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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author | imgteam |
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date | Mon, 13 Nov 2023 22:11:00 +0000 |
parents | e0af18405e37 |
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<tool id="ip_curve_fitting" name="Perform curve fitting" version="0.0.3-2" profile="20.05"> <description></description> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> <xrefs> <xref type="bio.tools">galaxy_image_analysis</xref> </xrefs> <requirements> <requirement type="package" version="1.20.2">numpy</requirement> <requirement type="package" version="3.0.7">openpyxl</requirement> <requirement type="package" version="1.2.4">pandas</requirement> <requirement type="package" version="1.6.2">scipy</requirement> </requirements> <command> <![CDATA[ python '$__tool_directory__/curve_fitting.py' '$fn_in' ./output.xlsx $degree $penalty $alpha ]]> </command> <inputs> <param name="fn_in" type="data" format="xlsx" label="File name of input data points (xlsx)" /> <param name="degree" type="select" label="Degree of the polynomial function"> <option value="2" selected="True">2nd degree</option> <option value="1">1st degree</option> </param> <param name="penalty" type="select" label="Optimization objective for fitting"> <option value="abs" selected="True">Least absolute deviations (LAD)</option> <option value="quadratic">Least squares (LS)</option> <option value="student-t">Robust non-convex penalty</option> </param> <param name="alpha" type="float" value="0.01" label="Significance level for generating assistive curves" /> </inputs> <outputs> <data format="xlsx" name="fn_out" from_work_dir="output.xlsx"/> </outputs> <tests> <test> <param name="fn_in" value="spots_linked.xlsx"/> <param name="degree" value="2"/> <param name="penalty" value="abs"/> <param name="alpha" value="0.01"/> <output name="fn_out" value="curves_fitted.xlsx" ftype="xlsx" compare="sim_size"/> </test> </tests> <help> **What it does** This tool fits (1st- or 2nd-degree) polynomial curves to data points. Optional: Given a significance level, assistive curves will also be generated. </help> <citations> <citation type="doi">10.1097/j.pain.0000000000002642</citation> </citations> </tool>