diff --git a/tools/recetox_aplcms/macros.xml b/tools/recetox_aplcms/macros.xml
index c9c3ad665..e510ef3b1 100644
--- a/tools/recetox_aplcms/macros.xml
+++ b/tools/recetox_aplcms/macros.xml
@@ -1,9 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.13.4</token>
+    <token name="@TOOL_VERSION@">0.14.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
-            <requirement type="package" version="2.5.2">pymzml</requirement>
+            <requirement type="package" version="2.5.11">pymzml</requirement>
+            <yield />
         </requirements>
     </xml>
 
diff --git a/tools/recetox_aplcms/recetox_aplcms_align_features.xml b/tools/recetox_aplcms/recetox_aplcms_align_features.xml
index 422be7789..739cfeacb 100644
--- a/tools/recetox_aplcms/recetox_aplcms_align_features.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_align_features.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy0" profile="23.0">
     <description>align peaks across samples</description>
     <macros>
         <import>macros.xml</import>
@@ -56,7 +56,18 @@
     </outputs>
 
     <tests>
-        <test expect_failure="true" />
+        <test expect_num_outputs="3">
+            <param name="files" ftype="parquet">
+                <collection type="list">
+                    <element name="RCX_06_shortened_extracted_clusters.parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/clusters/RCX_06_shortened_extracted_clusters.parquet?ref_type=heads&amp;inline=false"/>
+                    <element name="RCX_07_shortened_extracted_clusters.parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/clusters/RCX_07_shortened_extracted_clusters.parquet?ref_type=heads&amp;inline=false"/>
+                    <element name="RCX_08_shortened_extracted_clusters.parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/clusters/RCX_08_shortened_extracted_clusters.parquet?ref_type=heads&amp;inline=false"/>
+                </collection>
+            </param>
+            <output name="metadata_file" ftype="parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/aligned/metadata_table.parquet?ref_type=heads&amp;inline=false"/>
+            <output name="rt_file" ftype="parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/aligned/rt_table.parquet?ref_type=heads&amp;inline=false"/>
+            <output name="intensity_file" ftype="parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/aligned/intensity_table.parquet?ref_type=heads&amp;inline=false"/>
+        </test>
     </tests>
 
     <help>
diff --git a/tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml b/tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml
index 214517ed3..cdacd4128 100644
--- a/tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_compute_clusters" name="recetox-aplcms - compute clusters" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="recetox_aplcms_compute_clusters" name="recetox-aplcms - compute clusters" version="@TOOL_VERSION@+galaxy0" profile="23.0">
     <description>compute clusters of mz and rt across samples and assign cluster IDs to individual features</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/recetox_aplcms/recetox_aplcms_compute_template.xml b/tools/recetox_aplcms/recetox_aplcms_compute_template.xml
index 39fd57f97..0639b6db1 100644
--- a/tools/recetox_aplcms/recetox_aplcms_compute_template.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_compute_template.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_compute_template" name="recetox-aplcms - compute template" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="recetox_aplcms_compute_template" name="recetox-aplcms - compute template" version="@TOOL_VERSION@+galaxy0" profile="23.0">
     <description>compute retention time correction template feature table</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/recetox_aplcms/recetox_aplcms_correct_time.xml b/tools/recetox_aplcms/recetox_aplcms_correct_time.xml
index 82ea0ade1..f9e7ec86c 100644
--- a/tools/recetox_aplcms/recetox_aplcms_correct_time.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_correct_time.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0" profile="23.0">
     <description>correct retention time across samples for peak alignment</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml b/tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml
index 3b904c375..596483092 100644
--- a/tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy0" profile="23.0">
     <description>generate feature table from noise-removed HRMS profile data</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml b/tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml
index 72a2842f1..e3501063e 100644
--- a/tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_merge_known_table" name="recetox-aplcms - merge known table" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="recetox_aplcms_merge_known_table" name="recetox-aplcms - merge known table" version="@TOOL_VERSION@+galaxy0" profile="23.0">
     <description>join knowledge from aligned features and known table.</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml b/tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml
index 5dc555ecc..2317c161e 100644
--- a/tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_recover_weaker_signals" name="recetox-aplcms - recover weaker signals" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="recetox_aplcms_recover_weaker_signals" name="recetox-aplcms - recover weaker signals" version="@TOOL_VERSION@+galaxy0" profile="23.0">
     <description>recover weaker signals from raw data using an aligned feature table</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
index aa5d6d8a7..ea2dc2e76 100644
--- a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy0" profile="23.0">
     <description>filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data</description>
     <macros>
         <import>macros.xml</import>
@@ -10,18 +10,29 @@
     </edam_operations>
     <expand macro="refs"/>
     <expand macro="creator"/>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="1.10.2">bioconductor-rawrr</requirement>
+        <!-- <requirement type="package" version="6.12.0.199">mono</requirement> -->
+    </expand>
 
     <command detect_errors="aggressive"><![CDATA[
-        python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
-        Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
+        #if $input_file.ext == 'thermo.raw':
+            cp $input_file input.$input_file.ext &&
+            Rscript -e 'source("${install_rawrr}")' &&
+            Rscript -e 'source("${raw_id_getter}")' &&
+            Rscript -e "future::plan(future::multicore, workers = \${GALAXY_SLOTS:-1})" &&
+        #else:
+            ln -s $input_file input.$input_file.ext &&
+            python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
+        #end if
+        Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' -e 'future::plan(future::sequential)'
     ]]></command>
     <configfiles>
         <configfile name="run_script"><![CDATA[
             sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size)
 
             profile <- remove_noise(
-                filename = '$input_file',
+                filename = 'input.${input_file.ext}',
                 min_pres = $min_pres,
                 min_run = $min_run,
                 mz_tol = ${mz_tol}/1e6,
@@ -36,10 +47,21 @@
             profile <- save_sample_name(profile, sample_name)
             save_data_as_parquet_file(profile, '$output_file')
         ]]></configfile>
+
+        <configfile name="raw_id_getter"><![CDATA[
+            header <- rawrr::readFileHeader('input.${input_file.ext}')
+            writeLines(header[['Sample id']], "sample_name.txt")
+        ]]></configfile>
+
+        <configfile name="install_rawrr"><![CDATA[
+            rawrr::installRawFileReaderDLLs()
+            rawrr::installRawrrExe()
+            rawrr::rawrrAssemblyPath()
+        ]]></configfile>
     </configfiles>
 
     <inputs>
-        <param label="Input spectra data" name="input_file" type="data" format="mzml"
+        <param label="Input spectra data" name="input_file" type="data" format="mzml,thermo.raw"
                help="Sample data in .mzml format acquired in profile mode." />
         <expand macro="remove_noise_params"/>
     </inputs>
@@ -58,6 +80,11 @@
             <param name="grouping_threshold" value="2" />
             <output name="output_file" file="remove_noise_docker_threshold.parquet" ftype="parquet" />
         </test>
+        <test>
+            <param name="input_file" ftype="thermo.raw" location="https://zenodo.org/records/7890956/files/8_qc_no_dil_milliq.raw?download=1"/>
+            <param name="grouping_threshold" value="2" />
+            <output name="output_file" ftype="parquet" md5="a43a29b2e79c59d40bfb8c24c674f899"/>
+        </test>
     </tests>
 
     <help>
diff --git a/tools/recetox_aplcms/test-data/peak_table_galaxy.parquet b/tools/recetox_aplcms/test-data/peak_table_galaxy.parquet
index 256483e78..1f2defb8b 100644
Binary files a/tools/recetox_aplcms/test-data/peak_table_galaxy.parquet and b/tools/recetox_aplcms/test-data/peak_table_galaxy.parquet differ
diff --git a/tools/recetox_aplcms/test-data/remove_noise_docker.parquet b/tools/recetox_aplcms/test-data/remove_noise_docker.parquet
index 3430baa21..24a25aef4 100644
Binary files a/tools/recetox_aplcms/test-data/remove_noise_docker.parquet and b/tools/recetox_aplcms/test-data/remove_noise_docker.parquet differ
diff --git a/tools/recetox_aplcms/test-data/remove_noise_docker_threshold.parquet b/tools/recetox_aplcms/test-data/remove_noise_docker_threshold.parquet
index f22314f15..f76d51386 100644
Binary files a/tools/recetox_aplcms/test-data/remove_noise_docker_threshold.parquet and b/tools/recetox_aplcms/test-data/remove_noise_docker_threshold.parquet differ