--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aplcms_to_ramclustr_converter.py	Tue Mar 22 16:06:28 2022 +0000
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+
+import argparse
+import sys
+
+import pandas as pd
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--dataframe", help="Parquet dataframe")
+parser.add_argument('output')
+args = parser.parse_args()
+
+
+def main():
+    featureTable = pd.read_parquet(args.dataframe)
+
+    # Concatenate "mz" and "rt" columns; select relevant columns; pivot the table
+    featureTable["mz_rt"] = featureTable["mz"].astype(str) + "_" + featureTable["rt"].astype(str)
+    featureTable = featureTable[["sample", "mz_rt", "sample_intensity"]]
+    featureTable = pd.pivot_table(featureTable, columns="mz_rt", index="sample", values="sample_intensity")
+
+    try:
+        featureTable.to_csv(args.output, sep=',')
+        msg = f"Dataset of {len(featureTable)} samples is converted to a feature-by-sample table"
+        print(msg, file=sys.stdout)
+        return 0
+    except Exception:
+        print("Could not write the data", file=sys.stdout)
+        return 1
+
+
+if __name__ == "__main__":
+    main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aplcms_to_ramclustr_converter.xml	Tue Mar 22 16:06:28 2022 +0000
@@ -0,0 +1,31 @@
+<tool id="aplcms_to_ramclustr_converter" name="apLCMS to RamClustR converter" version="0.1.0+galaxy1" python_template_version="3.5">
+    <description>converts apLCMS output to RamClustR input</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
+    <requirements>
+        <requirement type="package" version="1.1.5">pandas</requirement>
+        <requirement type="package" version="4.0.0">pyarrow</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python $__tool_directory__/aplcms_to_ramclustr_converter.py --dataframe '${aplcms_dataframe}' '${out_file}'
+    ]]></command>
+    <inputs>
+        <param name="aplcms_dataframe" type="data" format="parquet" label="apLCMS Dataframe"/>
+    </inputs>
+    <outputs>
+        <data format="csv" name="out_file" label="Feature-by-sample ${aplcms_dataframe.name} table"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="aplcms_dataframe" value="input.parquet" ftype="parquet"/>
+            <output name="out_file" file="output.csv" ftype="csv"/>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+        @HELP@
+        ]]>
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Mar 22 16:06:28 2022 +0000
@@ -0,0 +1,31 @@
+<macros>
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Martin"
+                familyName="Čech"
+                url="https://github.com/martenson"
+                identifier="0000-0002-9318-1781" />
+            <person
+                givenName="Maksym"
+                familyName="Skoryk"
+                url="https://github.com/maximskorik"
+                identifier="0000-0003-2056-8018" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+    <token name="@HELP@">
+        <![CDATA[
+            Tool to convert apLCMS output to csv file formated in accordance to RamClustR (CSV) input requirements.
+
+            **Workflow position**
+
+            - Upstream tool: `apLCMS <https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms>`_  Unsupervised or Hybrid
+
+            - Downstream tool: `RamClustR <https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr>`_ (CSV)
+        ]]>
+    </token>
+</macros>

Binary file test-data/input.parquet has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.csv	Tue Mar 22 16:06:28 2022 +0000
@@ -0,0 +1,4 @@
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