From 881f5b063611b9c4929b8dffe48c338d47675d50 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Fri, 25 Jul 2025 17:08:51 +0200
Subject: [PATCH 1/5] updated tools and initial version

---
 tools/recetox_aplcms/macros.xml               |   5 +++--
 .../recetox_aplcms_align_features.xml         |   2 +-
 .../recetox_aplcms_compute_clusters.xml       |   2 +-
 .../recetox_aplcms_compute_template.xml       |   2 +-
 .../recetox_aplcms_correct_time.xml           |   2 +-
 .../recetox_aplcms_generate_feature_table.xml |   2 +-
 .../recetox_aplcms_merge_known_table.xml      |   2 +-
 .../recetox_aplcms_recover_weaker_signals.xml |   2 +-
 .../recetox_aplcms_remove_noise.xml           |   8 +++++---
 .../test-data/peak_table_galaxy.parquet       | Bin 163673 -> 163673 bytes
 .../test-data/remove_noise_docker.parquet     | Bin 364902 -> 364902 bytes
 .../remove_noise_docker_threshold.parquet     | Bin 1537 -> 1537 bytes
 12 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/tools/recetox_aplcms/macros.xml b/tools/recetox_aplcms/macros.xml
index c9c3ad665..071f8e4e4 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@">0.14.0</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="2.5.6">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..c041424f2 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>
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..5dca47606 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>
@@ -10,7 +10,9 @@
     </edam_operations>
     <expand macro="refs"/>
     <expand macro="creator"/>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="1.10.2">bioconductor-rawrr</requirement>
+    </expand>
 
     <command detect_errors="aggressive"><![CDATA[
         python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
@@ -39,7 +41,7 @@
     </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>
diff --git a/tools/recetox_aplcms/test-data/peak_table_galaxy.parquet b/tools/recetox_aplcms/test-data/peak_table_galaxy.parquet
index 256483e78afd5ba90f42a1dc2357b88ed75ddca7..1f2defb8be8e6ee99d753a652f4059308d698a49 100644
GIT binary patch
delta 24
fcmcclkMrg~&W0AoElgJRtd@EPdWO^O>zSkgg*ynL

delta 24
fcmcclkMrg~&W0AoElgJRtQL9(dIr<&>zSkgg)0c3

diff --git a/tools/recetox_aplcms/test-data/remove_noise_docker.parquet b/tools/recetox_aplcms/test-data/remove_noise_docker.parquet
index 3430baa21b690820dd24c3d2912445e4ae89801b..24a25aef4d49c85a897c7cd89a71617dfc2148fe 100644
GIT binary patch
delta 30
mcmaF1NbK1nv4$4L7N!>F7M3lnUK3d@^$he3r~6N26$b#b{t5X2

delta 30
mcmaF1NbK1nv4$4L7N!>F7M3lnUK3d@^bGV2ru$E16$b#b?g{q*

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 f22314f15f262420458f5f1e4110047bcbb1799d..f76d51386a7cd33244c6cdaa427cd9ebb3bc37b4 100644
GIT binary patch
delta 36
kcmZqVY2?}PlvT!3&p^*m(np4Y0gf1UvNA9PI0hL40FC7aZU6uP

delta 36
kcmZqVY2?}PlvTz;&p^*W(np4Y0gf1UvNA9PI0hL40FAK*YybcN


From 26dcd075addebaee586d414650dc0be583b19d88 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Wed, 13 Aug 2025 13:03:49 +0200
Subject: [PATCH 2/5] added dependencies and configfiles to install rawrr -
 currently waiting for next aplcms release to fix a bug in the package

---
 .../recetox_aplcms_remove_noise.xml           | 29 +++++++++++++++++--
 1 file changed, 26 insertions(+), 3 deletions(-)

diff --git a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
index 5dca47606..10698706e 100644
--- a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
@@ -12,10 +12,17 @@
     <expand macro="creator"/>
     <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';
+        ln $input_file input.$input_file.ext &&
+        #if $input_file.ext == 'thermo.raw':
+            Rscript -e 'source("${install_rawrr}")' &&
+            Rscript -e 'source("${raw_id_getter}")' &&
+        #else:
+            python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
+        #end if
         Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
     ]]></command>
     <configfiles>
@@ -23,7 +30,7 @@
             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 = ${mz_tol}/1e6,
@@ -38,6 +45,17 @@
             profile <- save_sample_name(profile, sample_name)
             save_data_as_parquet_file(profile, '$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>
@@ -51,7 +69,7 @@
     </outputs>
 
     <tests>
-        <test>
+        <!-- <test>
             <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
             <output name="output_file" file="remove_noise_docker.parquet" ftype="parquet" />
         </test>
@@ -59,6 +77,11 @@
             <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
             <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" file="raw.parquet"/>
         </test>
     </tests>
 

From 5c3b4d2c6fdb1b3d6a798e69837c9ff916d26cf7 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Fri, 15 Aug 2025 10:20:41 +0200
Subject: [PATCH 3/5] Fixed raw file reasing in the test and updated to 0.14.1

---
 tools/recetox_aplcms/macros.xml                      | 2 +-
 tools/recetox_aplcms/recetox_aplcms_remove_noise.xml | 9 +++++----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/tools/recetox_aplcms/macros.xml b/tools/recetox_aplcms/macros.xml
index 071f8e4e4..5a710b470 100644
--- a/tools/recetox_aplcms/macros.xml
+++ b/tools/recetox_aplcms/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.14.0</token>
+    <token name="@TOOL_VERSION@">0.14.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
diff --git a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
index 10698706e..ba5f4548e 100644
--- a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
@@ -20,10 +20,11 @@
         #if $input_file.ext == 'thermo.raw':
             Rscript -e 'source("${install_rawrr}")' &&
             Rscript -e 'source("${raw_id_getter}")' &&
+            Rscript -e "future::plan(future::multicore, workers = \${GALAXY_SLOTS:-1})" &&
         #else:
             python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
         #end if
-        Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
+        Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' -e 'future::plan(future::sequential)'
     ]]></command>
     <configfiles>
         <configfile name="run_script"><![CDATA[
@@ -69,7 +70,7 @@
     </outputs>
 
     <tests>
-        <!-- <test>
+        <test>
             <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
             <output name="output_file" file="remove_noise_docker.parquet" ftype="parquet" />
         </test>
@@ -77,11 +78,11 @@
             <param name="input_file" value="mbr_test0.mzml" ftype="mzml"/>
             <param name="grouping_threshold" value="2" />
             <output name="output_file" file="remove_noise_docker_threshold.parquet" ftype="parquet" />
-        </test> -->
+        </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" file="raw.parquet"/>
+            <output name="output_file" ftype="parquet" md5="a43a29b2e79c59d40bfb8c24c674f899"/>
         </test>
     </tests>
 

From 8cadee5616017b4f13a0a7d6b14b51602fce6dba Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Fri, 15 Aug 2025 14:13:53 +0200
Subject: [PATCH 4/5] using soft symlink or copying in case of raw file,
 currently there is no better solution

---
 tools/recetox_aplcms/macros.xml                      | 2 +-
 tools/recetox_aplcms/recetox_aplcms_remove_noise.xml | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/tools/recetox_aplcms/macros.xml b/tools/recetox_aplcms/macros.xml
index 5a710b470..e510ef3b1 100644
--- a/tools/recetox_aplcms/macros.xml
+++ b/tools/recetox_aplcms/macros.xml
@@ -3,7 +3,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
-            <requirement type="package" version="2.5.6">pymzml</requirement>
+            <requirement type="package" version="2.5.11">pymzml</requirement>
             <yield />
         </requirements>
     </xml>
diff --git a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
index ba5f4548e..ea2dc2e76 100644
--- a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
@@ -12,16 +12,17 @@
     <expand macro="creator"/>
     <expand macro="requirements">
         <requirement type="package" version="1.10.2">bioconductor-rawrr</requirement>
-        <requirement type="package" version="6.12.0.199">mono</requirement>
+        <!-- <requirement type="package" version="6.12.0.199">mono</requirement> -->
     </expand>
 
     <command detect_errors="aggressive"><![CDATA[
-        ln $input_file input.$input_file.ext &&
         #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)'

From 90f4834379084c45af7be7e3c8ca49b95044ce64 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Fri, 17 Oct 2025 09:50:46 +0200
Subject: [PATCH 5/5] trying tests with remote files urls

---
 .../recetox_aplcms_align_features.xml               | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/tools/recetox_aplcms/recetox_aplcms_align_features.xml b/tools/recetox_aplcms/recetox_aplcms_align_features.xml
index c041424f2..739cfeacb 100644
--- a/tools/recetox_aplcms/recetox_aplcms_align_features.xml
+++ b/tools/recetox_aplcms/recetox_aplcms_align_features.xml
@@ -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>