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comparison table_pandas_rename_column.xml @ 0:3f54cd56a65e draft

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