Mercurial > repos > recetox > table_pandas_rename_column

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
author recetox
date Wed, 29 Jan 2025 15:35:31 +0000 (3 months ago)
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3f54cd56a65e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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1 <tool id="table_pandas_rename_column" name="table rename column" version="@PANDAS_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
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2 <description>of a table</description>
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3 <!-- <xrefs>
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4 <xref type="bio.tools"></xref>
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5 </xrefs> -->
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6 <macros>
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7 <import>macros.xml</import>
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8 <token name="@VERSION_SUFFIX@">0</token>
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9 </macros>
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10 <!-- TODO: please annotate this tool with topics and operations from http://edamontology.org -->
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11 <!-- TODO: for more information see: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#edam-topics-and-operations -->
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12 <!-- <edam_topics>
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13 <edam_topic>topic_TODO</edam_topic>
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14 </edam_topics>
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15 <edam_operations>
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16 <edam_operation>operation_TODO</edam_operation>
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17 </edam_operations> -->
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18 <requirements>
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19 <expand macro="requirement_pandas_pyarrow"/>
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20 </requirements>
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21 <required_files>
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22 <include path="table_pandas_rename_column.py" />
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23 <include path="utils.py" />
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24 </required_files>
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25 <expand macro="creator" />
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26 <command detect_errors="exit_code"><![CDATA[
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27 #set rename_dict = " ".join([str($key_value_pair.column) + '=' + str($key_value_pair.new_name) for $key_value_pair in $columns_selection])
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28 python3 '$__tool_directory__/table_pandas_rename_column.py'
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29 --input_dataset '$input_dataset' '$input_dataset.ext'
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30 --rename $rename_dict
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31 --output_dataset '$output_dataset' '$output_dataset.ext'
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32 ]]></command>
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33 <inputs>
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34 <param name="input_dataset" type="data" format="csv,tsv,tabular,parquet" label="Input Dataset"/>
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35 <repeat name="columns_selection" title="Rename column" min="1">
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36 <param name="column" type="data_column" data_ref="input_dataset" use_header_names="true" label="Column" help="Column from the dataset to rename."/>
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37 <param argument="new_name" type="text" value="" label="New column name" help="New name for the column">
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38 <sanitizer invalid_char="">
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39 <valid initial="string.letters,string.digits">
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40 <add value="_" />
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41 </valid>
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42 </sanitizer>
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43 <validator type="regex">[0-9a-zA-Z_]+</validator>
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44 </param>
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45 </repeat>
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46 </inputs>
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47 <outputs>
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48 <data name="output_dataset" format_source="input_dataset" label="${tool.name} on ${on_string}">
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49 <change_format>
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50 <when input="input_dataset.ext" value="tsv" format="tabular" />
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51 </change_format>
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52 </data>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input_dataset" value="reference.txt" ftype="tabular"/>
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57 <param name="column" value="2"/>
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58 <param name="new_name" value="retention_time"/>
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59 <output name="output_dataset" file="rename/reference_rt_renamed.tabular" ftype="tabular"/>
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60 </test>
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61 <test>
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62 <param name="input_dataset" value="reference.txt" ftype="tabular"/>
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63 <repeat name="columns_selection">
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64 <param name="column" value="2"/>
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65 <param name="new_name" value="retention_time"/>
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66 </repeat>
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67 <repeat name="columns_selection">
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68 <param name="column" value="1"/>
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69 <param name="new_name" value="retention_index"/>
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70 </repeat>
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71 <output name="output_dataset" file="rename/reference_both_renamed.tabular" ftype="tabular"/>
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 This tool renames columns in a table.
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76
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77 Inputs
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78 ------
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79
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80 - **Input Dataset**: The input dataset in CSV, TSV, tabular, or Parquet format.
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81 - **Columns to Rename**: Specify the columns to rename and their new names. You can use the "repeat" function to rename multiple columns.
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82
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83 Outputs
3f54cd56a65e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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84 -------
3f54cd56a65e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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85
3f54cd56a65e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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86 - **Output Dataset**: The output dataset with the renamed columns.
3f54cd56a65e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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87
3f54cd56a65e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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88 ]]></help>
3f54cd56a65e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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89 <citations>
3f54cd56a65e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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90 <citation type="doi">10.5281/zenodo.3509134</citation>
3f54cd56a65e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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91 </citations>
3f54cd56a65e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
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92 </tool>