Mercurial > repos > bgruening > tabpfn

annotate tabpfn.xml @ 0:2a0c6d2090f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
author bgruening
date Wed, 15 Jan 2025 12:33:37 +0000
parents
children bb60469276fd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
1 <tool id="tabpfn" name="Tabular data prediction using TabPFN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
2 <description>with PyTorch</description>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
3 <macros>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
4 <token name="@TOOL_VERSION@">2.0.3</token>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
6 </macros>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
7 <creator>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
8 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
9 <person givenName="Anup" familyName="Kumar" email="kumara@informatik.uni-freiburg.de" />
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
10 <person givenName="Frank" familyName="Hutter" email="fh@cs.uni-freiburg.de" />
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
11 </creator>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
12 <requirements>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
13 <requirement type="package" version="@TOOL_VERSION@">tabpfn</requirement>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
14 <requirement type="package" version="2.2.2">pandas</requirement>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
15 <requirement type="package" version="3.9.2">matplotlib</requirement>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
16 </requirements>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
17 <version_command>echo "@VERSION@"</version_command>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
18 <command detect_errors="aggressive">
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
19 <![CDATA[
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
20 python '$__tool_directory__/main.py'
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
21 --train_data '$train_data'
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
22 --test_data '$test_data'
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
23 ]]>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
24 </command>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
25 <inputs>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
26 <param name="train_data" type="data" format="tabular" label="Train data" help="Please provide training data for training model."/>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
27 <param name="test_data" type="data" format="tabular" label="Test data" help="Please provide test data for evaluating model."/>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
28 </inputs>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
29 <outputs>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
30 <data format="tabular" name="output_predicted_data" from_work_dir="output_predicted_data" label="Predicted data"></data>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
31 <data format="png" name="output_prec_recall_curve" from_work_dir="output_prec_recall_curve" label="Precision-recall curve"></data>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
32 </outputs>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
33 <tests>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
34 <test>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
35 <param name="train_data" value="local_train_rows.tabular" ftype="tabular" />
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
36 <param name="test_data" value="local_test_rows.tabular" ftype="tabular" />
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
37 <output name="output_predicted_data">
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
38 <assert_contents>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
39 <has_n_columns n="42" />
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
40 <has_n_lines n="3" />
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
41 </assert_contents>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
42 </output>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
43 </test>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
44 </tests>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
45 <help>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
46 <![CDATA[
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
47 **What it does**
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
48
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
49 Classification on tabular data by TabPFN
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
50
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
51 **Input files**
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
52 - 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.
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
53 - 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.
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
54
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
55 **Output files**
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
56 - Predicted data along with predicted labels
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
57 ]]>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
58 </help>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
59 <citations>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
60 <citation type="doi">10.1038/s41586-024-08328-6</citation>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
61 </citations>
2a0c6d2090f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tabpfn commit bce8b0297bff54e7e29a6106a7f385fd1318c0aa
bgruening
parents:
diff changeset
62 </tool>