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comparison curve_fitting.xml @ 0:e08061d196ce draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
author imgteam
date Thu, 22 Jul 2021 19:34:07 +0000
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1 <tool id="ip_curve_fitting" name="Curve Fitting" version="0.0.1" profile="20.05">
2 <description>to data points using (1st- or 2nd-degree) polynomial function</description>
3 <requirements>
4 <requirement type="package" version="1.20.2">numpy</requirement>
5 <requirement type="package" version="3.0.7">openpyxl</requirement>
6 <requirement type="package" version="1.2.4">pandas</requirement>
7 <requirement type="package" version="1.6.2">scipy</requirement>
8 </requirements>
9 <command>
10 <![CDATA[
11 python '$__tool_directory__/curve_fitting.py'
12 '$fn_in'
13 ./output.xlsx
14 '$degree'
15 '$penalty'
16 '$alpha'
17 ]]>
18 </command>
19 <inputs>
20 <param name="fn_in" type="data" format="xlsx" label="File name of input data points (xlsx)" />
21 <param name="degree" type="integer" label="Degree of the polynomial function">
22 <option value="2" selected="True">2nd degree</option>
23 <option value="1">1st degree</option>
24 </param>
25 <param name="penalty" type="select" label="Optimization objective for fitting">
26 <option value="abs" selected="True">Least absolute deviations (LAD)</option>
27 <option value="quadratic">Least squares (LS)</option>
28 <option value="student-t">Robust non-convex penalty</option>
29 </param>
30 <param name="alpha" type="float" value="0.01" label="Significance level for generating assistive curves" />
31 </inputs>
32 <outputs>
33 <data format="xlsx" name="fn_out" from_work_dir="output.xlsx"/>
34 </outputs>
35 <tests>
36 <test>
37 <param name="fn_in" value="spots_linked.xlsx"/>
38 <param name="degree" value="2"/>
39 <param name="penalty" value="abs"/>
40 <param name="alpha" value="0.01"/>
41 <output name="fn_out" value="curves_fitted.xlsx" ftype="xlsx" compare="sim_size"/>
42 </test>
43 </tests>
44 <help>
45 **What it does**
46
47 This tool fits (1st- or 2nd-degree) polynomial curves to data points. Optional: Given a significance level, assistive curves will also be generated.
48 </help>
49 </tool>