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Merge pull request #16837 from lldelisle/ilastik
Add Interactive Tool Ilastik
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| <tool id="interactive_tool_ilastik" tool_type="interactive" name="Ilastik" version="@VERSION@" profile="23.0"> | ||
| <description>interactive learning and segmentation toolkit</description> | ||
| <macros> | ||
| <token name="@VERSION@">1.4.0</token> | ||
| </macros> | ||
| <requirements> | ||
| <container type="docker">quay.io/galaxy/ilastik:@VERSION@</container> | ||
| </requirements> | ||
| <entry_points> | ||
| <entry_point name="Ilastik" requires_domain="True"> | ||
| <port>5800</port> | ||
| </entry_point> | ||
| </entry_points> | ||
| <command detect_errors="exit_code"> | ||
| <![CDATA[ | ||
| ## Check inputs have no duplicated element_identifier: | ||
| #set labels = [input.element_identifier for input in $infiles] | ||
| #set duplicates = [label for label in labels if labels.count(label) > 1] | ||
| #if len(duplicates) > 0: | ||
| #set unique_duplicates = list(set(duplicates)) | ||
| echo "Cannot run ilastik because these identifiers are present more than once:" && | ||
| #for label in $unique_duplicates: | ||
| echo $label && | ||
| #end for | ||
| exit 1 && | ||
| #end if | ||
| export HOME=\$PWD && | ||
| ## Create a directory where the app user has access | ||
| mkdir -p ./output && | ||
| chown 1000:1000 ./output/ && | ||
| ## Make a copy of the existing project if exists | ||
| #if str($input_type.existing) == "existing": | ||
| cp '$input_type.project' ./output/MyProject.ilp && | ||
| #end if | ||
| ## Link input images to current working directory | ||
| #for input in $infiles: | ||
| ln -s '$input' ./'$input.element_identifier'.tif && | ||
| #end for | ||
| ## Write the bash script to run: | ||
| #if str($input_type.existing) == "new": | ||
| echo "ilastik --new_project \$HOME/output/MyProject.ilp --workflow '$input_type.Workflow'" > ./ilastik_with_args && | ||
| #else: | ||
| echo "ilastik --project \$HOME/output/MyProject.ilp" > ./ilastik_with_args && | ||
| #end if | ||
| ## Copy it to /bin/ so it will be used by the container: | ||
| chmod +x ./ilastik_with_args && | ||
| cp ./ilastik_with_args '/bin/' && | ||
| /init | ||
| ]]> | ||
| </command> | ||
| <inputs> | ||
| <conditional name="input_type"> | ||
| <param name="existing" type="select" label="Which project you want to work on?"> | ||
| <option value="new">Start a new project</option> | ||
| <option value="existing">Modify an existing project</option> | ||
| </param> | ||
| <when value="new"> | ||
| <param name="Workflow" type="select" label="Type of Workflow" > | ||
| <option value="PixelClassificationWorkflow">Pixel Classification</option> | ||
| <option value="AutocontextTwoStage">Autocontext (2-stage)</option> | ||
| <option value="ObjectClassificationWorkflowPixel">Pixel Classification + Object Classification</option> | ||
| <option value="ObjectClassificationWorkflowPrediction">Object Classification [Inputs: Raw Data, Pixel Prediction Map]</option> | ||
| <option value="ObjectClassificationWorkflowBinary">Object Classification [Inputs: Raw Data, Segmentation]</option> | ||
| <option value="ConservationTrackingWorkflowFromBinary">Tracking [Inputs: Raw Data, Segmentation Image]</option> | ||
| <option value="ConservationTrackingWorkflowFromPrediction">Tracking [Inputs: Raw Data, Pixel Prediction Map]</option> | ||
| <option value="AnimalConservationTrackingWorkflowFromBinary">Animal Tracking [Inputs: Raw Data, Segmentation Image]</option> | ||
| <option value="AnimalConservationTrackingWorkflowFromPrediction">Animal Tracking [Inputs: Raw Data, Pixel Prediction Map]</option> | ||
| <option value="StructuredTrackingWorkflowFromBinary">Tracking with Learning [Inputs: Raw Data, Segmentation Image]</option> | ||
| <option value="StructuredTrackingWorkflowFromPrediction">Tracking with Learning [Inputs: Raw Data, Pixel Prediction Map]</option> | ||
| <option value="EdgeTrainingWithMulticutWorkflow">Bounary-based Segmentation with Multicut</option> | ||
| <option value="CountingWorkflow">Cell Density Counting</option> | ||
| <option value="DataConversionWorkflow">Data Conversion</option> | ||
| <option value="neuralNetwork.RemoteWorkflow">Neural Network Classification (Remote)</option> | ||
| <option value="neuralNetwork.LocalWorkflow">Neural Network Classification (Local)</option> | ||
| </param> | ||
| </when> | ||
| <when value="existing"> | ||
| <param argument="--project" type="data" format="h5" label="Existing ilastik project" /> | ||
| </when> | ||
| </conditional> | ||
| <param name="infiles" type="data" format="tiff" multiple="true" label="Input files in TIFF format"/> | ||
| </inputs> | ||
|
|
||
| <outputs> | ||
| <data name="ilastik_project" format="h5" label="Ilastik project file" from_work_dir="output/MyProject.ilp"/> | ||
| </outputs> | ||
|
|
||
| <tests> | ||
| </tests> | ||
|
|
||
| <help><![CDATA[ | ||
| Leverage machine learning algorithms to easily segment, classify, track and count your cells or other experimental data. Most operations are interactive, even on large datasets: you just draw the labels and immediately see the result. No machine learning expertise required. | ||
| This tool has been designed uniquely to make/modify a project. | ||
| - It requires that input images have unique identifiers. | ||
| - When you have trained your project, save it and quit the application. The project called 'MyProject.ilp' will be imported into your history. | ||
| - If you want to modify a project, make sure you use at least the same images (with the same identifiers) as the first time (but you can add more). | ||
| Please, check the documentation at https://www.ilastik.org/documentation/. | ||
| ]]> | ||
| </help> | ||
| <citations> | ||
| <citation type="doi">10.1038/s41592-019-0582-9</citation> | ||
| </citations> | ||
| </tool> |