upgrade gsc_scran_normalize (#652)

* upgrade scran conda package

* Install dynamicTreeCut conda package now required by scran

* replace deprecated "normalize" by logNormCounts function of scran

* Update scran-normalize.R

* update .shed.yml with repo url

* update all tests

tools/gsc_scran_normalize/.shed.yml

@@ -7,6 +7,6 @@ long_description: |
 categories:
   - Transcriptomics
 homepage_url: http://artbio.fr
-remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize
+remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize
 toolshed:
   - toolshed

tools/gsc_scran_normalize/scran-normalize.R

@@ -1,15 +1,15 @@
-# load packages that are provided in the conda env
 options(show.error.messages = FALSE,
   error = function() {
     cat(geterrmessage(), file = stderr())
     q("no", 1, FALSE)
-    }
+  }
 )
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 warnings()
 
 library(optparse)
 library(scran)
+library(dynamicTreeCut)
 
 # Arguments
 option_list <- list(
@@ -19,12 +19,6 @@ option_list <- list(
     type = "character",
     help = "Input file that contains count values to transform"
   ),
-  make_option(
-    c("-s", "--sep"),
-    default = "\t",
-    type = "character",
-    help = "File separator [default : '%default' ]"
-  ),
   make_option(
     "--cluster",
     default = FALSE,
@@ -53,18 +47,15 @@ option_list <- list(
 )
 
 opt <- parse_args(OptionParser(option_list = option_list),
-                 args = commandArgs(trailingOnly = TRUE))
+                  args = commandArgs(trailingOnly = TRUE))
 
-if (opt$sep == "tab") {
-  opt$sep <- "\t"
-  }
 
 data <- read.table(
   opt$data,
   check.names = FALSE,
   header = TRUE,
   row.names = 1,
-  sep = opt$sep
+  sep = "\t"
 )
 
 ## Import data as a SingleCellExperiment object
@@ -81,7 +72,7 @@ if (opt$cluster) {
   sce <- computeSumFactors(sce)
 }
 
-sce <- normalize(sce)
+sce <- logNormCounts(sce)
 
 logcounts <- data.frame(genes = rownames(sce), round(logcounts(sce), digits = 5), check.names = FALSE)
 

tools/gsc_scran_normalize/scran_normalize.xml

@@ -1,16 +1,16 @@
-<tool id="scran_normalize" name="scran_normalize" version="0.2.1">
+<tool id="scran_normalize" name="scran_normalize" version="1.28.1+galaxy0">
     <description>Normalize raw counts expression values using deconvolution size factors</description>
     <requirements>
-        <requirement type="package" version="1.6.2">r-optparse</requirement>
-        <requirement type="package" version="1.12.1=r36he1b5a44_0">bioconductor-scran</requirement>
+        <requirement type="package" version="1.28.1">bioconductor-scran</requirement>
+        <requirement type="package" version="1.63_1">r-dynamictreecut</requirement>
+        <requirement type="package" version="1.7.3">r-optparse</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Tool exception" />
     </stdio>
     <command detect_errors="exit_code"><![CDATA[ 
         Rscript $__tool_directory__/scran-normalize.R 
             --data '$input'
-            --sep '$input_sep' 
             #if $metacell.cluster == "Yes":
                 --cluster
                 --method '$metacell.method'
@@ -19,11 +19,7 @@
             -o '${output}'
 ]]></command>
     <inputs>
-        <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data" help = "Must have an header"/>
-        <param name="input_sep" type="select" label="Input column separator">
-            <option value="tab" selected="true">Tabulation</option>
-            <option value=",">Comma</option>
-        </param>
+        <param name="input" type="data" format="tabular" label="Raw counts of expression data" help = "A tsv file that must have an header line"/>
         <conditional name="metacell">
             <param name="cluster" type="select" label = "Do you want to cluster cells ?" help="Perform scaling method on metacell, see Details">
                 <option value="Yes">Yes</option>
@@ -45,18 +41,18 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="counts.tab" ftype="tabular"/>
-            <output name="output" file="logcounts.tab" ftype="tabular"/>
+            <param name="input" value="counts.tsv" ftype="tabular"/>
+            <output name="output" file="logcounts.tsv" ftype="tabular"/>
         </test>
         <test>
-            <param name="input" value="counts.tab" ftype="tabular"/>
+            <param name="input" value="counts.tsv" ftype="tabular"/>
             <param name="cluster" value="Yes"/>
             <param name="method" value="igraph"/>
             <param name="size" value="25"/>
             <output name="output" file="logcounts_igraph.tsv" ftype="tabular"/>
         </test>
         <test>
-            <param name="input" value="counts.tab" ftype="tabular"/>
+            <param name="input" value="counts.tsv" ftype="tabular"/>
             <param name="cluster" value="Yes"/>
             <param name="method" value="hclust"/>
             <param name="size" value="25"/>