# HG changeset patch
# User iuc
# Date 1686138450 0
# Node ID d3e447dd52c8310283f3cb947e129fb65e40889b
# Parent  5f1cb4c28d73684825e3cabe0b8d0de997bd4e3f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93

diff -r 5f1cb4c28d73 -r d3e447dd52c8 macros.xml
--- a/macros.xml	Thu Jun 01 07:56:00 2023 +0000
+++ b/macros.xml	Wed Jun 07 11:47:30 2023 +0000
@@ -8,7 +8,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">0.30.1</token>
-    <token name="@SUFFIX_VERSION@">0</token>
+    <token name="@SUFFIX_VERSION@">1</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="citations">
         <citations>
diff -r 5f1cb4c28d73 -r d3e447dd52c8 sleuth.R
--- a/sleuth.R	Thu Jun 01 07:56:00 2023 +0000
+++ b/sleuth.R	Wed Jun 07 11:47:30 2023 +0000
@@ -26,39 +26,67 @@
 # Collect arguments from command line
 parser <- ArgumentParser(description = "Sleuth R script")
 
-parser$add_argument("--factorLevel", action = "append", required = TRUE)
+parser$add_argument("--factorLevel", action = "append", required = FALSE)
 parser$add_argument("--factorLevel_counts",
                     action = "append",
-                    required = TRUE)
-parser$add_argument("--factorLevel_n", action = "append",  required = TRUE)
-parser$add_argument("--cores",  type = "integer", required = TRUE)
+                    required = FALSE)
+parser$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$add_argument("--nbins", type = "integer", required = TRUE)
-parser$add_argument("--lwr", type = "numeric", required = TRUE)
-parser$add_argument("--upr", type = "numeric", required = TRUE)
+parser$add_argument("--nbins", type = "integer", required = FALSE)
+parser$add_argument("--lwr", type = "numeric", required = FALSE)
+parser$add_argument("--upr", type = "numeric", required = FALSE)
+parser$add_argument("--metadata_file",
+                    action = "append",
+                    required = FALSE)
+parser$add_argument("--experiment_design", required = FALSE)
 
 args <- parser$parse_args()
 
-all_files <- args$factorLevel_counts
+if (args$experiment_design == "complex") {
+  ## Complex experiment design
+  ############################
 
-conditions <- c()
-for (x in seq_along(args$factorLevel)) {
-  temp <- append(conditions, rep(args$factorLevel[[x]]))
-  conditions <- temp
-}
+  s2c  <-
+    read.table(file = args$metadata_file,
+               header = TRUE,
+               sep = "\t")
+  paths <- c()
+  for (x in s2c$data_filename) {
+    paths <- c(paths, paste("./kallisto_outputs/",  x, sep = ""))
+  }
+  for (f in paths) {
+    file.rename(f, gsub(".fastq.*", "", f))
+        file.rename(f, paste(gsub(".fastq.*", "", f), ".h5", sep = ""))
+  }
+  s2c$path <- paste(gsub(".fastq.*", ".h5", paths), ".h5", sep = "")
+
+  so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1)
+  so <- sleuth_fit(so)
 
-sample_names <- all_files %>%
-  str_replace(pattern = "\\.tab", "")
+} else {
+  ## Simple experiment design
+  ###########################
+
+  conditions <- c()
+  for (x in seq_along(args$factorLevel)) {
+    temp <- append(conditions, rep(args$factorLevel[[x]]))
+    conditions <- temp
+  }
 
-design <-
-  data.frame(list(
-    sample = sample_names,
-    condition = conditions,
-    path = all_files
-  ))
-so <- sleuth_prep(design,
-                  cores = args$cores,
-                  normalize = args$normalize)
+  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)
+}
 
 so <- sleuth_fit(
   so,
diff -r 5f1cb4c28d73 -r d3e447dd52c8 sleuth.xml
--- a/sleuth.xml	Thu Jun 01 07:56:00 2023 +0000
+++ b/sleuth.xml	Wed Jun 07 11:47:30 2023 +0000
@@ -21,23 +21,38 @@
     </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[
-        #set $factor_levels = list()
+        #import os
+        mkdir -p './kallisto_outputs' &&
         #set $cond_files = list()
-        #set $cond_n_files = list()
-        #for $level in $rep_factorLevel
-            $factor_levels.append(str($level.factorLevel))
-            $cond_n_files.append(len(str($level.countsFile).split(",")))
-            #for $i, $count in enumerate(str($level.countsFile).split(","))
-                #set $fname = str($level.factorLevel) + "_"  + str($i) + '.h5'
-                ln -s '${count}' "${fname}" &&
-                $cond_files.append($fname)
+        #if $experiment_design.selector == "single"
+            #set $factor_levels = list()
+            #set $cond_n_files = list()
+            #for $level in $experiment_design.rep_factorLevel
+                $factor_levels.append(str($level.factorLevel))
+                $cond_n_files.append(len(str($level.countsFile).split(",")))
+                #for $i, $count in enumerate(str($level.countsFile).split(","))
+                    #set $fname = str($level.factorLevel) + "_"  + str($i) + '.h5'
+                    #set $output_path =  "/".join(['./kallisto_outputs',$fname])
+                    ln -s '${count}' $output_path &&
+                    $cond_files.append($output_path)
+                #end for
             #end for
-        #end for
+        #else
+            #for $count in $experiment_design.countsFile
+                #set $output_path =  "/".join(['./kallisto_outputs',$count.element_identifier])
+                ln -s '${count}' $output_path &&
+                $cond_files.append($output_path)
+            #end for
+        #end if
         Rscript '${__tool_directory__}/sleuth.R'
-            #for $i, $factor in enumerate($factor_levels)
-                --factorLevel $factor
-                --factorLevel_n $cond_n_files[$i]
-            #end for
+            #if $experiment_design.selector == "single"
+                #for $i, $factor in enumerate($factor_levels)
+                    --factorLevel $factor
+                    --factorLevel_n $cond_n_files[$i]
+                #end for
+            #else
+                --metadata_file $experiment_design.metadata_file
+            #end if
             #for $file in $cond_files
                 --factorLevel_counts $file
             #end for
@@ -46,17 +61,30 @@
             --nbins $advanced_options.nbins
             --lwr $advanced_options.lwr
             --upr $advanced_options.upr
+            --experiment_design $experiment_design.selector
     ]]></command>
     <inputs>
-        <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
-            <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>
-                </sanitizer>
+        <conditional name="experiment_design">
+            <param name="selector" type="select" label="Experiment design" help="If you have multiple experimental conditions, you should use propably the complex design mode. In the help section you can find more information.">
+                <option value="single">Simple design mode (one experimental factor)</option>
+                <option value="complex">Complex design mode (two experimental factors)</option>
             </param>
-            <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/>
-        </repeat>
+            <when value="single">
+                <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
+                    <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>
+                        </sanitizer>
+                    </param>
+                    <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/>
+                </repeat>
+            </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 it 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 
@@ -68,6 +96,7 @@
             <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." />
         </section>
+
     </inputs>
     <outputs>
         <data name="sleuth_table" from_work_dir="sleuth_table.tab" format="tabular" label="${tool.name} on ${on_string}: DE table">
@@ -104,6 +133,35 @@
             <output name="pca_plot" file="test01_pca.pdf" ftype="pdf" compare="sim_size"/>
             <output name="density_plot" file="test01_density.pdf" ftype="pdf" compare="sim_size"/>
         </test>
+    <test expect_num_outputs="3">
+        <conditional name="experiment_design">
+            <param name="selector" value="complex"/>
+            <param name="countsFile">
+                <collection type="list">
+                    <element name="kallisto_output_01.h5" ftype="h5" value="kallisto_output_01.h5"/>
+                    <element name="kallisto_output_02.h5" ftype="h5" value="kallisto_output_02.h5"/>
+                    <element name="kallisto_output_03.h5" ftype="h5" value="kallisto_output_03.h5"/>
+                    <element name="kallisto_output_04.h5" ftype="h5" value="kallisto_output_04.h5"/>
+                </collection>
+            </param>
+            <param name="metadata_file" value="design.tab"/>
+        </conditional>
+        <section name="advanced_options">
+            <param name="normalization" value="true"/>
+            <param name="nbins" value="100"/>
+            <param name="lwr" value="0.25"/>
+            <param name="upr" value="0.75"/>
+        </section>
+        <output name="sleuth_table" ftype="tabular">
+            <assert_contents>
+                <has_size value="756310" delta="100"/>
+                <has_text text="ENST00000394894.8"/>
+                <has_text text="ENST00000524187.1"/>
+            </assert_contents>
+        </output>
+        <output name="pca_plot" file="test02_pca.pdf" ftype="pdf" compare="sim_size"/>
+        <output name="density_plot" file="test02_density.pdf" ftype="pdf" compare="sim_size"/>
+    </test>
     </tests>
     <help><![CDATA[
 
@@ -123,6 +181,24 @@
 These can serve as proxies for technical replicates, allowing for an ascertainment of the variability in estimates due to the random 
 processes underlying RNA-Seq as well as the statistical procedure of read assignment. 
 
+.. class:: infomark
+
+**Experimental design tabular input for complex experimental designs**
+
+The experimental design input should have this format:
+
+        ::
+        
+            data_filename	condition	sample
+            finename_01.fastq.gz	condition1	replicate1
+            filename_02.fastq.gz	condition1	replicate2
+            filename_03.fastq.gz	condition2	replicate1
+            filename_04.fastq.gz	condition2	replicate2
+
+
+The tabular file **requires to have the same column names** as the example (data_file, condition, sample). The data file column correspond to original FASTQ filenames uploaded to Galaxy. 
+Condition includes the information about the first factor, and sample includes information about the second factor. **Only alphanumeric characters, undescores and dots are allowed**.
+
     ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 5f1cb4c28d73 -r d3e447dd52c8 test-data/design.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/design.tab	Wed Jun 07 11:47:30 2023 +0000
@@ -0,0 +1,5 @@
+sample	condition	data_filename
+CAM_01	CAM	kallisto_output_01.h5
+CAM_02	CAM	kallisto_output_02.h5
+reC3_01	reC3	kallisto_output_03.h5
+reC3_02	reC3	kallisto_output_04.h5
diff -r 5f1cb4c28d73 -r d3e447dd52c8 test-data/test02_density.pdf
Binary file test-data/test02_density.pdf has changed
diff -r 5f1cb4c28d73 -r d3e447dd52c8 test-data/test02_pca.pdf
Binary file test-data/test02_pca.pdf has changed