Mercurial > repos > thomaswollmann > 2d_feature_extraction
diff 2d_feature_extraction.xml @ 0:4d6e6901df43 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author | thomaswollmann |
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date | Wed, 16 Jan 2019 15:32:39 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2d_feature_extraction.xml Wed Jan 16 15:32:39 2019 -0500 @@ -0,0 +1,88 @@ +<?xml version="1.0"?> +<tool name="2D Feature Extraction" id="ip_2d_feature_extraction" version="0.0.8"> + <description>Feature Extraction</description> + <requirements> + <requirement type="package" version="0.23.4">pandas</requirement> + <requirement type="package" version="0.14.0">scikit-image</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> + <requirement type="package" version="0.15.1">tifffile</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/2d_feature_extraction.py' + #if $feature_options['features'] == 'all' + --all + #else if $feature_options['features'] == 'select' + ${' '.join(str( $feature_options['selected_features'] ).split(','))} + #end if + #if $use_raw_option['use_raw'] == 'raw_image' + --raw '$input_raw' + #end if + '$input_label' '$output' + ]]> + </command> + <inputs> + <param name="input_label" type="data" format="tiff" label="Label file" /> + <conditional name="use_raw_option"> + <param label="Use original image to compute additional features" name="use_raw" type="select"> + <option selected="True" value="no_original">No original image</option> + <option value="raw_image">Use original image</option> + </param> + <when value="no_original"> </when> + <when value="raw_image"> + <param name="input_raw" type="data" format="tiff" label="Original image file" /> + </when> + </conditional> + <conditional name="feature_options"> + <param label="Select features to compute" name="features" type="select"> + <option selected="True" value="all">All features</option> + <option value="select">Select features</option> + </param> + <when value="all"> </when> + <when value="select"> + <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes"> + <option value="--label">Add label id of label image</option> + <option value="--patches">Patches (requires original image)</option> + <option value="--max_intensity">Max Intensity (requires original image)</option> + <option value="--mean_intensity">Mean Intensity (requires original image)</option> + <option value="--min_intensity">Minimum Intensity (requires original image)</option> + <option value="--moments_hu">Moments Hu</option> + <option value="--centroid">Centroid</option> + <option value="--bbox">Bounding Box</option> + <option value="--area">Area</option> + <option value="--filled_area">Filled Area</option> + <option value="--convex_area">Convex Area</option> + <option value="--perimeter">Perimeter</option> + <option value="--extent">Extent</option> + <option value="--eccentricity">Eccentricity</option> + <option value="--equivalent_diameter">Equivalent Diameter</option> + <option value="--euler_number">Euler Number</option> + <option value="--inertia_tensor_eigvals">Inertia Tensor Eigenvalues</option> + <option value="--major_axis_length">Major Axis Length</option> + <option value="--minor_axis_length">Minor Axis Length</option> + <option value="--orientation">Orientation</option> + <option value="--solidity">Solidity</option> + <option value="--moments">Moments</option> + <option value="--convexity">Convexity</option> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + <tests> + <test> + <param name="input_label" value="input.tiff"/> + <param name="features" value="select"/> + <param name="selected_features" value="--area"/> + <output name="output" ftype="tabular" value="out.csv"/> + </test> + </tests> + <help> + This tool computes several features of a 2D label image and optionally more features using the original image. + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>