# HG changeset patch
# User iuc
# Date 1730824451 0
# Node ID 2bfd55b87af3a9a3fa7af5c55cd3e3492d659ef7
# Parent  2af7c5086a96c23c1811ffb60a065be83fc69ac1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f

diff -r 2af7c5086a96 -r 2bfd55b87af3 macros.xml
--- a/macros.xml	Wed Aug 24 18:09:40 2022 +0000
+++ b/macros.xml	Tue Nov 05 16:34:11 2024 +0000
@@ -52,6 +52,11 @@
             <!-- <requirement type="package" version="1.6.2">bioconductor-scran</requirement> -->
         </requirements>
     </macro>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">RaceID</xref>
+        </xrefs>
+      </xml>
     <macro name="yesno_checkedno" >
         <option value="yes" >Yes</option>
         <option value="no" selected="true" >No</option>
diff -r 2af7c5086a96 -r 2bfd55b87af3 raceid_trajectory.xml
--- a/raceid_trajectory.xml	Wed Aug 24 18:09:40 2022 +0000
+++ b/raceid_trajectory.xml	Tue Nov 05 16:34:11 2024 +0000
@@ -4,6 +4,7 @@
         <import>macros.xml</import>
         <import>macros_cheetah.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command_config" prog="pseudotemporal.R" cheetah="TRAJECTORY_CHEETAH" />
 
@@ -136,7 +137,7 @@
 
 StemID is an algorithm for the inference of lineage trees and differentiation trajectories based on pseudo-temporal ordering of single-cell transcriptomes. It utilizies the clusters predicted by RaceID clustering tool.
 
-In a nutshell, StemID infers links between clusters which are more populated with intermediate single-cell transcriptomes than expected by chance. 
+In a nutshell, StemID infers links between clusters which are more populated with intermediate single-cell transcriptomes than expected by chance.
 
 This will generate an RDS object, and a PDF showing a minimal spanning tree between the clusters, with the strength between clusters given by the colour and thickness of the branches.
 
diff -r 2af7c5086a96 -r 2bfd55b87af3 scripts/cluster.R
--- a/scripts/cluster.R	Wed Aug 24 18:09:40 2022 +0000
+++ b/scripts/cluster.R	Tue Nov 05 16:34:11 2024 +0000
@@ -4,8 +4,8 @@
 args <- commandArgs(trailingOnly = TRUE)
 
 if (length(args) != 1) {
-     message(paste("VERSION:", VERSION))
-     stop("Please provide the config file")
+    message(paste("VERSION:", VERSION))
+    stop("Please provide the config file")
 }
 
 suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
@@ -17,8 +17,9 @@
     if (!is.null(filt.lbatch.regexes)) {
         lar <- filt.lbatch.regexes
         nn <- colnames(sc@expdata)
-        filt$LBatch <- lapply(1:length(lar), function(m) {  # nolint
-            return(nn[grep(lar[[m]], nn)])})
+        filt$LBatch <- lapply(1:length(lar), function(m) { # nolint
+            return(nn[grep(lar[[m]], nn)])
+        })
     }
 
     sc <- do.call(filterdata, c(sc, filt))
@@ -44,9 +45,12 @@
     unq <- unique(filt_feat)
     if (length(unq) == 1) {
         abline(v = unq, col = "red", lw = 2)
-        text(tmp$mids, table(filt_feat)[[1]] - 100, pos = 1,
-             paste(10^unq, "\nFeatures\nin remaining\nCells",
-                   sep = ""), cex = 0.8)
+        text(tmp$mids, table(filt_feat)[[1]] - 100,
+            pos = 1,
+            paste(10^unq, "\nFeatures\nin remaining\nCells",
+                sep = ""
+            ), cex = 0.8
+        )
     }
 
     if (filt.use.ccorrect) {
@@ -80,7 +84,7 @@
     ## Heatmaps
     test1 <- list()
     test1$side <- 3
-    test1$line <- 0  #1 #3
+    test1$line <- 0 # 1 #3
 
     x <- clustheatmap(sc, final = FALSE)
     print(do.call(mtext, c(paste("(Initial)"), test1)))
@@ -122,8 +126,10 @@
         test$line <- -1
         print(do.call(mtext, c(paste(buffer, "Sig. Genes"), test)))
         test$line <- 0
-        print(do.call(mtext, c(paste(buffer, "(fc > ",
-                                     genelist.foldchange, ")"), test)))
+        print(do.call(mtext, c(paste(
+            buffer, "(fc > ",
+            genelist.foldchange, ")"
+        ), test)))
     })
     write.table(df, file = out.genelist, sep = "\t", quote = FALSE)
 }
@@ -131,14 +137,18 @@
 
 writecellassignments <- function(sc) {
     dat <- sc@cluster$kpart
-    tab <- data.frame(row.names = NULL,
-                      cells = names(dat),
-                      cluster.initial = dat,
-                      cluster.final = sc@cpart,
-                      is.outlier = names(dat) %in% sc@out$out)
+    tab <- data.frame(
+        row.names = NULL,
+        cells = names(dat),
+        cluster.initial = dat,
+        cluster.final = sc@cpart,
+        is.outlier = names(dat) %in% sc@out$out
+    )
 
-    write.table(tab, file = out.assignments, sep = "\t",
-                quote = FALSE, row.names = FALSE)
+    write.table(tab,
+        file = out.assignments, sep = "\t",
+        quote = FALSE, row.names = FALSE
+    )
 }
 
 
@@ -146,19 +156,29 @@
 
 if (use.filtnormconf) {
     sc <- do.filter(sc)
-    message(paste(" - Source:: genes:", nrow(sc@expdata),
-                  ", cells:", ncol(sc@expdata)))
-    message(paste(" - Filter:: genes:", nrow(as.matrix(getfdata(sc))),
-                  ", cells:", ncol(as.matrix(getfdata(sc)))))
-    message(paste("         :: ",
-                  sprintf("%.1f", 100 * nrow(as.matrix(
-                                            getfdata(sc))) / nrow(sc@expdata)),
-                  "% of genes remain,",
-                  sprintf("%.1f", 100 * ncol(as.matrix(
-                                            getfdata(sc))) / ncol(sc@expdata)),
-                  "% of cells remain"))
-    write.table(as.matrix(sc@ndata), file = out.table, col.names = NA,
-                row.names = TRUE, sep = "\t", quote = FALSE)
+    message(paste(
+        " - Source:: genes:", nrow(sc@expdata),
+        ", cells:", ncol(sc@expdata)
+    ))
+    message(paste(
+        " - Filter:: genes:", nrow(as.matrix(getfdata(sc))),
+        ", cells:", ncol(as.matrix(getfdata(sc)))
+    ))
+    message(paste(
+        "         :: ",
+        sprintf("%.1f", 100 * nrow(as.matrix(
+            getfdata(sc)
+        )) / nrow(sc@expdata)),
+        "% of genes remain,",
+        sprintf("%.1f", 100 * ncol(as.matrix(
+            getfdata(sc)
+        )) / ncol(sc@expdata)),
+        "% of cells remain"
+    ))
+    write.table(as.matrix(sc@ndata),
+        file = out.table, col.names = NA,
+        row.names = TRUE, sep = "\t", quote = FALSE
+    )
 }
 
 if (use.cluster) {
diff -r 2af7c5086a96 -r 2bfd55b87af3 scripts/clusterinspect.R
--- a/scripts/clusterinspect.R	Wed Aug 24 18:09:40 2022 +0000
+++ b/scripts/clusterinspect.R	Tue Nov 05 16:34:11 2024 +0000
@@ -1,11 +1,11 @@
 #!/usr/bin/env R
-VERSION <- "0.5"  # nolint
+VERSION <- "0.5" # nolint
 
 args <- commandArgs(trailingOnly = TRUE)
 
 if (length(args) != 1) {
-     message(paste("VERSION:", VERSION))
-     stop("Please provide the config file")
+    message(paste("VERSION:", VERSION))
+    stop("Please provide the config file")
 }
 
 suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
@@ -49,15 +49,18 @@
 }
 
 
-do.inspect.symbolmap <- function(sc) {  # nolint
+do.inspect.symbolmap <- function(sc) { # nolint
     if (!is.null(plotsym.use.typeremoveregex)) {
-        plotsym$types <- sub(plotsym.use.typeremoveregex, "",
-                             colnames(sc@ndata))
+        plotsym$types <- sub(
+            plotsym.use.typeremoveregex, "",
+            colnames(sc@ndata)
+        )
 
         if (!is.null(plotsym.use.typeremoveregex.subselect)) {
             plotsym$subset <- plotsym$types[grep(
-                                          plotsym.use.typeremoveregex.subselect,
-                                          plotsym$types)]
+                plotsym.use.typeremoveregex.subselect,
+                plotsym$types
+            )]
         }
     }
     plotsym$fr <- FALSE
@@ -68,16 +71,16 @@
     print(do.call(mtext, c("Symbols FR", test)))
 }
 
-do.inspect.diffgene <- function(sc) {  # nolint
+do.inspect.diffgene <- function(sc) { # nolint
 
-    getSubNames <- function(lob, sc) {  # nolint
+    getSubNames <- function(lob, sc) { # nolint
         use_names <- NULL
         if (!is.null(lob$manual)) {
             use_names <- lob$manual
-        }else if (!is.null(lob$regex)) {
+        } else if (!is.null(lob$regex)) {
             nm <- colnames(sc@ndata)
             use_names <- nm[grep(lob$regex, nm)]
-        }else if (!is.null(lob$cln)) {
+        } else if (!is.null(lob$cln)) {
             use_names <- names(sc@cpart)[sc@cpart %in% lob$cln]
         }
         if (is.null(use_names)) {
@@ -98,7 +101,7 @@
 }
 
 
-do.inspect.genesofinterest <- function(sc) {  # nolint
+do.inspect.genesofinterest <- function(sc) { # nolint
     if (is.null(plotexp$n)) { ## No title, and one gene? Use gene name
         if (length(plotexp$g) == 1) {
             plotexp$n <- plotexp$g
diff -r 2af7c5086a96 -r 2bfd55b87af3 scripts/pseudotemporal.R
--- a/scripts/pseudotemporal.R	Wed Aug 24 18:09:40 2022 +0000
+++ b/scripts/pseudotemporal.R	Tue Nov 05 16:34:11 2024 +0000
@@ -4,8 +4,8 @@
 args <- commandArgs(trailingOnly = T) # nolint
 
 if (length(args) != 1) {
-     message(paste("VERSION:", VERSION))
-     stop("Please provide the config file")
+    message(paste("VERSION:", VERSION))
+    stop("Please provide the config file")
 }
 
 suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
@@ -29,20 +29,31 @@
     ltr <- do.call(comppvalue, c(ltr, pstc.comppval))
     x <- do.call(compscore, c(ltr, pstc.compscore))
     print(do.call(mtext, c("Compute Score", test)))
-    print(do.call(mtext, c(paste0("No. of inter-cluster links / ",
-                                  "Delta median entropy of each cluster / ",
-                                  "StemID2 score (combination of both)"),
-                           second)))
+    print(do.call(mtext, c(
+        paste0(
+            "No. of inter-cluster links / ",
+            "Delta median entropy of each cluster / ",
+            "StemID2 score (combination of both)"
+        ),
+        second
+    )))
     plotdistanceratio(ltr)
     print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test)))
-    print(do.call(mtext, c("Original vs High-dimensional Embedded Space",
-                           second)))
+    print(do.call(mtext, c(
+        "Original vs High-dimensional Embedded Space",
+        second
+    )))
     do.call(plotgraph, c(ltr, pstc.plotgraph))
     print(do.call(mtext, c(paste0(c("Lineage Trajectories", rep(" ", 54)),
-                                  collapse = ""), test)))
-    print(do.call(mtext, c(paste0(c(paste0("Colour = Level of Significance, ",
-                                           "Width = Link Score"),
-                                    rep(" ", 106)), collapse = ""), second)))
+        collapse = ""
+    ), test)))
+    print(do.call(mtext, c(paste0(c(
+        paste0(
+            "Colour = Level of Significance, ",
+            "Width = Link Score"
+        ),
+        rep(" ", 106)
+    ), collapse = ""), second)))
     plotspantree(ltr)
     print(do.call(mtext, c("Minimum Spanning Tree", test)))
     plotspantree(ltr, projections = TRUE)
diff -r 2af7c5086a96 -r 2bfd55b87af3 scripts/trajectoryinspect.R
--- a/scripts/trajectoryinspect.R	Wed Aug 24 18:09:40 2022 +0000
+++ b/scripts/trajectoryinspect.R	Tue Nov 05 16:34:11 2024 +0000
@@ -4,8 +4,8 @@
 args <- commandArgs(trailingOnly = TRUE)
 
 if (length(args) != 1) {
-     message(paste("VERSION:", VERSION))
-     stop("Please provide the config file")
+    message(paste("VERSION:", VERSION))
+    stop("Please provide the config file")
 }
 
 suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
@@ -34,7 +34,8 @@
     )
     write.table(
         head(bra$diffgenes$z, trjsid.numdiffgenes),
-        file = out.diffgenes)
+        file = out.diffgenes
+    )
 
     par(mfrow = c(3, 2), cex = 0.5)
     print(do.call(plotmap, c(bra$scl, final = FALSE, fr = FALSE)))
@@ -63,7 +64,7 @@
     trjfid_procsom$s1d <- s1d
     ps <- do.call(procsom, c(trjfid_procsom))
 
-    y    <- ltr@sc@cpart[n$f]
+    y <- ltr@sc@cpart[n$f]
     fcol <- ltr@sc@fcol
 
     trjfid_plotheat$xpart <- y
@@ -72,26 +73,32 @@
     test$side <- 3
     test$line <- 3
 
-    ##Plot average z-score for all modules derived from the SOM:
+    ## Plot average z-score for all modules derived from the SOM:
     trjfid_plotheat$x <- ps$nodes.z
     trjfid_plotheat$ypart <- unique(ps$nodes)
     print(do.call(plotheatmap, c(trjfid_plotheat)))
-    print(do.call(mtext, c("Average z-score for all modules derived from SOM",
-                           test)))
-    ##Plot z-score profile of each gene ordered by SOM modules:
+    print(do.call(mtext, c(
+        "Average z-score for all modules derived from SOM",
+        test
+    )))
+    ## Plot z-score profile of each gene ordered by SOM modules:
     trjfid_plotheat$x <- ps$all.z
     trjfid_plotheat$ypart <- ps$nodes
     print(do.call(plotheatmap, c(trjfid_plotheat)))
-    print(do.call(mtext, c(paste0("z-score profile of each gene",
-                                  "ordered by SOM modules"), test)))
-    ##Plot normalized expression profile of each gene ordered by SOM modules:
+    print(do.call(mtext, c(paste0(
+        "z-score profile of each gene",
+        "ordered by SOM modules"
+    ), test)))
+    ## Plot normalized expression profile of each gene ordered by SOM modules:
     trjfid_plotheat$x <- ps$all.e
     trjfid_plotheat$ypart <- ps$nodes
     print(do.call(plotheatmap, c(trjfid_plotheat)))
-    print(do.call(mtext, c(paste0("Normalized expression profile of each",
-                                  "gene ordered by SOM modules"), test)))
-    ##Plot binarized expression profile of each gene
-    ##(z-score < -1, -1 < z-score < 1, z-score > 1)
+    print(do.call(mtext, c(paste0(
+        "Normalized expression profile of each",
+        "gene ordered by SOM modules"
+    ), test)))
+    ## Plot binarized expression profile of each gene
+    ## (z-score < -1, -1 < z-score < 1, z-score > 1)
     trjfid_plotheat$x <- ps$all.b
     trjfid_plotheat$ypart <- ps$nodes
     print(do.call(plotheatmap, c(trjfid_plotheat)))