Mercurial > repos > recetox > table_pandas_rename_columns_regex

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author recetox
date Wed, 29 Jan 2025 15:35:08 +0000
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1 <tool id="table_pandas_rename_columns_regex" name="table rename columns via regex" version="@PANDAS_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
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2 <description>rename columns in a table using regex</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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8 <requirements>
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9 <expand macro="requirement_pandas_pyarrow"/>
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10 </requirements>
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12 <required_files>
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13 <include path="table_pandas_rename_columns_regex.py" />
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14 <include path="utils.py" />
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15 </required_files>
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17 <expand macro="creator" />
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19 <command detect_errors="exit_code"><![CDATA[
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20 python3 '$__tool_directory__/table_pandas_rename_columns_regex.py'
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21 --input_dataset '$input_dataset' '$input_dataset.ext'
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22 --columns '$columns'
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23 --regex_check '$regex_check'
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24 --regex_replace '$regex_replace'
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25 --output_dataset '$output_dataset' '$output_dataset.ext'
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26 ]]></command>
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27
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28 <inputs>
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29 <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."/>
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30 <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."/>
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31 <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.">
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32 <expand macro="regex_sanitizer"/>
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33 </param>
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34 <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.">
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35 <expand macro="regex_sanitizer"/>
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36 </param>
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37 </inputs>
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38
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39 <outputs>
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40 <data name="output_dataset" format_source="input_dataset" label="${tool.name} on ${on_string}">
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41 <change_format>
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42 <when input="input_dataset.ext" value="tsv" format="tabular" />
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43 </change_format>
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44 </data>
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45 </outputs>
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46
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47 <tests>
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48 <test expect_num_outputs="1">
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49 <param name="input_dataset" value="rename/reference_both_renamed.tabular" ftype="tabular"/>
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50 <param name="columns" value="1,2"/>
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51 <param name="regex_check" value="retention_"/>
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52 <param name="regex_replace" value=""/>
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53 <output name="output_dataset" ftype="tabular">
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54 <assert_contents>
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55 <has_text text="retention" negate="true"/>
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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60
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61 <help><![CDATA[
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62 This tool renames columns in a table using the specified regex patterns.
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63
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64 Inputs
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65 ------
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66
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67 - **Input Dataset**: The input dataset in CSV, TSV, tabular, or Parquet format.
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68 - **Columns to Rename**: Select one or more columns from the dataset to rename. You can select columns by their header names.
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69 - **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.
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70 - **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.
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71
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72 Outputs
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73 -------
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74
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75 - **Output Dataset**: The output dataset with the renamed columns.
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76 ]]></help>
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77
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78 <citations>
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79 <citation type="doi">10.5281/zenodo.3509134</citation>
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80 <citation type="doi">10.25080/Majora-92bf1922-00a</citation>
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81 </citations>
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82 </tool>