view table_pandas_rename_columns_regex.xml @ 0:505a8e975968 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6

<tool id="table_pandas_rename_columns_regex" name="table rename columns via regex" version="@PANDAS_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>rename columns in a table using regex</description>
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>

    <requirements>
        <expand macro="requirement_pandas_pyarrow"/>
    </requirements>

    <required_files>
        <include path="table_pandas_rename_columns_regex.py" />
        <include path="utils.py" />
    </required_files>

    <expand macro="creator" />

    <command detect_errors="exit_code"><![CDATA[
        python3 '$__tool_directory__/table_pandas_rename_columns_regex.py' 
            --input_dataset '$input_dataset' '$input_dataset.ext'
            --columns '$columns'
            --regex_check '$regex_check'
            --regex_replace '$regex_replace'
            --output_dataset '$output_dataset' '$output_dataset.ext'
    ]]></command>
    
    <inputs>
        <param name="input_dataset" type="data" format="csv,tsv,tabular,parquet" label="Input Dataset" help="The input dataset in CSV, TSV, tabular, or Parquet format."/>
        <param name="columns" type="data_column" data_ref="input_dataset" multiple="true" use_header_names="true" min="1" label="Columns to Rename"  help="Select one or more columns from the dataset to rename. You can select columns by their header names."/>
        <param name="regex_check" type="text" label="Regex to Check For" help="The regular expression pattern to search for in the column names. This pattern will be used to identify parts of the column names to be replaced.">
            <expand macro="regex_sanitizer"/>
        </param>
        <param name="regex_replace" type="text" label="Regex to Replace With" optional="true" help="The regular expression pattern to replace the matched parts of the column names with. This pattern will be used to rename the columns.">
            <expand macro="regex_sanitizer"/>
        </param>
    </inputs>

    <outputs>
        <data name="output_dataset" format_source="input_dataset" label="${tool.name} on ${on_string}">
            <change_format>
                <when input="input_dataset.ext" value="tsv" format="tabular" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <test expect_num_outputs="1">
            <param name="input_dataset" value="rename/reference_both_renamed.tabular" ftype="tabular"/>
            <param name="columns" value="1,2"/>
            <param name="regex_check" value="retention_"/>
            <param name="regex_replace" value=""/>
            <output name="output_dataset" ftype="tabular">
                <assert_contents>
					<has_text text="retention" negate="true"/>
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
This tool renames columns in a table using the specified regex patterns.

Inputs
------

- **Input Dataset**: The input dataset in CSV, TSV, tabular, or Parquet format.
- **Columns to Rename**: Select one or more columns from the dataset to rename. You can select columns by their header names.
- **Regex to Check For**: The regular expression pattern to search for in the column names. This pattern will be used to identify parts of the column names to be replaced.
- **Regex to Replace With**: The regular expression pattern to replace the matched parts of the column names with. This pattern will be used to rename the columns.

Outputs
-------

- **Output Dataset**: The output dataset with the renamed columns.
    ]]></help>

    <citations>
        <citation type="doi">10.5281/zenodo.3509134</citation>
        <citation type="doi">10.25080/Majora-92bf1922-00a</citation>
    </citations>
</tool>