Mercurial > repos > imgteam > curve_fitting

diff curve_fitting.xml @ 0:8bf2c507af3a 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 19:34:36 +0000
parents
children c54cf4ce6baf
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/curve_fitting.xml	Thu Jul 22 19:34:36 2021 +0000
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+<tool id="ip_curve_fitting" name="Curve Fitting" version="0.0.1" profile="20.05"> 
+    <description>to data points using (1st- or 2nd-degree) polynomial function</description>
+    <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="integer" 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>
+</tool>