Mercurial > repos > bgruening > run_jupyter_job

annotate 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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f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
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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">
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
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2 <description>inside a Docker container</description>
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3 <requirements>
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4 <container type="docker">docker.io/anupkumar/docker-ml-jupyterlab:galaxy-integration-0.1</container>
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7 python '${__tool_directory__}/main.py'
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8 --ml_paths '$ml_h5_dataset_paths'
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
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9 --loaded_file '$select_file'
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10 --working_dir `pwd`
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11 --output_array '$outfile_output_arrays'
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12 --output_zip '$outfile_output_zip'
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13 --ml_h5_files '$ml_h5_datasets'
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="ml_h5_dataset_paths" type="text" label="Data paths" optional="true" />
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18 <param name="select_file" type="data" label="Load file" format="txt" />
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19 <param name="ml_h5_datasets" type="data" label="Input h5 dataset" format="h5" multiple="true" optional="true" />
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20 </inputs>
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21 <outputs>
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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"
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23 <data format="zip" name="outfile_output_zip" label="Zipped files"></data>
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24 <collection name="onnx_models" type="list" label="Trained models">
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25 <discover_datasets format="onnx" pattern="__name__" visible="false" directory="model_outputs" />
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26 </collection>
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27 </outputs>
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28 <tests>
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29 <test expect_num_outputs="3">
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30 <param name="select_file" value="tf-script.py" />
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31 <output name="outfile_output_zip" file="zipped_file_tf.zip" ftype="zip" compare="sim_size" delta="50" />
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32 <output name="outfile_output_arrays">
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33 <assert_contents>
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34 <has_h5_keys keys="loss_history,mnist_images,mnist_labels,tot_loss"/>
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35 </assert_contents>
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36 </output>
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37 </test>
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38 <test expect_num_outputs="3">
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39 <param name="select_file" value="scikit-script.py" />
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40 <output name="outfile_output_zip" file="zipped_file_sk.zip" ftype="zip" compare="sim_size" delta="5" />
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41 <output name="outfile_output_arrays">
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42 <assert_contents>
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43 <has_h5_keys keys="X,X_test,X_train,loss,y,y_test,y_train" />
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44 </assert_contents>
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45 </output>
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46 </test>
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47 <test>
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48 <param name="select_file" value="tf-script.py" />
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49 <output_collection name="onnx_models" type="list">
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50 <element name="onnx_model_mnist_model.onnx" file="onnx_model_mnist_model.onnx" ftype="onnx" compare="sim_size" delta="100" />
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51 </output_collection>
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52 </test>
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53 <test>
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54 <param name="select_file" value="scikit-script.py" />
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55 <output_collection name="onnx_models" type="list">
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56 <element name="onnx_model_clr.onnx" file="onnx_model_clr.onnx" ftype="onnx" compare="sim_size" delta="50" />
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57 </output_collection>
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58 </test>
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59 </tests>
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60 <help>
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61 <![CDATA[
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
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62 **What it does**
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63
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
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64 **Description**
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65
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
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66 Runs a long running job on Galaxy's cluster.
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67
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68 -----
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69
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
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70 **Output file**
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71
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
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72 Returns a model.
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73
f4619200cb0a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit f945b1bff5008ba01da31c7de64e5326579394d6"
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74 ]]>
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75 </help>
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76 <citations>
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77 <citation type="bibtex">
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78 @ARTICLE{anuprulez_galaxytools,
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79 Author = {Anup Kumar and Björn Grüning},
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80 keywords = {Galaxy tool},
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81 title = {{Tool for long running jobs}},
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82 url = {}
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83 }
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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>