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Enable column renaming for parquet files until the implementation of the parquet types is finished #762

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Enable column renaming for parquet files until the implementation of the parquet types is finished #762

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f9b7f21
added test to rename parquet
hechth Jun 16, 2026
732529c
fixed linting
hechth Jun 16, 2026
61a8b81
Merge branch 'master' into table-rename-parquet
hechth Jun 18, 2026
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75 changes: 49 additions & 26 deletions tools/tables/table_pandas_rename_column.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
</xrefs> -->
<macros>
<import>macros.xml</import>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
</macros>
<!-- TODO: please annotate this tool with topics and operations from http://edamontology.org -->
<!-- TODO: for more information see: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#edam-topics-and-operations -->
Expand All @@ -31,18 +31,41 @@
--output_dataset '$output_dataset' '$output_dataset.ext'
]]></command>
<inputs>
<param name="input_dataset" type="data" format="csv,tsv,tabular,parquet" label="Input Dataset"/>
<repeat name="columns_selection" title="Rename column" min="1">
<param name="column" type="data_column" data_ref="input_dataset" use_header_names="true" label="Column" help="Column from the dataset to rename."/>
<param argument="new_name" type="text" value="" label="New column name" help="New name for the column">
<sanitizer invalid_char="">
<valid initial="string.letters,string.digits">
<add value="_" />
</valid>
</sanitizer>
<validator type="regex">[0-9a-zA-Z_]+</validator>
<conditional name="input_type">
<param name="type" type="select" label="Input type" help="TODO">
<option value="text">Text (csv/tsv/tabular)</option>
<option value="binary">Binary (parquet)</option>
</param>
</repeat>
<when value="text">
<param name="input_dataset" type="data" format="csv,tsv,tabular" label="Input Dataset"/>
<repeat name="columns_selection" title="Rename column" min="1">
<param name="column" type="data_column" data_ref="input_dataset" use_header_names="true" label="Column" help="Column from the dataset to rename."/>
<param argument="new_name" type="text" label="New column name" help="New name for the column" optional="false">
<sanitizer invalid_char="">
<valid initial="string.letters,string.digits">
<add value="_" />
</valid>
</sanitizer>
<validator type="regex">[0-9a-zA-Z_]+</validator>
</param>
</repeat>
</when>
<when value="binary">
<param name="input_dataset" type="data" format="parquet" label="Input Dataset"/>
<repeat name="columns_selection" title="Rename column" min="1">
<param name="column" type="integer" label="Column" min="1" help="Column index from the dataset to rename."/>
<param argument="new_name" type="text" label="New column name" help="New name for the column" optional="false">
<sanitizer invalid_char="">
<valid initial="string.letters,string.digits">
<add value="_" />
</valid>
</sanitizer>
<validator type="regex">[0-9a-zA-Z_]+</validator>
</param>
</repeat>
</when>
</conditional>

</inputs>
<outputs>
<data name="output_dataset" format_source="input_dataset" label="${tool.name} on ${on_string}">
Expand All @@ -53,23 +76,23 @@
</outputs>
<tests>
<test>
<param name="input_dataset" value="reference.txt" ftype="tabular"/>
<repeat name="columns_selection">
<param name="column" value="2"/>
<param name="new_name" value="retention_time"/>
</repeat>
<param name="input_type|input_dataset" value="reference.txt" ftype="tabular"/>
<param name="input_type|columns_selection_0|column" value="2"/>
<param name="input_type|columns_selection_0|new_name" value="retention_time"/>
<output name="output_dataset" file="rename/reference_rt_renamed.tabular" ftype="tabular"/>
</test>
<test>
<param name="input_dataset" value="reference.txt" ftype="tabular"/>
<repeat name="columns_selection">
<param name="column" value="2"/>
<param name="new_name" value="retention_time"/>
</repeat>
<repeat name="columns_selection">
<param name="column" value="1"/>
<param name="new_name" value="retention_index"/>
</repeat>
<param name="input_type|input_dataset" value="query.parquet" ftype="parquet"/>
<param name="input_type|columns_selection_0|column" value="3"/>
<param name="input_type|columns_selection_0|new_name" value="ri"/>
<output name="output_dataset" file="rename/query_retention_index_renamed.parquet" ftype="parquet"/>
</test>
<test>
<param name="input_type|input_dataset" value="reference.txt" ftype="tabular"/>
<param name="input_type|columns_selection_0|column" value="2"/>
<param name="input_type|columns_selection_0|new_name" value="retention_time"/>
<param name="input_type|columns_selection_1|column" value="1"/>
<param name="input_type|columns_selection_1|new_name" value="retention_index"/>
<output name="output_dataset" file="rename/reference_both_renamed.tabular" ftype="tabular"/>
</test>
</tests>
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