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Merge pull request #737 from RECETOX/copilot/update-to-version-0-2-0
rcx-tk: 0.1.0 → 0.2.0, rename metadata→sequence, add msdial corrections tool
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‎tools/rcx-tk/.shed.yml‎

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name: rcx_tk
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owner: recetox
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remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/"
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homepage_url: "https://github.com/RECETOX/rcx-tk"
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categories:
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- Metabolomics
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description: "Tools to process metadata or alkane files."
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long_description: "rcx-tk package provides tools to process the metadata or alkane files. On the input, the user is expected to supply a path to the metadata/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."
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type: unrestricted
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name: rcx_tk
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description: "Tools to process sequence or alkane files and to correct MSDial alignment results by grouping duplicate alignments."
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long_description: |
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"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."
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type: unrestricted

‎tools/rcx-tk/macros.xml‎

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<macros>
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<token name="@TOOL_VERSION@">0.2.0</token>
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<xml name="creator">
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<creator>
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<person
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givenName="Zargham"
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familyName="Ahmad"
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url="https://github.com/zargham-ahmad"
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identifier="0000-0000-0000-0000"/>
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<person
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givenName="Kristina"
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familyName="Gomoryova"
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url="https://github.com/KristinaGomoryova"
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identifier="0000-0003-4407-3917" />
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<person
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givenName="Helge"
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familyName="Hecht"
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url="https://github.com/hechth"
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identifier="0000-0001-6744-996X" />
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<organization
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url="https://www.recetox.muni.cz/"
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email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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name="RECETOX MUNI" />
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</creator>
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</xml>
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</macros>

‎tools/rcx-tk/rcx-tk.xml‎

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<tool id="rcx-tk" name="rcx-tk" version="@TOOL_VERSION@+galaxy1" profile="23.05">
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<description>Processes and standardizes metadata or alkane files by rearranging columns, validating file names, and deriving new columns for downstream analysis.</description>
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<tool id="rcx-tk" name="rcx-tk" version="@TOOL_VERSION@+galaxy0" profile="23.05">
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<description>Processes and standardizes sequence, alkane or MSDial output files for downstream analysis.</description>
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<macros>
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<token name="@TOOL_VERSION@">0.1.0</token>
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<import>macros.xml</import>
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</macros>
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<edam_topics>
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<edam_topic>topic_3172</edam_topic>
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<requirements>
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<requirement type="package" version="@TOOL_VERSION@">rcx-tk</requirement>
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</requirements>
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<creator>
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<person
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givenName="Zargham"
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familyName="Ahmad"
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url="https://github.com/zargham-ahmad"
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identifier="0000-0000-0000-0000"/>
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<person
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givenName="Kristina"
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familyName="Gomoryova"
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url="https://github.com/KristinaGomoryova"
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identifier="0000-0003-4407-3917" />
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<person
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givenName="Helge"
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familyName="Hecht"
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url="https://github.com/hechth"
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identifier="0000-0001-6744-996X" />
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<organization
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url="https://www.recetox.muni.cz/"
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email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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name="RECETOX MUNI" />
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</creator>
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<expand macro="creator"/>
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<command detect_errors="aggressive"><![CDATA[
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#if $input_file.ext == "tabular"
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#set $input_file_new = 'input.tsv'
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python3 -m rcx_tk --method ${method} ${input_file_new} 'output.tsv'
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]]></command>
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<inputs>
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<param name="input_file" type="data" format="csv,tabular,tsv,xls,xlsx,txt" label="Input data file" help="Upload your sample metadata (sequence) or alkane file."/>
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<param name="method" type="select" label="Processing method" help="Select whether to process a metadata file or an alkane file. This determines the column arrangement and validation steps.">
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<option value="metadata" selected="true">Metadata file</option>
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<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."/>
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<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.">
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<option value="sequence" selected="true">Sequence file</option>
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<option value="alkanes">Alkane file</option>
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<option value="msdial">MS-DIAL file</option>
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</param>
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</inputs>
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<outputs>
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<data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed ${method} (dataset ${input_file.id})"/>
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<data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed as ${method} on dataset ${input_file.id}"/>
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</outputs>
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<tests>
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<test>
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<param name="input_file" value="input_metadata.tabular"/>
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<param name="method" value="metadata"/>
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<param name="method" value="sequence"/>
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<output name="output_file" file="output_metadata.tsv"/>
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</test>
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<test>
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.. _rcx_tk:
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======================================
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rcx-tk: Metadata/Alkane File Processor
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rcx-tk: Sequence/Alkane File Processor
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======================================
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**Tool Description**
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rcx-tk is a tool for processing sample metadata (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.
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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.
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How it works
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------------
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------
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1. **Input data file**
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Upload your sample metadata (sequence) or alkane file. Supported formats: CSV, TSV, tabular, XLS, XLSX, or TXT.
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Upload your sample sequence or alkane file. Supported formats: CSV, TSV, tabular, XLS, XLSX, or TXT.
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2. **Processing method**
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Select whether to process a metadata file or an alkane file. This determines the column arrangement and validation steps.
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Select whether to process a sequence file or an alkane file. This determines the column arrangement and validation steps.
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Outputs
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Example
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Suppose you have a metadata file in CSV or tabular format. Select "Metadata file" as the processing method and upload your file. The tool will output a processed TSV file with standardized columns and additional identifiers.
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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.
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Notes
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