From be63963cb11e3b87cad0a549ce01eea76b5959c2 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Fri, 3 May 2024 09:16:43 +0200
Subject: [PATCH 1/2] updated csv output to tsv

---
 tools/waveica/macros.xml                    | 6 +++++-
 tools/waveica/test-data/normalized_data.csv | 6 ------
 tools/waveica/waveica.xml                   | 8 ++++----
 tools/waveica/waveica_wrapper.R             | 8 +++-----
 4 files changed, 12 insertions(+), 16 deletions(-)
 delete mode 100644 tools/waveica/test-data/normalized_data.csv

diff --git a/tools/waveica/macros.xml b/tools/waveica/macros.xml
index 090d8470..344bd533 100644
--- a/tools/waveica/macros.xml
+++ b/tools/waveica/macros.xml
@@ -99,7 +99,11 @@
 
     <xml name="outputs">
         <outputs>
-             <data format_source="data" name="normalized_data"/>
+            <data name="normalized_data" format_source="data" >
+                <change_format>
+                    <when input="data.ext" value="parquet" format="parquet" />
+                </change_format>
+            </data>
         </outputs>
     </xml>
 
diff --git a/tools/waveica/test-data/normalized_data.csv b/tools/waveica/test-data/normalized_data.csv
deleted file mode 100644
index 19b09281..00000000
--- a/tools/waveica/test-data/normalized_data.csv
+++ /dev/null
@@ -1,6 +0,0 @@
-sampleName,class,sampleType,injectionOrder,batch,M85T34,M86T41,M86T518,M86T539
-VT_160120_002,sample,sample,1,1,355200.506508035,75115889.9077485,6101488.54615418,2007379.02604984
-VT_160120_004,sample,sample,2,1,216897.826587868,75204863.1495248,6170882.26270475,2069979.64992079
-VT_160120_006,sample,sample,3,1,362337.195084504,76490295.1450204,12588041.969092,1818589.63912375
-VT_160120_008,sample,sample,4,1,143303.377379009,83771659.9549148,6181538.46316058,1975712.25920485
-VT_160120_010,sample,sample,5,1,189065.516447239,84108898.7658797,6103964.42378424,1935671.32085241
diff --git a/tools/waveica/waveica.xml b/tools/waveica/waveica.xml
index 8e53a8d5..67b080c8 100644
--- a/tools/waveica/waveica.xml
+++ b/tools/waveica/waveica.xml
@@ -1,4 +1,4 @@
-<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy4" python_template_version="3.5">
+<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy5" python_template_version="3.5">
     <description>removal of batch effects for untargeted metabolomics data</description>
     <macros>
         <import>macros.xml</import>
@@ -103,7 +103,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.csv"/>
+            <output name="normalized_data" file="normalized_data.tsv"/>
         </test>
         <test><!-- TEST 2 -->
             <param name="data" value="input_data.tsv" ftype="tsv"/>
@@ -138,7 +138,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.csv"/>
+            <output name="normalized_data" file="normalized_data.tsv"/>
         </test>
         <test><!-- TEST 5 -->
             <param name="input_choice" value="2"/>
@@ -192,7 +192,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.csv"/>
+            <output name="normalized_data" file="normalized_data.tsv"/>
         </test>
         <!-- The following test has different results on three platform I've tried -->
         <!-- <test>
diff --git a/tools/waveica/waveica_wrapper.R b/tools/waveica/waveica_wrapper.R
index 0a883a65..cb100c04 100644
--- a/tools/waveica/waveica_wrapper.R
+++ b/tools/waveica/waveica_wrapper.R
@@ -231,15 +231,13 @@ exclude_group <- function(data, group) {
 }
 
 store_data <- function(data, output, ext) {
-  if (ext == "csv") {
-    write.csv(data, file = output, row.names = FALSE, quote = FALSE)
-  } else if (ext == "tsv") {
+  if (ext == "parquet") {
+    arrow::write_parquet(data, sink = output)
+  } else {
     write.table(data,
       file = output, sep = "\t",
       row.names = FALSE, quote = FALSE
     )
-  } else {
-    arrow::write_parquet(data, sink = output)
   }
   cat("Normalization has been completed.\n")
 }

From c03952195db19fca92321211fbbe043c586d3c7f Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Fri, 3 May 2024 11:00:23 +0200
Subject: [PATCH 2/2] fixed ext issue

---
 tools/waveica/macros.xml        |  4 ++--
 tools/waveica/waveica.xml       | 18 +++++++++---------
 tools/waveica/waveica_wrapper.R |  2 +-
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/tools/waveica/macros.xml b/tools/waveica/macros.xml
index 344bd533..551d1321 100644
--- a/tools/waveica/macros.xml
+++ b/tools/waveica/macros.xml
@@ -99,9 +99,9 @@
 
     <xml name="outputs">
         <outputs>
-            <data name="normalized_data" format_source="data" >
+            <data name="normalized_data" format="tsv">
                 <change_format>
-                    <when input="data.ext" value="parquet" format="parquet" />
+                    <when input_dataset="data" attribute="ext" value="parquet" format="parquet" />
                 </change_format>
             </data>
         </outputs>
diff --git a/tools/waveica/waveica.xml b/tools/waveica/waveica.xml
index 67b080c8..d6219c6b 100644
--- a/tools/waveica/waveica.xml
+++ b/tools/waveica/waveica.xml
@@ -1,4 +1,4 @@
-<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy5" python_template_version="3.5">
+<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy5" profile="21.09">
     <description>removal of batch effects for untargeted metabolomics data</description>
     <macros>
         <import>macros.xml</import>
@@ -103,7 +103,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.tsv"/>
+            <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
         </test>
         <test><!-- TEST 2 -->
             <param name="data" value="input_data.tsv" ftype="tsv"/>
@@ -114,7 +114,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.tsv"/>
+            <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
         </test>
         <test><!-- TEST 3 -->
             <param name="data" value="input_data.parquet" ftype="parquet"/>
@@ -125,7 +125,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.parquet"/>
+            <output name="normalized_data" file="normalized_data.parquet" ftype="parquet"/>
         </test>
         <test><!-- TEST 4 -->
             <param name="input_choice" value="2"/>
@@ -138,7 +138,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.tsv"/>
+            <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
         </test>
         <test><!-- TEST 5 -->
             <param name="input_choice" value="2"/>
@@ -151,7 +151,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.tsv"/>
+            <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
         </test>
         <test><!-- TEST 6 -->
             <param name="input_choice" value="2"/>
@@ -164,7 +164,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/>
+            <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
         </test>
         <test><!-- TEST 7 -->
             <param name="input_choice" value="2"/>
@@ -178,7 +178,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/>
+            <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/>
         </test>
         <test><!-- TEST 8 -->
             <param name="input_choice" value="2"/>
@@ -192,7 +192,7 @@
             <param name="t" value="0.05"/>
             <param name="t2" value="0.05"/>
             <param name="alpha" value="0"/>
-            <output name="normalized_data" file="normalized_data.tsv"/>
+            <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/>
         </test>
         <!-- The following test has different results on three platform I've tried -->
         <!-- <test>
diff --git a/tools/waveica/waveica_wrapper.R b/tools/waveica/waveica_wrapper.R
index cb100c04..fc0c865e 100644
--- a/tools/waveica/waveica_wrapper.R
+++ b/tools/waveica/waveica_wrapper.R
@@ -232,7 +232,7 @@ exclude_group <- function(data, group) {
 
 store_data <- function(data, output, ext) {
   if (ext == "parquet") {
-    arrow::write_parquet(data, sink = output)
+    arrow::write_parquet(data, output)
   } else {
     write.table(data,
       file = output, sep = "\t",