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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 15:36:02 +0000
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1 <tool id="table_scipy_interpolate" name="table scipy interpolate" version="@SCIPY_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description>interpolate data using the scipy.interpolate library</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 <requirement type="package" version="@SCIPY_VERSION@">scipy</requirement>
20 <expand macro="requirement_pandas_pyarrow"/>
21 </requirements>
22 <required_files>
23 <include path="table_scipy_interpolate.py" />
24 <include path="utils.py" />
25 </required_files>
26 <expand macro="creator" />
27 <command detect_errors="exit_code"><![CDATA[
28 python3 '${__tool_directory__}/table_scipy_interpolate.py'
29 --reference_dataset '$reference_dataset' '$reference_dataset.ext'
30 --query_dataset '$query_dataset' '$query_dataset.ext'
31 --x_col $x_col
32 --y_col $y_col
33 --xnew_col $xnew_col
34 --model '$model'
35 --output_dataset '$output_dataset' '$output_dataset.ext'
36 ]]></command>
37
38 <inputs>
39 <param argument="--reference_dataset" type="data" format="tabular,csv,tsv,parquet" label="Reference data" help="Reference dataset to use fopr the interpolation" />
40 <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."/>
41 <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."/>
42 <param argument="--query_dataset" type="data" format="tabular,csv,tsv,parquet" label="Query dataset" help="Query dataset for which to interpolate the values." />
43 <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."/>
44
45 <param name="model" type="select" label="Interpolation model" help="Interpolation model from scipy to use. For more details see [1].">
46 <option value="linear">Piecewise linear</option>
47 <option value="cubic" selected="true">Cubic spline</option>
48 <option value="pchip">Pchip</option>
49 <option value="akima">Akima1D</option>
50 </param>
51 </inputs>
52 <outputs>
53 <data name="output_dataset" format_source="query_dataset" label="${tool.name} on ${on_string}">
54 <change_format>
55 <when input="query_dataset.ext" value="tsv" format="tabular" />
56 </change_format>
57 </data>
58 </outputs>
59 <tests>
60 <test>
61 <param name="reference_dataset" value="reference.txt" ftype="tabular"/>
62 <param name="x_col" value="1"/>
63 <param name="y_col" value="2"/>
64 <param name="query_dataset" value="query.tabular" ftype="tabular"/>
65 <param name="xnew_col" value="3"/>
66 <output name="output_dataset" file="interpolate/query_interpolate_rt.tabular" ftype="tabular"/>
67 </test>
68 </tests>
69 <help><![CDATA[
70 .. class:: infomark
71
72 **What it does**
73 This tool interpolates the values for a column to be added
74
75 Usage
76 .....
77 [1] (https://docs.scipy.org/doc/scipy/tutorial/interpolate.html)
78
79 **Input**
80 Input a reference table and choose the X (source) and Y (target) columns for the interpolation.
81 Choose a query table and the X (source) column for which to calculate the new Y values.
82
83
84 **Output**
85 A table with the interpolated Y column.
86
87 ]]></help>
88 <citations>
89 <citation type="doi">10.25080/Majora-92bf1922-00a</citation>
90 <citation type="doi">10.1038/s41592-019-0686-2</citation>
91 </citations>
92 </tool>