Mercurial > repos > bgruening > run_jupyter_job

comparison run_jupyter_job.xml @ 0:f4619200cb0a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
author bgruening
date Sat, 11 Dec 2021 17:56:38 +0000
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children c93b2676a27d
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1 <tool id="run_jupyter_job" name="Run long running jupyterlab script" hidden="true" version="0.0.1" profile="21.09">
2 <description>inside a Docker container</description>
3 <requirements>
4 <container type="docker">docker.io/anupkumar/docker-ml-jupyterlab:galaxy-integration-0.1</container>
5 </requirements>
6 <command detect_errors="aggressive"><![CDATA[
7 python '${__tool_directory__}/main.py'
8 --ml_paths '$ml_h5_dataset_paths'
9 --loaded_file '$select_file'
10 --working_dir `pwd`
11 --output_array '$outfile_output_arrays'
12 --output_zip '$outfile_output_zip'
13 --ml_h5_files '$ml_h5_datasets'
14 ]]>
15 </command>
16 <inputs>
17 <param name="ml_h5_dataset_paths" type="text" label="Data paths" optional="true" />
18 <param name="select_file" type="data" label="Load file" format="txt" />
19 <param name="ml_h5_datasets" type="data" label="Input h5 dataset" format="h5" multiple="true" optional="true" />
20 </inputs>
21 <outputs>
22 <data format="h5" name="outfile_output_arrays" label="Saved arrays"></data>
23 <data format="zip" name="outfile_output_zip" label="Zipped files"></data>
24 <collection name="onnx_models" type="list" label="Trained models">
25 <discover_datasets format="onnx" pattern="__name__" visible="false" directory="model_outputs" />
26 </collection>
27 </outputs>
28 <tests>
29 <test expect_num_outputs="3">
30 <param name="select_file" value="tf-script.py" />
31 <output name="outfile_output_zip" file="zipped_file_tf.zip" ftype="zip" compare="sim_size" delta="50" />
32 <output name="outfile_output_arrays">
33 <assert_contents>
34 <has_h5_keys keys="loss_history,mnist_images,mnist_labels,tot_loss"/>
35 </assert_contents>
36 </output>
37 </test>
38 <test expect_num_outputs="3">
39 <param name="select_file" value="scikit-script.py" />
40 <output name="outfile_output_zip" file="zipped_file_sk.zip" ftype="zip" compare="sim_size" delta="5" />
41 <output name="outfile_output_arrays">
42 <assert_contents>
43 <has_h5_keys keys="X,X_test,X_train,loss,y,y_test,y_train" />
44 </assert_contents>
45 </output>
46 </test>
47 <test>
48 <param name="select_file" value="tf-script.py" />
49 <output_collection name="onnx_models" type="list">
50 <element name="onnx_model_mnist_model.onnx" file="onnx_model_mnist_model.onnx" ftype="onnx" compare="sim_size" delta="100" />
51 </output_collection>
52 </test>
53 <test>
54 <param name="select_file" value="scikit-script.py" />
55 <output_collection name="onnx_models" type="list">
56 <element name="onnx_model_clr.onnx" file="onnx_model_clr.onnx" ftype="onnx" compare="sim_size" delta="50" />
57 </output_collection>
58 </test>
59 </tests>
60 <help>
61 <![CDATA[
62 **What it does**
63
64 **Description**
65
66 Runs a long running job on Galaxy's cluster.
67
68 -----
69
70 **Output file**
71
72 Returns a model.
73
74 ]]>
75 </help>
76 <citations>
77 <citation type="bibtex">
78 @ARTICLE{anuprulez_galaxytools,
79 Author = {Anup Kumar and Björn Grüning},
80 keywords = {Galaxy tool},
81 title = {{Tool for long running jobs}},
82 url = {}
83 }
84 </citation>
85 </citations>
86 </tool>