view rename_annotated_feature.xml @ 0:268fcec93d9c draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28

<tool id="rename_annotated_feature" name="Rename Annotated Feature" version="@TOOL_VERSION@+galaxy0" profile="21.09">
    <description>Rename columns in abundance table based on annotations table</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="2.2.1">pandas</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python3 '${__tool_directory__}/rename_annotated_feature.py'
        --annotations_table_path '$annotations_table_path' 
        --abundance_table_path '$abundance_table_path' 
        --mode '$mode'
        --output_path '$output_path'
    ]]></command>
    <inputs>
        <param name="annotations_table_path" type="data" format="tabular" label="Annotations table file" help="Path to the annotations table file."/>
        <param name="abundance_table_path" type="data" format="tabular" label="Abundance table file" help="Path to the abundance table file."/>
        <param name="mode" type="select" label="Mode to use for renaming" help="Can be single or multiple.">
            <option value="single" selected="true">Single</option>
            <option value="multiple">Multiple</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_path" format="tabular" label="Renamed abundance table"/>
    </outputs>
    <tests>
        <test>
            <param name="annotations_table_path" value="annotated_table.tsv" ftype="tabular"/>
            <param name="abundance_table_path" value="abundance_table.tsv" ftype="tabular"/>
            <param name="mode" value="single"/>
            <output name="output_path" file="single_mode_output.tsv"/>
        </test>
        <test>
            <param name="annotations_table_path" value="annotated_table.tsv" ftype="tabular"/>
            <param name="abundance_table_path" value="abundance_table.tsv" ftype="tabular" />
            <param name="mode" value="multiple"/>
            <output name="output_path" file="multi_mode_output.tsv"/>
        </test>
    </tests>
    <help>
        <![CDATA[
        @HELP@
        ]]>
    </help>
    <!-- Update to the correct citation for this tool -->
    <citations>
            <citation type="doi">10.5281/zenodo.7178586</citation>
            <citation type="doi">10.21105/joss.02411</citation>
            <citation type="doi">10.1021/ac501530d</citation>            
    </citations>
</tool>