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annotate tabpfn.xml @ 1:5112462f2dd3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit 0544107f87c3df249ecc89a64dfd390f8708b736
author bgruening
date Wed, 15 Jan 2025 20:34:13 +0000
parents 3dc3c7443c8e
children c081e5e1d7ce
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3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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1 <tool id="tabpfn" name="Tabular data prediction using TabPFN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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2 <description>with PyTorch</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.0.3</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <creator>
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8 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
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9 <person givenName="Anup" familyName="Kumar" email="kumara@informatik.uni-freiburg.de" />
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10 <person givenName="Frank" familyName="Hutter" email="fh@cs.uni-freiburg.de" />
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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11 </creator>
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">tabpfn</requirement>
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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14 <requirement type="package" version="2.2.2">pandas</requirement>
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15 <requirement type="package" version="3.9.2">matplotlib</requirement>
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16 </requirements>
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17 <version_command>echo "@VERSION@"</version_command>
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18 <command detect_errors="aggressive">
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19 <![CDATA[
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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20 python '$__tool_directory__/main.py'
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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21 --train_data '$train_data'
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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22 --test_data '$test_data'
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param name="train_data" type="data" format="tabular" label="Train data" help="Please provide training data for training model."/>
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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27 <param name="test_data" type="data" format="tabular" label="Test data" help="Please provide test data for evaluating model."/>
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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28 </inputs>
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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29 <outputs>
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30 <data format="tabular" name="output_predicted_data" from_work_dir="output_predicted_data" label="Predicted data"></data>
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5112462f2dd3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit 0544107f87c3df249ecc89a64dfd390f8708b736
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31 <data format="png" name="output_prec_recall_curve" from_work_dir="output_prec_recall_curve.png" label="Precision-recall curve"></data>
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3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="train_data" value="local_train_rows.tabular" ftype="tabular" />
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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36 <param name="test_data" value="local_test_rows.tabular" ftype="tabular" />
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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37 <output name="output_predicted_data">
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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38 <assert_contents>
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39 <has_n_columns n="42" />
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40 <has_n_lines n="3" />
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41 </assert_contents>
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42 </output>
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43 </test>
1
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44 <test>
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45 <param name="train_data" value="local_train_rows.tabular" ftype="tabular" />
5112462f2dd3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit 0544107f87c3df249ecc89a64dfd390f8708b736
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46 <param name="test_data" value="local_test_rows.tabular" ftype="tabular" />
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47 <output name="output_prec_recall_curve" file="pr_curve.png" compare="sim_size" />
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48 </test>
0
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49 </tests>
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50 <help>
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51 <![CDATA[
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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52 **What it does**
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53
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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54 Classification on tabular data by TabPFN
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55
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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56 **Input files**
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57 - Training data: the training data should contain features and the last column should be the class labels. It could either be tabular or in CSV format.
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58 - Test data: the test data should also contain the same features as the training data and the last column should be the class labels. It could either be tabular or in CSV format.
3dc3c7443c8e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
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59
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60 **Output files**
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61 - Predicted data along with predicted labels
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62 ]]>
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63 </help>
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64 <citations>
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65 <citation type="doi">10.1038/s41586-024-08328-6</citation>
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66 </citations>
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67 </tool>