Updating tools/rcx-tk from version 0.2.2 to 0.3.1 (#767)

* Updating tools/rcx-tk from version 0.2.2 to 0.3.1

* updated command section to comply with 0.3.1

---------

Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Co-authored-by: Helge Hecht <helge.hecht@recetox.muni.cz>

Author: 3 people

tools/rcx-tk/macros.xml

@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.2.2</token>
+    <token name="@TOOL_VERSION@">0.3.1</token>
     <xml name="creator">
         <creator>
             <person

tools/rcx-tk/rcx-tk.xml

@@ -1,5 +1,5 @@
 <tool id="rcx-tk" name="rcx-tk" version="@TOOL_VERSION@+galaxy0" profile="23.05">
-    <description>Processes and standardizes sequence, alkane or MSDial output files for downstream analysis.</description>
+    <description>Processes and standardizes sequence, alkane, or MSDial output files for downstream analysis.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -17,65 +17,80 @@
     </requirements>
     <expand macro="creator"/>
     <command detect_errors="aggressive"><![CDATA[
-       #set $input_file_new = 'input.' + str($input_file.ext)
-       cp ${input_file} ${input_file_new} &&
-       python3 -m rcx_tk --method ${method} ${input_file_new} 'output.tsv' 
+        #set $input_file_new = 'input.' + str($input_file.ext)
+        cp ${input_file} ${input_file_new} &&
+        #if $method == "msdial"
+        python3 -m rcx_tk ${method} ${input_file_new} 'output.tsv' $mz_tol_ppm
+        #else
+        python3 -m rcx_tk ${method} ${input_file_new} 'output.tsv'
+        #end if
     ]]></command>
     <inputs>
-        <param name="input_file" type="data" format="csv,tabular,tsv,xls,xlsx,txt" label="Input data file" help="Upload your sample sequence or alkane file."/>
-        <param name="method" type="select" label="Processing method" help="Select whether to process a sequence file or an alkane file. This determines the column arrangement and validation steps.">
-            <option value="sequence" selected="true">Sequence file</option>
-            <option value="alkanes">Alkane file</option>
-            <option value="msdial">MS-DIAL file</option>
-        </param>
+        <param name="input_file" type="data" format="csv,tabular,tsv,xls,xlsx,txt" label="Input data file" help="Upload your sample sequence, alkane, or MS-DIAL file."/>
+        <conditional name="command">
+            <param name="method" type="select" label="Processing method" help="Select the rcx-tk subcommand to run. This determines the column arrangement, validation steps, and CLI invocation.">
+                <option value="sequence" selected="true">Sequence file</option>
+                <option value="alkanes">Alkane file</option>
+                <option value="msdial">MS-DIAL file</option>
+            </param>
+            <when value="sequence"/>
+            <when value="alkanes" />
+            <when value="msdial">
+                <param argument="mz_tol_ppm" type="integer" min="1" max="100" value="5" label="m/z tolerance [ppm]" help="Tolerance for splitting clusters from different ions." />
+            </when>
+        </conditional>
+
     </inputs>
     <outputs>
         <data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed as ${method} on dataset ${input_file.id}"/>
     </outputs>
     <tests>
         <test>
             <param name="input_file" value="input_metadata.tabular"/>
-            <param name="method" value="sequence"/>
+            <param name="command|method" value="sequence"/>
             <output name="output_file" file="output_metadata.tsv"/>
         </test>
          <test>
             <param name="input_file" value="input_alkanes.txt"/>
-            <param name="method" value="alkanes"/>
+            <param name="command|method" value="alkanes"/>
             <output name="output_file" file="output_alkanes.tsv"/>
         </test>
         <test>
-            <param name="input_file" location="https://raw.githubusercontent.com/RECETOX/rcx-tk/refs/tags/v0.2.2/tests/test_data/msdial_katka.tsv"/>
-            <param name="method" value="msdial"/>
-            <output name="output_file" location="https://raw.githubusercontent.com/RECETOX/rcx-tk/refs/tags/v0.2.2/tests/test_data/msdial_katka_corrected.tsv"/>
+            <param name="input_file" location="https://raw.githubusercontent.com/RECETOX/rcx-tk/refs/tags/v0.3.1/tests/test_data/msdial_katka.tsv"/>
+            <param name="command|method" value="msdial"/>
+            <output name="output_file" location="https://raw.githubusercontent.com/RECETOX/rcx-tk/refs/tags/v0.3.1/tests/test_data/msdial_katka_corrected.tsv"/>
         </test>
     </tests>
     <help><![CDATA[
 
 .. _rcx_tk:
 
-======================================
-rcx-tk: Sequence/Alkane File Processor
-======================================
+====================================================
+rcx-tk: Sequence, Alkane, and MS-DIAL File Processor
+====================================================
 
 **Tool Description**
 
-rcx-tk is a tool for processing sample sequence and alkane files. It standardizes your input by rearranging columns, validating file names, and deriving new columns such as `sampleName`, `sequenceIdentifier`, `sampleIdentifier`, and `localOrder`. This ensures your data is ready for downstream analysis and compatible with standardized workflows.
+rcx-tk is a tool for processing sequence metadata, alkane retention index, and MS-DIAL output files. It standardizes inputs by rearranging columns, validating file names, and deriving new columns such as `sampleName`, `sequenceIdentifier`, `subjectIdentifier`, and `localOrder`. For MS-DIAL files, it also merges duplicate alignments using the package's click-based subcommand interface.
 
 How it works
 ------------
 
-- **Column rearrangement**: Ensures columns are in the correct order for further processing.
-- **File name validation**: Checks that file names follow expected conventions.
-- **Derivation of new columns**: Automatically generates useful columns for sample tracking and analysis.
+- **Sequence files**: validates file names, checks that `injectionOrder` is an integer, and derives metadata columns from the file name.
+- **Alkane files**: keeps the alkane columns used by rcx-tk and renames them to the normalized output format.
+- **MS-DIAL files**: reads the MS-DIAL table, identifies duplicate alignments, and refines them using the tolerance value.
 
 Inputs
 ------
 
 1. **Input data file**  
-   Upload your sample sequence or alkane file. Supported formats: CSV, TSV, tabular, XLS, XLSX, or TXT.
+    Upload your sample sequence, alkane, or MS-DIAL file. Supported formats: CSV, TSV, tabular, XLS, XLSX, or TXT.
 
 2. **Processing method**  
-   Select whether to process a sequence file or an alkane file. This determines the column arrangement and validation steps.
+    Select which rcx-tk subcommand to run. This determines the column arrangement, validation steps, and whether MS-DIAL duplicate merging is applied.
+
+3. **MS-DIAL tolerance**  
+   When processing MS-DIAL files, you can provide an optional m/z tolerance in parts per million. The default used by rcx-tk is 5.
 
 Outputs
 -------
@@ -86,7 +101,7 @@ Outputs
 Example
 -------
 
-Suppose you have a sequence file in CSV or tabular format. Select "Sequence file" as the processing method and upload your file. The tool will output a processed TSV file with standardized columns and additional identifiers.
+Suppose you have a sequence file in CSV or tabular format. Select "Sequence file" as the processing method and upload your file. The tool will output a processed TSV file with standardized columns and additional identifiers. For MS-DIAL files, the tool invokes the `msdial` subcommand with the package's default tolerance unless you extend the wrapper to expose that argument.
 
 Notes
 -----