annotate table_scipy_interpolate.xml @ 0:0112f08c95ed draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6

<tool id="table_scipy_interpolate" name="table scipy interpolate" version="@SCIPY_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>interpolate data using the scipy.interpolate library</description>
    <!-- <xrefs>
        <xref type="bio.tools"></xref>
    </xrefs> -->
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">0</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 -->
    <!-- <edam_topics>
        <edam_topic>topic_TODO</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_TODO</edam_operation>
    </edam_operations> -->
    <requirements>
        <requirement type="package" version="@SCIPY_VERSION@">scipy</requirement>
        <expand macro="requirement_pandas_pyarrow"/>
    </requirements>
    <required_files>
        <include path="table_scipy_interpolate.py" />
        <include path="utils.py" />
    </required_files>
    <expand macro="creator" />
    <command detect_errors="exit_code"><![CDATA[
        python3 '${__tool_directory__}/table_scipy_interpolate.py' 
        --reference_dataset '$reference_dataset' '$reference_dataset.ext'
        --query_dataset '$query_dataset' '$query_dataset.ext'
        --x_col $x_col
        --y_col $y_col
        --xnew_col $xnew_col
        --model '$model'
        --output_dataset '$output_dataset' '$output_dataset.ext'
        ]]></command>

    <inputs>
        <param argument="--reference_dataset" type="data" format="tabular,csv,tsv,parquet" label="Reference data" help="Reference dataset to use fopr the interpolation" />
        <param name="x_col" type="data_column" data_ref="reference_dataset" use_header_names="true" label="x (reference)" help="Column from the reference dataset to use as X axis for the interpolator."/>
        <param name="y_col" type="data_column" data_ref="reference_dataset" use_header_names="true" label="y (reference)" help="Column from the reference dataset to use as Y axis for the interpolator."/>
        <param argument="--query_dataset" type="data" format="tabular,csv,tsv,parquet" label="Query dataset" help="Query dataset for which to interpolate the values." />
        <param name="xnew_col" type="data_column" data_ref="query_dataset" use_header_names="true" label="x (query)" help="Column from the query dataset for which to interpolate."/>

        <param name="model" type="select" label="Interpolation model" help="Interpolation model from scipy to use. For more details see [1].">
            <option value="linear">Piecewise linear</option>
            <option value="cubic" selected="true">Cubic spline</option>
            <option value="pchip">Pchip</option>
            <option value="akima">Akima1D</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_dataset" format_source="query_dataset" label="${tool.name} on ${on_string}">
            <change_format>
                <when input="query_dataset.ext" value="tsv" format="tabular" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="reference_dataset" value="reference.txt" ftype="tabular"/>
            <param name="x_col" value="1"/>
            <param name="y_col" value="2"/>
            <param name="query_dataset" value="query.tabular" ftype="tabular"/>
            <param name="xnew_col" value="3"/>
            <output name="output_dataset" file="interpolate/query_interpolate_rt.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**
This tool interpolates the values for a column to be added

Usage
.....
[1] (https://docs.scipy.org/doc/scipy/tutorial/interpolate.html)

**Input**
Input a reference table and choose the X (source) and Y (target) columns for the interpolation.
Choose a query table and the X (source) column for which to calculate the new Y values.


**Output**
A table with the interpolated Y column.

    ]]></help>
    <citations>
        <citation type="doi">10.25080/Majora-92bf1922-00a</citation>
        <citation type="doi">10.1038/s41592-019-0686-2</citation>
    </citations>
</tool>