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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:11:00 +0000
parents e0af18405e37
children
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6
2dc244356765 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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1 <tool id="ip_curve_fitting" name="Perform curve fitting" version="0.0.3-2" profile="20.05">
2dc244356765 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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2 <description></description>
2dc244356765 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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3 <edam_operations>
2dc244356765 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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4 <edam_operation>operation_3443</edam_operation>
2dc244356765 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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5 </edam_operations>
2dc244356765 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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6 <xrefs>
2dc244356765 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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7 <xref type="bio.tools">galaxy_image_analysis</xref>
2dc244356765 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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8 </xrefs>
0
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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9 <requirements>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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10 <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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11 <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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12 <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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13 <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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14 </requirements>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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15 <command>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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16 <![CDATA[
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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17 python '$__tool_directory__/curve_fitting.py'
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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18 '$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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19 ./output.xlsx
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e0af18405e37 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit cd63bc5e6eb7254111012209fac9154569355f20
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20 $degree
e0af18405e37 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit cd63bc5e6eb7254111012209fac9154569355f20
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21 $penalty
e0af18405e37 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit cd63bc5e6eb7254111012209fac9154569355f20
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22 $alpha
0
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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23 ]]>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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24 </command>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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25 <inputs>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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26 <param name="fn_in" type="data" format="xlsx" label="File name of input data points (xlsx)" />
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00feb1ecd040 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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27 <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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28 <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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29 <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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30 </param>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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31 <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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32 <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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33 <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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34 <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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35 </param>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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36 <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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37 </inputs>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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38 <outputs>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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39 <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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40 </outputs>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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41 <tests>
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 <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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44 <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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45 <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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46 <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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47 <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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48 </test>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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49 </tests>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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50 <help>
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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51 **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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52
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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53 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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54 </help>
4
004c57179c61 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ae389b10be46633407effcc6856167f6e8bb2122"
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55 <citations>
004c57179c61 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ae389b10be46633407effcc6856167f6e8bb2122"
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56 <citation type="doi">10.1097/j.pain.0000000000002642</citation>
004c57179c61 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ae389b10be46633407effcc6856167f6e8bb2122"
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57 </citations>
0
8bf2c507af3a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ commit ef82d0882741042922349499cafa35d20d70ce70"
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58 </tool>