Mercurial > repos > iuc > sleuth

changeset 3:2c3d294dbe42 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 4adb19064a6973121680119529444286c24c1ac1
author iuc
date Mon, 02 Jun 2025 21:31:22 +0000
parents d6b5fc94062c
children
files macros.xml sleuth.R sleuth.xml
diffstat 3 files changed, 103 insertions(+), 92 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Jun 08 19:57:53 2023 +0000
+++ b/macros.xml	Mon Jun 02 21:31:22 2025 +0000
@@ -3,13 +3,13 @@
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">r-sleuth</requirement>
             <requirement type="package" version="0.2.0">r-annotables</requirement>
-            <requirement type="package" version="2.2.1">r-argparse</requirement>
+            <requirement type="package" version="2.2.5">r-argparse</requirement>
             <requirement type="package" version="2.0.0">r-tidyverse</requirement>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.30.1</token>
-    <token name="@SUFFIX_VERSION@">2</token>
-    <token name="@PROFILE@">20.01</token>
+    <token name="@TOOL_VERSION@">0.30.2</token>
+    <token name="@SUFFIX_VERSION@">0</token>
+    <token name="@PROFILE@">23.2</token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1038/nmeth.4324</citation>
--- a/sleuth.R	Thu Jun 08 19:57:53 2023 +0000
+++ b/sleuth.R	Mon Jun 02 21:31:22 2025 +0000
@@ -1,6 +1,7 @@
 library(sleuth,
-        quietly = TRUE,
-        warn.conflicts = FALSE)
+    quietly = TRUE,
+    warn.conflicts = FALSE
+)
 library(annotables, quietly = TRUE, warn.conflicts = FALSE)
 library(argparse, quietly = TRUE, warn.conflicts = FALSE)
 library(tidyverse)
@@ -8,11 +9,11 @@
 
 # setup R error handling to go to stderr
 options(
-  show.error.messages = FALSE,
-  error = function() {
-    cat(geterrmessage(), file = stderr())
-    q("no", 1, FALSE)
-  }
+    show.error.messages = FALSE,
+    error = function() {
+        cat(geterrmessage(), file = stderr())
+        q("no", 1, FALSE)
+    }
 )
 
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
@@ -28,113 +29,123 @@
 
 parser$add_argument("--factorLevel", action = "append", required = FALSE)
 parser$add_argument("--factorLevel_counts",
-                    action = "append",
-                    required = FALSE)
-parser$add_argument("--factorLevel_n", action = "append",  required = FALSE)
-parser$add_argument("--cores",  type = "integer", required = FALSE)
+    action = "append",
+    required = FALSE
+)
+parser$add_argument("--factorLevel_n", action = "append", required = FALSE)
+parser$add_argument("--cores", type = "integer", required = FALSE)
 parser$add_argument("--normalize", action = "store_true", required = FALSE)
 parser$add_argument("--nbins", type = "integer", required = FALSE)
 parser$add_argument("--lwr", type = "numeric", required = FALSE)
 parser$add_argument("--upr", type = "numeric", required = FALSE)
 parser$add_argument("--metadata_file",
-                    action = "append",
-                    required = FALSE)
+    action = "append",
+    required = FALSE
+)
 parser$add_argument("--experiment_design", required = FALSE)
 
 args <- parser$parse_args()
 
 if (args$experiment_design == "complex") {
-  ## Complex experiment design
-  ############################
-
-  s2c  <-
-    read.table(file = args$metadata_file,
-               header = TRUE,
-               sep = "\t")
+    ## Complex experiment design
+    ############################
 
-  s2c$path <- file.path("./kallisto_outputs/", paste(s2c$path, ".h5", sep = ""))
-  for (f in args$factorLevel_counts) {
-    file.rename(f, paste(f, ".h5", sep = ""))
-  }
+    s2c <-
+        read.table(
+            file = args$metadata_file,
+            header = TRUE,
+            sep = "\t"
+        )
 
-  so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1)
-  so <- sleuth_fit(so)
+    s2c$path <- file.path("./kallisto_outputs/", paste(s2c$path, ".h5", sep = ""))
+    for (f in args$factorLevel_counts) {
+        file.rename(f, paste(f, ".h5", sep = ""))
+    }
 
+    so <- sleuth_prep(s2c, full_model = ~condition, num_cores = 1)
+    so <- sleuth_fit(so)
 } else {
-  ## Simple experiment design
-  ###########################
+    ## Simple experiment design
+    ###########################
 
-  conditions <- c()
-  for (x in seq_along(args$factorLevel)) {
-    temp <- append(conditions, rep(args$factorLevel[[x]]))
-    conditions <- temp
-  }
+    conditions <- c()
+    for (x in seq_along(args$factorLevel)) {
+        temp <- append(conditions, rep(args$factorLevel[[x]]))
+        conditions <- temp
+    }
 
-  sample_names <-
-    gsub(".fastq.+", "", basename(args$factorLevel_counts))
+    sample_names <-
+        gsub(".fastq.+", "", basename(args$factorLevel_counts))
 
-  design <-
-    data.frame(list(
-      sample = sample_names,
-      condition = conditions,
-      path = args$factorLevel_counts
-    ))
-  so <- sleuth_prep(design,
-                    cores = args$cores,
-                    normalize = args$normalize)
+    design <-
+        data.frame(list(
+            sample = sample_names,
+            condition = conditions,
+            path = args$factorLevel_counts
+        ))
+    so <- sleuth_prep(design,
+        cores = args$cores,
+        normalize = args$normalize
+    )
 }
 
 so <- sleuth_fit(
-  so,
-  ~ condition,
-  "full",
-  n_bins = args$nbins,
-  lwr = args$lwr,
-  upr = args$upr
+    so,
+    ~condition,
+    "full",
+    n_bins = args$nbins,
+    lwr = args$lwr,
+    upr = args$upr
 )
 
 so <- sleuth_fit(
-  so,
-  ~ 1,
-  "reduced",
-  n_bins = args$nbins,
-  lwr = args$lwr,
-  upr = args$upr
+    so,
+    ~1,
+    "reduced",
+    n_bins = args$nbins,
+    lwr = args$lwr,
+    upr = args$upr
 )
 
 so <- sleuth_lrt(so, "reduced", "full")
 
 sleuth_table <-
-  sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
+    sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
 
 write.table(
-  sleuth_table,
-  file = "sleuth_table.tab",
-  quote = FALSE,
-  sep = "\t",
-  col.names = TRUE,
-  row.names = FALSE
+    sleuth_table,
+    file = "sleuth_table.tab",
+    quote = FALSE,
+    sep = "\t",
+    col.names = TRUE,
+    row.names = FALSE
 )
 
 
 outputFile <- file.path(getwd(), "pca_plot.pdf")
-pdf(file = outputFile,
+pdf(
+    file = outputFile,
     height = 6,
-    width = 9)
+    width = 9
+)
 plot_pca(so, color_by = "condition")
 dev.off()
 
 outputFile <- file.path(getwd(), "group_density.pdf")
-pdf(file = outputFile,
+pdf(
+    file = outputFile,
     height = 6,
-    width = 9)
+    width = 9
+)
 plot_group_density(
-  so,
-  use_filtered = TRUE,
-  units = "est_counts",
-  trans = "log",
-  grouping = setdiff(colnames(so$sample_to_covariates),
-                     "sample"),
-  offset = 1
+    so,
+    use_filtered = TRUE,
+    units = "est_counts",
+    trans = "log",
+    grouping = setdiff(
+        colnames(so$sample_to_covariates),
+        "sample"
+    ),
+    offset = 1
 )
 dev.off()
--- a/sleuth.xml	Thu Jun 08 19:57:53 2023 +0000
+++ b/sleuth.xml	Mon Jun 02 21:31:22 2025 +0000
@@ -1,5 +1,5 @@
 <tool id="sleuth" name="Sleuth" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE@">
-    <description>differential expression analysis</description>
+    <description>Differential expression analysis</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -9,15 +9,15 @@
         <regex match="Execution halted"
            source="both"
            level="fatal"
-           description="Execution halted." />
+           description="Execution halted."/>
         <regex match="Error in"
            source="both"
            level="fatal"
-           description="An undefined error occurred, please check your input carefully and contact your administrator." />
+           description="An undefined error occurred, please check your input carefully and contact your administrator."/>
         <regex match="Fatal error"
            source="both"
            level="fatal"
-           description="An undefined error occurred, please check your input carefully and contact your administrator." />
+           description="An undefined error occurred, please check your input carefully and contact your administrator."/>
     </stdio>
     <version_command><![CDATA[echo $(R --version | grep version | grep -v GNU)", sleuth version" $(R --vanilla --slave -e "library(sleuth); cat(sessionInfo()\$otherPkgs\$sleuth\$Version)" 2> /dev/null | grep -v -i "WARNING: ")]]></version_command>
     <command><![CDATA[
@@ -74,7 +74,7 @@
                     <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
                         help="Only letters, numbers and underscores will be retained in this field">
                         <sanitizer>
-                            <valid initial="string.letters,string.digits"><add value="_" /></valid>
+                            <valid initial="string.letters,string.digits"><add value="_"/></valid>
                         </sanitizer>
                     </param>
                     <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/>
@@ -82,26 +82,26 @@
             </when>
             <when value="complex">
                 <param name="countsFile" type="data_collection" format="h5" multiple="true" label="Counts file(s)"/>
-                <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about the format of the design table in the help section." />
+                <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about the format of the design table in the help section."/>
             </when>
         </conditional>
         <section name="advanced_options" title="Advanced options" expanded="true">
             <param argument="normalization" type="boolean" truevalue="--normalize" falsevalue="" checked="true" label="Normalize data" 
                 help="If this is set to false, bootstraps will not be read and transformation of the data will not be done. This should 
-                    only be set to false if one desires to do a quick check of the raw data. " />
+                    only be set to false if one desires to do a quick check of the raw data. "/>
             <param argument="nbins" type="integer" min="0" value="100" label="NBins" help="The number of bins that the data should be 
-                split for the sliding window shrinkage using the mean-variance curve." />
+                split for the sliding window shrinkage using the mean-variance curve."/>
             <param argument="lwr" type="float" min="0" max="1" value="0.25" label="LWR" help="The lower range of variances within each 
-                bin that should be included for the shrinkage procedure. " />
+                bin that should be included for the shrinkage procedure. "/>
             <param argument="upr" type="float" min="0" max="1" value="0.75" label="UPR" help="The upper range of variances within each 
-                bin that should be included for the shrinkage procedure." />
+                bin that should be included for the shrinkage procedure."/>
         </section>
 
     </inputs>
     <outputs>
         <data name="sleuth_table" from_work_dir="sleuth_table.tab" format="tabular" label="${tool.name} on ${on_string}: DE table">
             <actions>
-                <action name="column_names" type="metadata" default="target_id,pval,qval,test_stat,rss,degrees_free,mean_obs,var_obs,tech_var,sigma_sq,smooth_sigma_sq,final_sigma_sq" />
+                <action name="column_names" type="metadata" default="target_id,pval,qval,test_stat,rss,degrees_free,mean_obs,var_obs,tech_var,sigma_sq,smooth_sigma_sq,final_sigma_sq"/>
             </actions>
         </data>
         <data name="pca_plot" from_work_dir="pca_plot.pdf" format="pdf" label="${tool.name} on ${on_string}: PCA plot"/>
@@ -154,7 +154,7 @@
             </section>
             <output name="sleuth_table" ftype="tabular">
                 <assert_contents>
-                    <has_size value="756310" delta="100"/>
+                    <has_size value="756425" delta="100"/>
                     <has_text text="ENST00000394894.8"/>
                     <has_text text="ENST00000524187.1"/>
                 </assert_contents>
@@ -183,7 +183,7 @@
             </section>
             <output name="sleuth_table" ftype="tabular">
                 <assert_contents>
-                    <has_size value="756310" delta="100"/>
+                    <has_size value="756425" delta="100"/>
                     <has_text text="ENST00000394894.8"/>
                     <has_text text="ENST00000524187.1"/>
                 </assert_contents>
@@ -230,5 +230,5 @@
 Additional factors can be included in the design table.
 
     ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>