnamarker2) + ggplot2::ggtitle(paste0(rnamarker, " vs ", rnamarker2))\n+ print(plot)\n+ }\n+ }\n+ for(protmarker in prot_labels) {\n+ protmarker <- paste("adt_", protmarker, sep = "")\n+ for(protmarker2 in prot_labels) {\n+ protmarker2 <- paste("adt_", protmarker2, sep="")\n+ plot <- Seurat::FeatureScatter(seuset, feature1 = protmarker, feature2 = protmarker2) + ggplot2::ggtitle(paste0(protmarker, " vs ", protmarker2))\n+ print(plot)\n+ }\n+ }\n+ dev.off()\n+}\n+\n+# nolint end\n' |
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| diff -r c0fd285eb553 -r fab6ff46e019 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jul 07 01:43:02 2023 +0000 |
| [ |
| @@ -0,0 +1,67 @@ +<macros> + <token name="@TOOL_VERSION@">4.3.0.1</token> + <token name="@FUNCTION_BASE@">function['function_select'] == "base"</token> + <token name="@FUNCTION_CITE@">function['function_select'] == "cite"</token> + <token name="@VARIABLE_CONTINUE@">function['variable_continue']['variable_continue'] == "yes"</token> + <token name="@PCA_CONTINUE@">function['variable_continue']['pca_continue']['pca_continue'] == "yes"</token> + <token name="@CLUSTERS_CONTINUE@">function['variable_continue']['pca_continue']['clusters_continue']['clusters_continue'] == "yes"</token> + <token name="@MARKERS_CONTINUE@">function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_continue'] == "yes"</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement> + <requirement type="package" version="2.22">r-rmarkdown</requirement> + <requirement type="package" version="1.14.2">r-data.table</requirement> + </requirements> + </xml> + <xml name="norm" label="Normalizing data" expanded="true"> + <param name="low_thresholds" type="integer" value="1" min="0" label="Low threshold for filtering cells" /> + <param name="high_thresholds" type="integer" value="20000000" min="1" label="High threshold for filtering cells" /> + <param name="vlnfeat" type="boolean" truevalue="T" falsevalue="F" label="Include violin plot and scatter plot of cell features"/> + <param name="norm_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after data normalization"/> + </xml> + <xml name="variable" label="Variable features" expanded="true"> + <param name="featplot" type="boolean" truevalue="T" falsevalue="F" label="Include plot of variable features"/> + <param name="var_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after data scaling"/> + </xml> + <xml name="pca" label="Principal component analysis" expanded="true"> + <param name="num_PCs" type="integer" min="0" value="10" label="Number of PCs to use in plots" help="Uses this number of PCs in PCHEatmap, JackStrawPlot, FindClusters, RunTSNE" /> + <param name="pc_plots" type="boolean" truevalue="T" falsevalue="F" label="Include PCA plots"/> + <param name="pca_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after PCA analysis"/> + </xml> + <xml name="clusters" label="Multidimensional scaling and Clustering" expanded="true"> + <param name="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" min="1"/> + <param name="resolution" type="float" value="0.6" min="0" label="Resolution parameter" help="Value of the resolution parameter used in FindClusters, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities" /> + <param name="nmds" type="boolean" truevalue="T" falsevalue="F" label="Include UMAP and TSNE plots"/> + <param name="clusters_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after TSNE and UMAP analysis"/> + </xml> + <xml name="markers" label="Marker genes" expanded="true"> + <param name="min_pct" type="float" value="0.1" min="0" max="1.0" label="Minimum percent cells" help="With FindMarkers, only test genes that are detected in at least this percentage of cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed" /> + <param name="logfc_threshold" type="float" min="0" value="0.25" label="Log fold change threshold" + help="With FindMarkers, limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Increasing this parameter speeds up the function, but can miss weaker signals" /> + <param name="heatmaps" type="boolean" truevalue="T" falsevalue="F" label="Include heatmaps of markers"/> + <param name="markers_file" type="boolean" truevalue="T" falsevalue="F" label="Output marker data"/> + </xml> + <xml name="cite-seq" label="Cite-seq analysis" expanded="true"> + <param name="cite_markers" type="boolean" truevalue="T" falsevalue="F" label="Output list of cite-seq markers"/> + <conditional name="comparison"> + <param name="comparison" type="select" label="Compare specific feature's effect on protein and rna expression?"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <param name="feat_comp" type="text" label="Feature(s) to inspect" help="Comma-separated list of features to directly compare with protein and RNA expression"/> + </when> + <when value="no"/> + </conditional> + <conditional name="marker_compare"> + <param name="marker_compare" type="select" label="Compare top RNA and protein features graphically against themselves and one another"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="top_x" type="integer" min="1" value="5" label="How many of the top features should be shown"/> + </when> + <when value="no"/> + </conditional> + </xml> +</macros> \ No newline at end of file |
| b |
| diff -r c0fd285eb553 -r fab6ff46e019 seurat.xml --- a/seurat.xml Mon Nov 21 14:35:28 2022 +0000 +++ b/seurat.xml Fri Jul 07 01:43:02 2023 +0000 |
| [ |
| b'@@ -1,119 +1,322 @@\n-<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy0">\n+<tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy1">\n <description>- toolkit for exploration of single-cell RNA-seq data</description>\n <macros>\n- <token name="@TOOL_VERSION@">4.3.0</token>\n+ <import>macros.xml</import>\n </macros>\n- <requirements>\n- <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>\n- <requirement type="package" version="2.18">r-rmarkdown</requirement>\n- </requirements>\n+ <expand macro="requirements"/>\n <command detect_errors="exit_code"><![CDATA[\n-#if "vln" in $meta.plots:\n- #set $vln = \'T\'\n-#else\n- #set $vln = \'F\'\n-#end if\n-#if "feat" in $meta.plots:\n- #set $feat = \'T\'\n-#else\n- #set $feat = \'F\'\n-#end if\n-#if "PCs" in $meta.plots:\n- #set $PCs = \'T\'\n-#else\n- #set $PCs = \'F\'\n-#end if\n-#if "tsne" in $meta.plots:\n- #set $tsne = \'T\'\n-#else\n- #set $tsne = \'F\'\n-#end if\n-#if "heat" in $meta.plots:\n- #set $heatmaps = \'T\'\n-#else\n- #set $heatmaps = \'F\'\n-#end if\n-#if not str($adv.perplexity):\n- #set $adv_perplexity = -1\n-#else:\n- #set $adv_perplexity = $adv.perplexity\n-#end if\n-Rscript -e "library(\\"rmarkdown\\"); render(\\"$__tool_directory__/Seurat.R\\",\n- params = list(counts = \\"${counts}\\",\n- min_cells = \\"${adv.min_cells}\\",\n- min_genes = \\"${adv.min_genes}\\",\n- low_thresholds = \\"${adv.low_thresholds}\\",\n- high_thresholds = \\"${adv.high_thresholds}\\",\n- numPCs = \\"${adv.num_PCs}\\",\n- cells_use = \\"${adv.cells_use}\\",\n- resolution = \\"${adv.resolution}\\",\n- perplexity = \\"${adv_perplexity}\\",\n- min_pct = \\"${adv.min_pct}\\",\n- logfc_threshold = \\"${adv.logfc_threshold}\\",\n+ #if $function.function_select == "base": \n+ Rscript -e "library(\\"rmarkdown\\"); render(\\"$__tool_directory__/Seurat.R\\",\n+ params = list(counts = \\"${function.input}\\",\n+ min_cells = \\"${function.min_cells}\\",\n+ min_genes = \\"${function.min_genes}\\",\n+ low_thresholds = \\"${function.low_thresholds}\\",\n+ high_thresholds = \\"${function.high_thresholds}\\",\n+ vlnfeat = \\"${function.vlnfeat}\\",\n+ norm_out = \\"${function.norm_file}\\",\n+ #if $function.variable_continue.variable_continue == "yes":\n+ featplot = \\"${function.variable_continue.featplot}\\",\n+ variable_out = \\"${function.variable_continue.var_file}\\",\n+ #if $function.variable_continue.pca_continue.pca_continue == "yes":\n+ numPCs = \\"${function.variable_continue.pca_continue.num_PCs}\\",\n+ PCplots = \\"${function.variable_continue.pca_continue.pc_plots}\\",\n+ pca_out = \\"${function.variable_continue.pca_continue.pca_file}\\",\n+ #if $function.variable_continue.pca_continue.clusters_continue.clusters_continue == "yes":\n+ perplexity = \\"${function.variable_continue.pca_continue.clusters_continue.perplexity}\\",\n+ resolution = \\"${function.variable_continue.pca_continue.clusters_continue.resolution}\\",\n+ nmds = \\"${function.variable_continue.pca_continue.clusters_continue.nmds}\\",\n+ clusters_out = \\"${function.variable_continue.pca_continue.clusters_continue.clusters_file}\\",\n+ #if $function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_continue == "yes":\n+ min_pct = \\"${function.variable_continue.pca_continue.clusters_continue.markers_continue.min_pct}\\",\n+ logfc_threshold = \\"${function.variable_continue.pca_continue.clusters_continue.markers_continue.logfc_threshold}\\",\n+ heatmaps = \\"${function.variable_continue.pca_continue.clusters_continue.markers_continue.heatmaps}\\",\n+ markers_out = \\"${function.variable_continue.pca_continue.clusters_continue.mar'..b'aram name="low_thresholds" value="1" />\n+ <param name="high_thresholds" value="20000000" />\n+ <param name="vlnfeat" value="F"/>\n+ <param name="norm_file" value="F"/>\n+ <param name="featplot" value="T"/>\n+ <param name="var_file" value="F"/>\n+ <param name="num_PCs" value="20" />\n+ <param name="pc_plots" value="T"/>\n+ <param name="pca_file" value="F"/>\n+ <param name="resolution" value="0.6" />\n+ <param name="nmds" value="F"/>\n+ <param name="clusters_file" value="F"/>\n+ <param name="min_pct" value="0.25" />\n+ <param name="logfc_threshold" value="0.25" />\n+ <param name="heatmaps" value="T"/>\n+ <param name="markers_file" value="F"/>\n+ <param name="cite_markers" value="T"/>\n+ <conditional name="comparison">\n+ <param name="comparison" value="yes"/>\n+ <param name="feat_comp" value="CD4,CD19"/>\n+ </conditional>\n+ <conditional name="marker_compare">\n+ <param name="marker_compare" value="yes"/>\n+ <param name="top_x" value="3"/>\n+ </conditional>\n+ </conditional>\n+ <section name="meta">\n+ <param name="showcode" value="T"/>\n+ <param name="warn" value="F"/>\n+ <param name="varstate" value="F"/>\n+ </section>\n+ <output name="rnamarkerst" ftype="tabular" file="rna_out.tsv" compare="sim_size" delta="500" />\n+ <output name="protmarkerst" ftype="tabular" file="protein_out.tsv" compare="sim_size" delta="500" />\n+ </test>\n+ <test expect_num_outputs="9">\n+ <conditional name="function">\n+ <param name="function_select" value="cite"/>\n+ <param name="rna" ftype="tabular" value="rna.tab.gz"/>\n+ <param name="prot" ftype="tabular" value="adt.tab.gz"/>\n+ <param name="min_cells" value="0"/>\n+ <param name="min_genes" value="0"/>\n+ <param name="low_thresholds" value="1" />\n+ <param name="high_thresholds" value="20000000" />\n+ <param name="vlnfeat" value="F"/>\n+ <param name="norm_file" value="T"/>\n+ <param name="featplot" value="T"/>\n+ <param name="var_file" value="T"/>\n+ <param name="num_PCs" value="20" />\n+ <param name="pc_plots" value="T"/>\n+ <param name="pca_file" value="T"/>\n+ <param name="resolution" value="0.6" />\n+ <param name="nmds" value="T"/>\n+ <param name="clusters_file" value="T"/>\n+ <param name="min_pct" value="0.25" />\n+ <param name="logfc_threshold" value="0.25" />\n+ <param name="heatmaps" value="T"/>\n+ <param name="markers_file" value="T"/>\n+ <param name="cite_markers" value="F"/>\n+ <conditional name="comparison">\n+ <param name="comparison" value="yes"/>\n+ <param name="feat_comp" value="CD4,CD19"/>\n+ </conditional>\n+ <conditional name="marker_compare">\n+ <param name="marker_compare" value="yes"/>\n+ <param name="top_x" value="3"/>\n+ </conditional>\n+ </conditional>\n+ <section name="meta">\n+ <param name="showcode" value="T"/>\n+ <param name="warn" value="F"/>\n+ <param name="varstate" value="F"/>\n+ </section>\n </test>\n </tests>\n <help><![CDATA[\n@@ -167,6 +473,8 @@\n **Inputs**\n \n * Gene count matrix in TAB-separated format\n+ or\n+ * RNA and Protein count matrices in TAB-separated formats\n \n -----\n \n' |
| b |
| diff -r c0fd285eb553 -r fab6ff46e019 test-data/adt.tab.gz |
| b |
| Binary file test-data/adt.tab.gz has changed |
| b |
| diff -r c0fd285eb553 -r fab6ff46e019 test-data/markers.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/markers.tsv Fri Jul 07 01:43:02 2023 +0000 |
| b |
| b'@@ -0,0 +1,773 @@\n+""\tp_val\tavg_log2FC\tpct.1\tpct.2\tp_val_adj\tcluster\tgene\n+Nucks1\t1.18411323850772e-16\t1.00561994844169\t1\t1\t1.09767297209666e-13\t0\tNucks1\n+Gpi1\t1.79982790200504e-16\t1.4397713415714\t1\t0.975\t1.66844046515867e-13\t0\tGpi1\n+Trp53\t4.43575005074525e-16\t1.67570868184123\t0.986\t0.949\t4.11194029704085e-13\t0\tTrp53\n+Gdf3\t6.15314650265127e-15\t1.75957711466652\t0.944\t0.802\t5.70396680795773e-12\t0\tGdf3\n+Rpl4\t9.94148370705165e-15\t0.555534334164376\t1\t1\t9.21575539643688e-12\t0\tRpl4\n+Ralb\t1.5603785645578e-14\t1.92721605141292\t0.93\t0.695\t1.44647092934508e-11\t0\tRalb\n+Ftl1\t5.38929343854758e-14\t0.896518520873592\t1\t1\t4.99587501753361e-11\t0\tFtl1\n+Zfp704\t3.48560933499829e-13\t1.54864588651405\t0.972\t0.838\t3.23115985354342e-10\t0\tZfp704\n+Tns1\t5.77529013908346e-13\t1.68280690355749\t0.887\t0.503\t5.35369395893037e-10\t0\tTns1\n+Gcat\t3.87561669839796e-12\t1.69793512322551\t0.958\t0.807\t3.59269667941491e-09\t0\tGcat\n+St3gal4\t6.49102709874417e-12\t1.10146192261782\t0.606\t0.173\t6.01718212053585e-09\t0\tSt3gal4\n+Gpa33\t1.33561520892938e-11\t2.12256764711496\t0.592\t0.208\t1.23811529867753e-08\t0\tGpa33\n+Xrn2\t3.29473696699025e-11\t0.770133884184816\t1\t0.995\t3.05422116839996e-08\t0\tXrn2\n+Mrpl17\t3.50012211643864e-11\t0.746796177121439\t1\t0.99\t3.24461320193862e-08\t0\tMrpl17\n+Ceacam2\t5.36266305938498e-11\t0.659994093618872\t0.761\t0.345\t4.97118865604987e-08\t0\tCeacam2\n+Adi1\t5.64090996263144e-11\t1.48358282742796\t0.972\t0.888\t5.22912353535935e-08\t0\tAdi1\n+Sept2\t7.01918447074417e-11\t0.868969458163974\t1\t1\t6.50678400437984e-08\t0\tSept2\n+Ppp1r11\t7.44523196438785e-11\t0.918592139758593\t1\t0.959\t6.90173003098754e-08\t0\tPpp1r11\n+Eif4e2\t2.22092667324463e-10\t0.824779756130801\t1\t0.995\t2.05879902609777e-07\t0\tEif4e2\n+Cacybp\t2.68829218185697e-10\t1.00228344950431\t0.986\t0.995\t2.49204685258141e-07\t0\tCacybp\n+Eno1\t6.96987523876623e-10\t0.40016030945526\t0.93\t0.599\t6.4610743463363e-07\t0\tEno1\n+Myeov2\t1.9990246379103e-09\t0.685539965183034\t0.986\t0.985\t1.85309583934285e-06\t0\tMyeov2\n+Gng10\t3.94623730908105e-09\t1.17130525771998\t0.859\t0.457\t3.65816198551814e-06\t0\tGng10\n+Cd109\t4.39844362440024e-09\t1.91175145685468\t0.408\t0.107\t4.07735723981902e-06\t0\tCd109\n+Hnrnpa0\t1.58290267057998e-08\t0.811216726627202\t0.986\t0.98\t1.46735077562765e-05\t0\tHnrnpa0\n+Msrb2\t5.48032890646332e-08\t1.24147534501256\t0.732\t0.381\t5.08026489629149e-05\t0\tMsrb2\n+Ptcd3\t6.19767456859678e-08\t0.800091440706327\t1\t0.99\t5.74524432508921e-05\t0\tPtcd3\n+Rai14\t8.40068444688735e-08\t1.31175247785821\t0.845\t0.538\t7.78743448226457e-05\t0\tRai14\n+Hint2\t2.26929636291787e-07\t0.715455167813889\t0.859\t0.497\t0.000210363772842486\t0\tHint2\n+Sra1\t2.68967121984332e-07\t0.93977408723431\t0.972\t0.924\t0.000249332522079476\t0\tSra1\n+Fth1\t1.19897530626167e-06\t0.631968616609468\t1\t1\t0.00111145010890457\t0\tFth1\n+2810432D09Rik\t1.3935121021676e-06\t1.08796030099265\t0.93\t0.782\t0.00129178571870937\t0\t2810432D09Rik\n+Cycs\t1.65526495315875e-06\t0.480425114297169\t1\t0.995\t0.00153443061157816\t0\tCycs\n+Npr1\t1.91352582651328e-06\t0.832258895946477\t0.972\t0.766\t0.00177383844117781\t0\tNpr1\n+Oas1a\t2.40234815360308e-06\t1.18028761558635\t0.817\t0.66\t0.00222697673839006\t0\tOas1a\n+Fancm\t2.50675446923527e-06\t0.894104496016523\t1\t0.99\t0.0023237613929811\t0\tFancm\n+Pnpla6\t2.84941771941601e-06\t1.15711866758003\t0.958\t0.929\t0.00264141022589864\t0\tPnpla6\n+Fkbp2\t3.35210087424692e-06\t0.681209438799815\t0.958\t0.909\t0.00310739751042689\t0\tFkbp2\n+Egfl7\t3.83761020774903e-06\t1.06164633323232\t0.732\t0.467\t0.00355746466258335\t0\tEgfl7\n+Ctnnb1\t4.95946741674435e-06\t0.468455673768554\t1\t0.99\t0.00459742629532201\t0\tCtnnb1\n+Amdhd2\t5.51993168968458e-06\t1.07601984805959\t0.901\t0.822\t0.0051169766763376\t0\tAmdhd2\n+Il1f9\t6.41757293244151e-06\t0.496713211958332\t0.394\t0.67\t0.00594909010837328\t0\tIl1f9\n+Mrpl51\t7.56282674299504e-06\t0.506391556742938\t1\t0.995\t0.0070107403907564\t0\tMrpl51\n+Exosc8\t1.06283094770493e-05\t0.502095828075973\t1\t1\t0.00985244288522468\t0\tExosc8\n+Prelid1\t1.43265849490701e-05\t0.491961820886089\t0.986\t0.995\t0.0132807442477879\t0\tPrelid1\n+Gabra1\t2.67122398852359e-05\t1.43236925093549\t0.268\t0.081\t0.0247622463736137\t0\tGabra1\n+Mbtps1\t2.72739402167582e-05\t0.87046171'..b'9e-06\t0.441003772850919\t0.96\t0.547\t0.0020627233127515\t4\tSec14l1\n+Gpatch31\t2.28602215776352e-06\t1.71564636112472\t0.84\t0.37\t0.00211914254024678\t4\tGpatch3\n+1700029F12Rik\t3.16670921538127e-06\t1.25920332789257\t0.6\t0.206\t0.00293553944265843\t4\t1700029F12Rik\n+D1Bwg0212e\t3.54092462883736e-06\t1.09075409376934\t0.96\t0.819\t0.00328243713093223\t4\tD1Bwg0212e\n+Agbl5\t3.63234366845022e-06\t0.359000375003823\t0.88\t0.51\t0.00336718258065336\t4\tAgbl5\n+Kif91\t4.01899120973089e-06\t0.768464087196651\t0.88\t0.403\t0.00372560485142053\t4\tKif9\n+Ctnna2\t4.18835867427856e-06\t0.489080438185307\t0.4\t0.107\t0.00388260849105622\t4\tCtnna2\n+Traf7\t4.59597118765464e-06\t0.70767916224615\t1\t0.959\t0.00426046529095585\t4\tTraf7\n+Rbm22\t5.36974645549668e-06\t0.730087432476789\t1\t0.992\t0.00497775496424542\t4\tRbm22\n+Rspry11\t5.69095110889555e-06\t1.0141365217818\t0.96\t0.716\t0.00527551167794617\t4\tRspry1\n+Mecp2\t6.73951105806661e-06\t0.990901622242648\t0.88\t0.551\t0.00624752675082775\t4\tMecp2\n+Ogfrl1\t7.83911040043734e-06\t0.426596561676906\t0.96\t0.56\t0.00726685534120541\t4\tOgfrl1\n+Nmb1\t8.1467937980205e-06\t1.48728600328544\t1\t0.728\t0.007552077850765\t4\tNmb\n+Nin2\t8.41338109135364e-06\t1.03986152957422\t0.96\t0.761\t0.00779920427168482\t4\tNin\n+Ccnyl1\t8.75230930750994e-06\t1.19543145693502\t1\t0.7\t0.00811339072806172\t4\tCcnyl1\n+Tex14\t9.56222447108374e-06\t0.494746429430875\t0.84\t0.436\t0.00886418208469463\t4\tTex14\n+St5\t1.14940659749145e-05\t0.605165682719874\t1\t0.638\t0.0106549991587457\t4\tSt5\n+Nbeal1\t1.21823749551211e-05\t0.832173404655711\t0.96\t0.897\t0.0112930615833972\t4\tNbeal1\n+Clk21\t1.68162380954407e-05\t1.21176749980517\t0.96\t0.852\t0.0155886527144735\t4\tClk2\n+Pip5k1c\t1.80263888169973e-05\t0.716186824000705\t0.96\t0.757\t0.0167104624333565\t4\tPip5k1c\n+Tmem87b1\t1.81967024576279e-05\t0.686361617836365\t1\t0.835\t0.016868343178221\t4\tTmem87b\n+Ercc4\t2.93090146915522e-05\t1.22254679642911\t1\t0.877\t0.0271694566190689\t4\tErcc4\n+Alox121\t2.9986865925419e-05\t0.814366019417343\t0.96\t0.691\t0.0277978247128634\t4\tAlox12\n+Cotl1\t3.55238391783376e-05\t0.291812126661166\t0.8\t0.387\t0.032930598918319\t4\tCotl1\n+Vps39\t3.62481073948892e-05\t1.28853126628222\t0.96\t0.827\t0.0336019955550623\t4\tVps39\n+4632434I11Rik1\t3.93389287722145e-05\t0.608031235714694\t0.96\t0.934\t0.0364671869718429\t4\t4632434I11Rik\n+Ankrd27\t4.13605244951355e-05\t0.78336551232952\t1\t0.794\t0.0383412062069906\t4\tAnkrd27\n+Fah1\t4.76477821526752e-05\t0.331144383476058\t0.4\t0.107\t0.0441694940555299\t4\tFah\n+Zmym4\t4.99487631936679e-05\t0.819479010245981\t0.96\t0.93\t0.0463025034805301\t4\tZmym4\n+Mosc21\t8.75878249805554e-05\t0.804360337949048\t0.96\t0.753\t0.0811939137569749\t4\tMosc2\n+Fem1c1\t0.000134144950945859\t1.59351176629955\t0.96\t0.831\t0.124352369526812\t4\tFem1c\n+D4Bwg0951e1\t0.000137801588617095\t0.565645554404937\t0.8\t0.403\t0.127742072648047\t4\tD4Bwg0951e\n+Zkscan141\t0.00014549216540626\t0.583843128566121\t0.92\t0.576\t0.134871237331603\t4\tZkscan14\n+Cry21\t0.000155364520126801\t0.42931037311356\t0.92\t0.531\t0.144022910157544\t4\tCry2\n+Dtnb1\t0.000163437118936719\t0.485702200066726\t1\t0.7\t0.151506209254338\t4\tDtnb\n+Abcc32\t0.000168288248321098\t0.250119026164717\t0.88\t0.514\t0.156003206193658\t4\tAbcc3\n+Zfp523\t0.000191398072795126\t0.329049002394344\t0.36\t0.107\t0.177426013481082\t4\tZfp523\n+Sec31a\t0.000344008370420095\t0.924496462911904\t1\t0.984\t0.318895759379428\t4\tSec31a\n+Ercc5\t0.000413521809768657\t0.419204737728817\t0.88\t0.584\t0.383334717655545\t4\tErcc5\n+Tnrc6a\t0.000536560574620653\t0.406801300987023\t0.96\t0.988\t0.497391652673345\t4\tTnrc6a\n+Ctnnd1\t0.000892942115112949\t0.766388544590886\t1\t0.984\t0.827757340709703\t4\tCtnnd1\n+Zmym31\t0.00106377539780854\t0.443295470931702\t1\t0.815\t0.986119793768515\t4\tZmym3\n+Zfp8301\t0.00119573195456822\t0.556755544900666\t1\t0.889\t1\t4\tZfp830\n+Hells1\t0.00123148933789219\t0.320858221286585\t0.96\t0.979\t1\t4\tHells\n+Nlrp31\t0.00167546658564824\t0.682913638083824\t0.48\t0.23\t1\t4\tNlrp3\n+Serpine21\t0.00170095741538562\t0.492169327022354\t0.96\t0.757\t1\t4\tSerpine2\n+Ttll5\t0.00173194686095845\t0.334901585350436\t0.96\t0.823\t1\t4\tTtll5\n+Shprh\t0.00223213166460002\t0.455600408375772\t0.96\t0.881\t1\t4\tShprh\n+Dcdc2c1\t0.00228198449889257\t1.55885090391374\t0.84\t0.675\t1\t4\tDcdc2c\n' |
| b |
| diff -r c0fd285eb553 -r fab6ff46e019 test-data/protein_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/protein_out.tsv Fri Jul 07 01:43:02 2023 +0000 |
| b |
| @@ -0,0 +1,103 @@ +p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene +1.67295292546245e-13 0.326405715743977 1 1 2.17483880310118e-12 1 CD3 +1.5642098215071e-44 0.495970381707604 1 1 2.03347276795923e-43 3 CD3 +1.14196527784025e-35 0.40085553451009 1 1 1.48455486119233e-34 3 CD4 +1.00171227157907e-42 0.49278398824099 1 1 1.30222595305279e-41 4 CD3 +4.45804690128427e-32 0.383908885768934 1 1 5.79546097166956e-31 4 CD4 +2.3270323108152e-64 0.535858744002285 1 1 3.02514200405976e-63 6 CD11c +4.59697497155158e-71 0.582642681231806 1 1 5.97606746301705e-70 8 CD11c +5.42829982399312e-23 0.310022335647084 1 1 7.05678977119106e-22 9 CD11c +5.34022845897306e-70 0.60889940093635 1 1 6.94229699666497e-69 10 CD11c +1.94515080115917e-75 0.987231181827462 1 1 2.52869604150692e-74 11 CD19 +1.3401718411323e-32 0.27534720926661 1 1 1.74222339347199e-31 11 CD45RA +6.82783507401538e-62 0.57275793552547 1 1 8.87618559621999e-61 12 CD11c +2.04431843457248e-31 0.449927697936415 1 1 2.65761396494422e-30 15 CD11c +3.39342323568419e-26 0.404810867237044 1 1 4.41145020638945e-25 16 CD11c +7.88511793517547e-29 0.465776338611985 1 1 1.02506533157281e-27 17 CD11c +1.91570514633727e-46 0.56726960905273 1 1 2.49041669023845e-45 18 CD11c +5.1260483533881e-82 1.18155234784116 1 1 6.66386285940453e-81 20 CD8 +1.57361935775751e-47 0.391899061098195 1 1 2.04570516508476e-46 20 CD45RA +8.74284608877472e-39 0.546627661446195 1 1 1.13656999154071e-37 23 CD11c +1.96816328438562e-27 0.525377309779508 1 1 2.55861226970131e-26 24 CD3 +2.80113243084789e-26 0.445779372516199 1 1 3.64147216010226e-25 24 CD4 +2.08891825701061e-32 0.359032672171917 1 1 2.71559373411379e-31 25 CD45RA +6.38184609794435e-23 0.314402863729703 1 1 8.29639992732766e-22 25 CD56 +2.33924416208311e-19 0.275395941678534 1 1 3.04101741070804e-18 25 CD16 +1.23100762344444e-72 0.527654790808374 1 1 1.60030991047777e-71 26 CD45RA +1.00222124580754e-61 0.47303501407078 1 1 1.3028876195498e-60 26 CD56 +5.04433216574995e-61 0.499525696517984 1 1 6.55763181547493e-60 26 CD16 +2.57942814886754e-19 0.397056393594097 1 1 3.3532565935278e-18 26 CD8 +3.80436056159182e-21 0.471090809116061 1 1 4.94566873006937e-20 27 CD3 +5.62262803624727e-14 0.365368408368207 1 1 7.30941644712145e-13 27 CD4 +8.05030043675788e-29 0.556377398183442 1 1 1.04653905677852e-27 28 CD3 +5.68183022990689e-24 0.462604140851 1 1 7.38637929887895e-23 28 CD4 +4.32372215869929e-27 0.492374012295227 1 1 5.62083880630908e-26 30 CD4 +8.80072296811784e-27 0.562209188025505 1 1 1.14409398585532e-25 30 CD3 +5.86102527405308e-30 0.514318772298818 1 1 7.619332856269e-29 31 CD4 +1.10478058693055e-26 0.551831262152829 1 1 1.43621476300972e-25 31 CD3 +6.38562416996792e-11 0.407403482613083 1 1 8.30131142095829e-10 32 CD3 +4.17895569544475e-06 0.272549702717712 1 1 5.43264240407818e-05 32 CD4 +3.72341120344556e-39 0.63404032335664 1 1 4.84043456447923e-38 33 CD11c +3.47626583425057e-31 0.298415769867169 1 1 4.51914558452574e-30 33 CD14 +1.61092774622993e-19 0.32674447986965 1 1 2.09420607009891e-18 35 CD45RA +7.8712241758892e-27 0.572421953528271 1 1 1.0232591428656e-25 36 CD11c +2.53970993841925e-22 0.278363837640406 1 1 3.30162291994503e-21 36 CD14 +1.35360047893276e-42 1.32718688149546 1 1 1.75968062261259e-41 37 CD8 +5.24757172988244e-13 0.263336896623814 1 1 6.82184324884717e-12 37 CD45RA +0.00411967300711807 0.251455582065055 1 1 0.0535557490925349 37 CD3 +5.08213840057668e-09 0.388143218090763 1 1 6.60677992074969e-08 38 CD3 +5.78899385075161e-07 0.325099136996257 1 1 7.52569200597709e-06 38 CD4 +4.66505722311064e-22 0.586604170424365 1 1 6.06457439004383e-21 39 CD3 +3.76660069557731e-21 0.514611202436318 1 1 4.8965809042505e-20 39 CD4 +5.55663908351586e-38 0.515577202059993 1 1 7.22363080857062e-37 40 CD45RA +6.27348968932591e-32 0.472480692520507 1 1 8.15553659612369e-31 40 CD16 +1.42947043118412e-28 0.415013457906016 1 1 1.85831156053936e-27 40 CD56 +1.8793375763755e-14 0.352665542997354 1 1 2.44313884928815e-13 40 CD8 +5.6008185645827e-24 0.602331877466961 1 1 7.2810641339575e-23 41 CD11c +2.57123247695116e-20 0.285387697218841 1 1 3.34260222003651e-19 41 CD14 +1.49095077292205e-14 0.49697275611693 1 1 1.93823600479867e-13 43 CD4 +2.08946196531086e-14 0.555739574445692 1 1 2.71630055490412e-13 43 CD3 +2.19758957676378e-05 0.399823538718023 1 1 0.000285686644979291 44 CD3 +6.14864318795116e-05 0.326473015534509 1 1 0.00079932361443365 44 CD4 +1.27620616488274e-20 0.48718207480276 1 1 1.65906801434756e-19 46 CD45RA +5.73473851777945e-19 0.463918420273511 1 1 7.45516007311328e-18 46 CD16 +8.88217928924765e-16 0.402449826305318 1 1 1.15468330760219e-14 46 CD56 +3.86899212782144e-09 0.403347559498734 1 1 5.02968976616787e-08 46 CD8 +7.82441161756527e-14 0.54974339100417 1 1 1.01717351028348e-12 47 CD4 +1.64611664916494e-12 0.593590803126451 1 1 2.13995164391443e-11 47 CD3 +1.50261128404362e-08 0.444698278386498 1 1 1.9533946692567e-07 48 CD4 +3.0693920280249e-08 0.485806405732138 1 1 3.99020963643237e-07 48 CD3 +3.75064021004935e-05 0.426060220487989 1 1 0.000487583227306415 49 CD3 +0.000142612327520314 0.368345962674295 1 1 0.00185396025776409 49 CD4 +1.75303069982881e-08 0.553523232257216 1 1 2.27893990977745e-07 50 CD3 +2.92205657488682e-07 0.472836909811648 1 1 3.79867354735287e-06 50 CD4 +1.58132516634947e-07 0.546611394241725 1 1 2.05572271625431e-06 52 CD3 +1.9461168179332e-07 0.488063324884708 1 1 2.52995186331316e-06 52 CD4 +8.03593559106167e-08 0.569767489448342 1 1 1.04467162683802e-06 54 CD3 +1.06870991801859e-06 0.487932704728795 1 1 1.38932289342417e-05 54 CD4 +0.000814556186990549 0.351686671472014 1 1 0.0105892304308771 56 CD3 +2.51009951330222e-06 0.493665228200334 1 1 3.26312936729289e-05 57 CD4 +2.42776604502913e-05 0.523629664434363 1 1 0.000315609585853786 57 CD3 +5.42134770798451e-06 0.496080353437594 1 1 7.04775202037986e-05 58 CD4 +4.89589551780272e-05 0.519918267191007 1 1 0.000636466417314353 58 CD3 +1.06083275668956e-05 0.518183248473891 1 1 0.000137908258369643 59 CD3 +2.28373871872614e-05 0.448662008549807 1 1 0.000296886033434398 59 CD4 +2.95127375391735e-07 0.545865093820575 1 1 3.83665588009256e-06 60 CD4 +6.89510261130472e-07 0.5873278673037 1 1 8.96363339469613e-06 60 CD3 +5.96266228093642e-07 0.6022052282127 1 1 7.75146096521734e-06 61 CD3 +2.05697616928793e-05 0.492874477040793 1 1 0.00026740690200743 61 CD4 +4.40285876196449e-05 0.50357982780149 1 1 0.000572371639055384 62 CD3 +0.00232951066979824 0.369528572352012 1 1 0.0302836387073771 62 CD4 +0.0032270997397837 0.343040055579376 1 1 0.0419522966171881 63 CD4 +0.00444570306598577 0.373769928678549 1 1 0.057794139857815 63 CD3 +0.00134937804457614 0.409801469287103 1 1 0.0175419145794898 64 CD3 +6.14108702172555e-07 0.526255271530294 1 1 7.98341312824321e-06 65 CD4 +4.59012879700512e-06 0.564101106006382 1 1 5.96716743610665e-05 65 CD3 +0.000265824057131672 0.474857735628406 1 1 0.00345571274271173 66 CD3 +0.00165866588427592 0.408084027476855 1 1 0.021562656495587 66 CD4 +0.000236342795052248 0.458031750173302 1 1 0.00307245633567922 67 CD3 +0.00268645559141873 0.374370937282443 1 1 0.0349239226884434 67 CD4 +2.3591660433204e-05 0.543103607805673 1 1 0.000306691585631652 69 CD3 +0.000647898842261096 0.415466628025077 1 1 0.00842268494939425 69 CD4 +0.000517321179939829 0.449086058194056 1 1 0.00672517533921778 70 CD3 +0.00369469052975548 0.372007896439794 1 1 0.0480309768868212 70 CD4 |
| b |
| diff -r c0fd285eb553 -r fab6ff46e019 test-data/rna.tab.gz |
| b |
| Binary file test-data/rna.tab.gz has changed |
| b |
| diff -r c0fd285eb553 -r fab6ff46e019 test-data/rna_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rna_out.tsv Fri Jul 07 01:43:02 2023 +0000 |
| b |
| b'@@ -0,0 +1,582 @@\n+p_val\tavg_log2FC\tpct.1\tpct.2\tp_val_adj\tcluster\tgene\n+0\t6.05663691346878\t1\t0.014\t0\t0\tCD9\n+1.9822323994606e-32\t0.892085602138872\t0.845\t0.67\t5.33220515454903e-30\t0\tCD74\n+1.15168092712414e-08\t0.478645233478619\t0.323\t0.19\t3.09802169396393e-06\t0\tCD36\n+2.8479031688574e-07\t0.475224325321269\t0.342\t0.22\t7.66085952422642e-05\t0\tCD68\n+1.19367791108326e-06\t0.319116267570157\t0.356\t0.236\t0.000321099358081397\t0\tCD14\n+1.25526626910762e-300\t2.55646528238641\t0.997\t0.174\t3.37666626389951e-298\t1\tCD247\n+4.9467417746979e-104\t1.38113679016585\t1\t0.491\t1.33067353739374e-101\t1\tCD7\n+3.26887578464599e-22\t0.738081621550979\t0.711\t0.447\t8.79327586069771e-20\t1\tCD3D\n+1.67975517808425e-21\t0.6897744848159\t0.646\t0.375\t4.51854142904665e-19\t1\tCD3E\n+5.06329852867774e-18\t0.772122890497265\t0.523\t0.295\t1.36202730421431e-15\t1\tCD3G\n+1.27114026491996e-14\t0.540176080901698\t0.729\t0.537\t3.41936731263469e-12\t1\tCD69\n+4.22106923632502e-12\t0.628229473292235\t0.431\t0.256\t1.13546762457143e-09\t1\tCD27\n+1.59191271885828e-09\t0.923324279812694\t0.28\t0.161\t4.28224521372878e-07\t1\tCD96\n+6.33331731091395e-06\t0.635612480130467\t0.3\t0.202\t0.00170366235663585\t1\tCD2\n+1.2084710019556e-05\t0.652639529253708\t0.266\t0.176\t0.00325078699526057\t1\tAAK1\n+7.18353005289289e-05\t0.45395573069296\t0.36\t0.264\t0.0193236958422819\t1\tCDC42SE2\n+0\t7.28866683945211\t1\t0.01\t0\t2\tCDC34\n+6.2438029160881e-11\t0.287473417951871\t0.837\t0.671\t1.6795829844277e-08\t2\tCD74\n+1.67553729019084e-291\t2.5252687279094\t1\t0.161\t4.50719531061337e-289\t3\tCDC42SE1\n+1.81222647838563e-48\t0.774911191999161\t1\t0.494\t4.87488922685735e-46\t3\tCD7\n+1.59722179115194e-38\t0.979326889347329\t0.758\t0.372\t4.29652661819873e-36\t3\tCD3E\n+7.84242124211886e-35\t0.885592128425985\t0.81\t0.444\t2.10961131412997e-32\t3\tCD3D\n+1.99915714824053e-33\t1.11040695652189\t0.611\t0.293\t5.37773272876704e-31\t3\tCD3G\n+2.3333724887806e-29\t1.01503304498776\t0.549\t0.252\t6.27677199481982e-27\t3\tCD27\n+1.04002760149565e-21\t0.661402834305967\t0.833\t0.534\t2.79767424802329e-19\t3\tCD69\n+2.11673614992016e-20\t0.44565536712769\t0.961\t0.849\t5.69402024328522e-18\t3\tCD52\n+4.16399404112572e-16\t1.17812983627874\t0.261\t0.108\t1.12011439706282e-13\t3\tCD6\n+6.12847805829085e-12\t0.906143067361228\t0.307\t0.156\t1.64856059768024e-09\t3\tCCR7\n+3.64114850082905e-09\t0.669170386110504\t0.346\t0.2\t9.79468946723015e-07\t3\tCD2\n+4.14796430174784e-09\t0.753573810220556\t0.294\t0.161\t1.11580239717017e-06\t3\tCD96\n+1.5417100566513e-06\t0.656281233809736\t0.284\t0.175\t0.0004147200052392\t3\tAAK1\n+3.81221452867488e-06\t0.523887078268232\t0.382\t0.264\t0.00102548570821354\t3\tCDC42SE2\n+3.97949109644182e-05\t0.443250782597945\t0.379\t0.271\t0.0107048310494285\t3\tCCT3\n+0.000406152806467521\t0.369291108612562\t0.376\t0.279\t0.109255104939763\t3\tCCT4\n+2.86179772528272e-140\t1.69823655981722\t1\t0.494\t7.69823588101052e-138\t4\tCD7\n+5.75083718491135e-41\t1.12108078531178\t0.734\t0.373\t1.54697520274115e-38\t4\tCD3E\n+2.87854133026334e-40\t0.975825622716567\t0.826\t0.444\t7.74327617840839e-38\t4\tCD3D\n+3.21739743549182e-23\t0.915070086700084\t0.566\t0.294\t8.65479910147299e-21\t4\tCD3G\n+1.07571393161663e-22\t0.703404470988817\t0.809\t0.535\t2.89367047604873e-20\t4\tCD69\n+5.66376326372948e-21\t0.998065485935792\t0.493\t0.254\t1.52355231794323e-18\t4\tCD27\n+5.60713087816813e-17\t0.410160383521315\t0.967\t0.849\t1.50831820622723e-14\t4\tCD52\n+5.74774963343849e-14\t1.097599612095\t0.309\t0.156\t1.54614465139495e-11\t4\tCCR7\n+4.99928644683509e-12\t0.95149999528962\t0.355\t0.2\t1.34480805419864e-09\t4\tCD2\n+7.61741524350528e-07\t0.566723778496881\t0.388\t0.27\t0.000204908470050292\t4\tCCT3\n+0.00597813707088682\t0.325303001531855\t0.28\t0.217\t1\t4\tCCT2\n+0\t6.3624837958636\t1\t0.012\t0\t5\tABCB7\n+0\t3.58747133818528\t0.88\t0.073\t0\t6\tABI3\n+1.42748858021799e-58\t1.53828071963406\t0.634\t0.212\t3.83994428078639e-56\t6\tCD68\n+1.07762676060828e-50\t1.09102064840927\t0.942\t0.669\t2.89881598603628e-48\t6\tCD74\n+5.07731529501781e-32\t1.3974890987987\t0.33\t0.1\t1.36579781435979e-29\t6\tCD86\n+6.97336181247085e-29\t1.45563803514765\t0.293\t0.088\t1.87583432755466e-26\t6\tCD300E\n+6.62536629976547e-23\t0.979237343350899\t0.507\t0.232\t1.78222353463691e-20\t6\tCD14\n+1.29879352423192'..b'8595059\t0.667\t0.262\t0.0300974343544684\t61\tCD27\n+0.000404998028111006\t1.14360651693177\t0.524\t0.205\t0.108944469561861\t61\tCD2\n+0.00325008416209062\t1.35697019849102\t0.524\t0.268\t0.874272639602378\t61\tCDC42SE2\n+0.00481829874618626\t0.98912520838801\t0.571\t0.303\t1\t61\tCD3G\n+0.00817202071604155\t0.642746565867117\t0.905\t0.544\t1\t61\tCD69\n+7.24611611446303e-06\t1.32003445589636\t0.857\t0.456\t0.00194920523479056\t62\tCD3D\n+0.000135130354289854\t1.63135403132032\t0.571\t0.262\t0.0363500653039708\t62\tCD27\n+0.00786163265781978\t0.814130760974114\t0.619\t0.409\t1\t62\tABRACL\n+0.00929561210732165\t0.991993254650952\t0.619\t0.385\t1\t62\tCD3E\n+0.00100151451502045\t0.985211935922848\t0.81\t0.544\t0.269407404540502\t63\tCD69\n+0.00140164320290821\t2.03211575223649\t0.429\t0.205\t0.377042021582309\t63\tCD2\n+0.0028110331662747\t0.966838796433823\t0.714\t0.457\t0.756167921727894\t63\tCD3D\n+0.0042739888518399\t1.42636035169469\t0.381\t0.179\t1\t63\tAAK1\n+0.00454958074894623\t0.836310251185253\t0.667\t0.385\t1\t63\tCD3E\n+0.00694858195731693\t0.557889545219698\t1\t0.853\t1\t63\tCD52\n+0.00714727517925193\t1.58210815517271\t0.333\t0.155\t1\t63\tABHD14B\n+0.00110319769218366\t0.903585518242311\t0.85\t0.544\t0.296760179197406\t64\tCD69\n+0.00148232064011444\t1.14761294230867\t0.75\t0.457\t0.398744252190784\t64\tCD3D\n+0.00642810796024993\t1.95574099974102\t0.35\t0.166\t1\t64\tCD96\n+2.42129765572733e-10\t2.00752214617334\t0.85\t0.261\t6.51329069390652e-08\t65\tCD27\n+5.76124142720778e-08\t2.03540694606857\t0.5\t0.113\t1.54977394391889e-05\t65\tCD6\n+3.25135565904384e-07\t2.85543958113225\t0.3\t0.051\t8.74614672282793e-05\t65\tCDCA7\n+8.43429615411452e-07\t2.21633445744274\t0.35\t0.07\t0.000226882566545681\t65\tABT1\n+3.53415724250826e-05\t1.05714306727267\t0.85\t0.385\t0.00950688298234722\t65\tCD3E\n+0.000140898983429988\t1.04671232639444\t0.9\t0.544\t0.0379018265426667\t65\tCD69\n+0.000283242576302817\t0.793604334287641\t0.95\t0.456\t0.0761922530254577\t65\tCD3D\n+0.00283529997397836\t0.514586942910608\t1\t0.853\t0.76269569300018\t65\tCD52\n+0.00340246674824964\t1.66926896855698\t0.25\t0.077\t0.915263555279153\t65\tCD40LG\n+0.00420406168813611\t1.14034407827933\t0.4\t0.161\t1\t65\tCCR7\n+0.00827065968049449\t1.5203844891369\t0.35\t0.155\t1\t65\tABHD14B\n+1.089560479526e-06\t1.33753090935073\t0.895\t0.385\t0.000293091768992493\t66\tCD3E\n+1.4129844504618e-06\t1.5789233757261\t0.737\t0.262\t0.000380092817174226\t66\tCD27\n+6.50886453713584e-05\t1.91249503683349\t0.368\t0.099\t0.0175088456048954\t66\tCCSER2\n+0.000131192836723538\t1.01054714777336\t0.895\t0.456\t0.0352908730786317\t66\tCD3D\n+0.000310537463949175\t0.907993053471882\t0.947\t0.544\t0.0835345778023282\t66\tCD69\n+0.00119147122927957\t0.608040991330872\t1\t0.853\t0.320505760676203\t66\tCD52\n+0.00151344246528663\t1.40627428091189\t0.421\t0.161\t0.407116023162102\t66\tCCR7\n+0.00770613574973099\t0.965383360144156\t0.421\t0.179\t1\t66\tAAK1\n+1.99394300815168e-06\t1.67397188957183\t0.842\t0.385\t0.000536370669192802\t67\tCD3E\n+0.00721868484936139\t1.36363253432037\t0.474\t0.262\t1\t67\tCD27\n+0.00877685171030327\t1.77884134972083\t0.263\t0.099\t1\t67\tCCSER2\n+0.000121082194768989\t1.42934247953002\t0.474\t0.16\t0.0325711103928581\t68\tCCR7\n+0.000653422794496296\t0.683045963502556\t1\t0.853\t0.175770731719504\t68\tCD52\n+0.00138765394116794\t1.30303667873644\t0.684\t0.385\t0.373278910174175\t68\tCD3E\n+0.00227347524038789\t0.954888155764406\t0.789\t0.544\t0.611564839664343\t68\tCD69\n+0.00270991774514855\t1.19273307152492\t0.579\t0.303\t0.728967873444959\t68\tCD3G\n+1.18945658282419e-05\t1.29850680560603\t0.895\t0.544\t0.00319963820779707\t69\tCD69\n+3.24568022150215e-05\t1.3633659373819\t0.737\t0.303\t0.00873087979584077\t69\tCD3G\n+0.0002195008780272\t1.07052905045681\t0.842\t0.457\t0.0590457361893169\t69\tCD3D\n+0.00703706170020798\t0.85755211311989\t0.684\t0.385\t1\t69\tCD3E\n+7.80489030433116e-05\t1.27349257904159\t0.778\t0.385\t0.0209951549186508\t70\tCD3E\n+0.00039423165375324\t1.08035764255708\t0.833\t0.457\t0.106048314859621\t70\tCD3D\n+0.000483402587592305\t0.975759148107562\t0.889\t0.544\t0.13003529606233\t70\tCD69\n+0.000554825609359925\t1.55708817466902\t0.556\t0.274\t0.14924808891782\t70\tCCT3\n+0.00375929385790544\t1.62746392034211\t0.444\t0.219\t1\t70\tCCT2\n+0.00391030643136033\t1.28281486642971\t0.444\t0.205\t1\t70\tCD2\n' |