Mercurial > repos > bgruening > run_jupyter_job

annotate run_jupyter_job.xml @ 2:bf2963c9bcdc draft default tip

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/jupyter_job commit c21261bb8373090c26cf5195134b30538b5bc714
author bgruening
date Fri, 20 Jan 2023 10:49:03 +0000
parents c93b2676a27d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
bf2963c9bcdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit c21261bb8373090c26cf5195134b30538b5bc714
bgruening
parents: 1
diff changeset
1 <tool id="run_jupyter_job" name="Run long running jupyterlab script" hidden="true" version="0.0.1" profile="22.01">
0
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
2 <description>inside a Docker container</description>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
3 <requirements>
2
bf2963c9bcdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit c21261bb8373090c26cf5195134b30538b5bc714
bgruening
parents: 1
diff changeset
4 <container type="docker">docker.io/anupkumar/docker-ml-jupyterlab:galaxy-integration-0.2</container>
0
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
5 </requirements>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
6 <command detect_errors="aggressive"><![CDATA[
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
7 python '${__tool_directory__}/main.py'
1
c93b2676a27d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit 6817ef65c64c0800e21815822c38beba52075f75"
bgruening
parents: 0
diff changeset
8 --ml_paths '$ml_h5_dataset_paths'
c93b2676a27d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit 6817ef65c64c0800e21815822c38beba52075f75"
bgruening
parents: 0
diff changeset
9 --loaded_file '$select_file'
0
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
10 --working_dir `pwd`
1
c93b2676a27d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit 6817ef65c64c0800e21815822c38beba52075f75"
bgruening
parents: 0
diff changeset
11 --output_array '$outfile_output_arrays'
c93b2676a27d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit 6817ef65c64c0800e21815822c38beba52075f75"
bgruening
parents: 0
diff changeset
12 --output_zip '$outfile_output_zip'
c93b2676a27d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit 6817ef65c64c0800e21815822c38beba52075f75"
bgruening
parents: 0
diff changeset
13 --ml_h5_files '$ml_h5_datasets'
0
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
14 ]]>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
15 </command>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
16 <inputs>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
17 <param name="ml_h5_dataset_paths" type="text" label="Data paths" optional="true" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
18 <param name="select_file" type="data" label="Load file" format="txt" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
19 <param name="ml_h5_datasets" type="data" label="Input h5 dataset" format="h5" multiple="true" optional="true" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
20 </inputs>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
21 <outputs>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
22 <data format="h5" name="outfile_output_arrays" label="Saved arrays"></data>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
23 <data format="zip" name="outfile_output_zip" label="Zipped files"></data>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
24 <collection name="onnx_models" type="list" label="Trained models">
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
25 <discover_datasets format="onnx" pattern="__name__" visible="false" directory="model_outputs" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
26 </collection>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
27 </outputs>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
28 <tests>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
29 <test expect_num_outputs="3">
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
30 <param name="select_file" value="tf-script.py" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
31 <output name="outfile_output_zip" file="zipped_file_tf.zip" ftype="zip" compare="sim_size" delta="50" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
32 <output name="outfile_output_arrays">
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
33 <assert_contents>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
34 <has_h5_keys keys="loss_history,mnist_images,mnist_labels,tot_loss"/>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
35 </assert_contents>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
36 </output>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
37 </test>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
38 <test expect_num_outputs="3">
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
39 <param name="select_file" value="scikit-script.py" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
40 <output name="outfile_output_zip" file="zipped_file_sk.zip" ftype="zip" compare="sim_size" delta="5" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
41 <output name="outfile_output_arrays">
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
42 <assert_contents>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
43 <has_h5_keys keys="X,X_test,X_train,loss,y,y_test,y_train" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
44 </assert_contents>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
45 </output>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
46 </test>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
47 <test>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
48 <param name="select_file" value="tf-script.py" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
49 <output_collection name="onnx_models" type="list">
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
50 <element name="onnx_model_mnist_model.onnx" file="onnx_model_mnist_model.onnx" ftype="onnx" compare="sim_size" delta="100" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
51 </output_collection>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
52 </test>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
53 <test>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
54 <param name="select_file" value="scikit-script.py" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
55 <output_collection name="onnx_models" type="list">
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
56 <element name="onnx_model_clr.onnx" file="onnx_model_clr.onnx" ftype="onnx" compare="sim_size" delta="50" />
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
57 </output_collection>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
58 </test>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
59 </tests>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
60 <help>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
61 <![CDATA[
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
62 **What it does**
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
63
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
64 **Description**
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
65
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
66 Runs a long running job on Galaxy's cluster.
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
67
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
68 -----
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
69
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
70 **Output file**
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
71
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
72 Returns a model.
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
73
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
74 ]]>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
75 </help>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
76 <citations>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
77 <citation type="bibtex">
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
78 @ARTICLE{anuprulez_galaxytools,
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
79 Author = {Anup Kumar and Björn Grüning},
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
80 keywords = {Galaxy tool},
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
81 title = {{Tool for long running jobs}},
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
82 url = {}
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
83 }
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
84 </citation>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
85 </citations>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
bgruening
parents:
diff changeset
86 </tool>