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annotate curve_fitting.xml @ 1:c54cf4ce6baf draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 7eed123c4116a9f47a8d3f6ab31565fa07b62013"
author imgteam
date Thu, 22 Jul 2021 22:16:12 +0000
parents 8bf2c507af3a
children dd5fede16ee4
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8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
imgteam
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1 <tool id="ip_curve_fitting" name="Curve Fitting" version="0.0.1" profile="20.05">
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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2 <description>to data points using (1st- or 2nd-degree) polynomial function</description>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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3 <requirements>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
imgteam
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4 <requirement type="package" version="1.20.2">numpy</requirement>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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5 <requirement type="package" version="3.0.7">openpyxl</requirement>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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6 <requirement type="package" version="1.2.4">pandas</requirement>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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7 <requirement type="package" version="1.6.2">scipy</requirement>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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8 </requirements>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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9 <command>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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10 <![CDATA[
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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11 python '$__tool_directory__/curve_fitting.py'
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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12 '$fn_in'
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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13 ./output.xlsx
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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14 '$degree'
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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15 '$penalty'
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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16 '$alpha'
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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17 ]]>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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18 </command>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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19 <inputs>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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20 <param name="fn_in" type="data" format="xlsx" label="File name of input data points (xlsx)" />
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c54cf4ce6baf "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 7eed123c4116a9f47a8d3f6ab31565fa07b62013"
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21 <param name="degree" type="select" label="Degree of the polynomial function">
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8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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22 <option value="2" selected="True">2nd degree</option>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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23 <option value="1">1st degree</option>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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24 </param>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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25 <param name="penalty" type="select" label="Optimization objective for fitting">
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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26 <option value="abs" selected="True">Least absolute deviations (LAD)</option>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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27 <option value="quadratic">Least squares (LS)</option>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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28 <option value="student-t">Robust non-convex penalty</option>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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29 </param>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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30 <param name="alpha" type="float" value="0.01" label="Significance level for generating assistive curves" />
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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31 </inputs>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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32 <outputs>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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33 <data format="xlsx" name="fn_out" from_work_dir="output.xlsx"/>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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34 </outputs>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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35 <tests>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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36 <test>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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37 <param name="fn_in" value="spots_linked.xlsx"/>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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38 <param name="degree" value="2"/>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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39 <param name="penalty" value="abs"/>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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40 <param name="alpha" value="0.01"/>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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41 <output name="fn_out" value="curves_fitted.xlsx" ftype="xlsx" compare="sim_size"/>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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42 </test>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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43 </tests>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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44 <help>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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45 **What it does**
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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46
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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47 This tool fits (1st- or 2nd-degree) polynomial curves to data points. Optional: Given a significance level, assistive curves will also be generated.
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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48 </help>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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49 </tool>