new implementation

Author: hechth

tools/rcx-tk/.shed.yml

@@ -5,16 +5,9 @@ categories:
   - Metabolomics
 repositories:
   rcx_tk:
-    description: "Tools to process sequence or alkane files."
-    long_description: "rcx-tk package provides tools to process the sequence or alkane files. On the input, the user is expected to supply a path to the sequence/alkane file in tsv/csv/xls/xlsx file. The file is then converted to a dataframe which is further processed. The main steps are columns rearrangement, validation of the file names and derivation of new metadata: sampleName, sequenceIdentifier, sampleIdentifier and localOrder. Finally, the processed dataframe is saved into user-defined location."
+    description: "Tools to process sequence or alkane files and to correct MSDial alignment results by grouping duplicate alignments."
+    long_description: "rcx-tk package provides tools to process the sequence or alkane files. On the input, the user is expected to supply a path to the sequence/alkane file in tsv/csv/xls/xlsx file. The file is then converted to a dataframe which is further processed. The main steps are columns rearrangement, validation of the file names and derivation of new metadata: sampleName, sequenceIdentifier, sampleIdentifier and localOrder. Duplicate rows sharing identical non-zero abundance values in any sample column are clustered and aggregated: metadata is concatenated and abundances are reduced using the maximum value."
     include:
       - rcx-tk.xml
       - macros.xml
       - test-data
-  rcx_tk_msdial:
-    description: "Tool to correct MSDial alignment results by grouping duplicate alignments."
-    long_description: "rcx-tk msdial correction tool processes MSDial alignment result files to identify and merge duplicate alignments. Duplicate rows sharing identical non-zero abundance values in any sample column are clustered and aggregated: metadata is concatenated and abundances are reduced using the maximum value."
-    include:
-      - rcx-tk-msdial.xml
-      - macros.xml
-      - test-data

tools/rcx-tk/rcx-tk-msdial.xml

@@ -1,5 +1,5 @@
 <tool id="rcx-tk" name="rcx-tk" version="@TOOL_VERSION@+galaxy0" profile="23.05">
-    <description>Processes and standardizes sequence or alkane files by rearranging columns, validating file names, and deriving new columns for downstream analysis.</description>
+    <description>Processes and standardizes sequence, alkane or MSDial output files for downstream analysis.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -30,10 +30,11 @@
         <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>
     </inputs>
     <outputs>
-        <data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed ${method} (dataset ${input_file.id})"/>
+        <data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed as ${method} on dataset ${input_file.id}"/>
     </outputs>
     <tests>
         <test>