Mercurial > repos > imgteam > 2d_filter_segmentation_by_features
changeset 1:6ad1d3cfdea1 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
| author | imgteam |
|---|---|
| date | Mon, 13 Nov 2023 22:10:21 +0000 |
| parents | e576b73a2e2f |
| children | 8f76184ca03f |
| files | 2d_filter_segmentation_by_features.py 2d_filter_segmentation_by_features.xml |
| diffstat | 2 files changed, 22 insertions(+), 14 deletions(-) [+] |
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--- a/2d_filter_segmentation_by_features.py Mon Jul 22 05:00:03 2019 -0400 +++ b/2d_filter_segmentation_by_features.py Mon Nov 13 22:10:21 2023 +0000 @@ -1,8 +1,10 @@ import argparse import sys -import skimage.io + +import pandas as pd +import skimage.io import skimage.util -import pandas as pd + if __name__ == "__main__": parser = argparse.ArgumentParser(description='Filter segmentation by features') @@ -15,8 +17,8 @@ img_in = skimage.io.imread(args.input_file.name) features = pd.read_csv(args.feature_file, delimiter="\t") rules = pd.read_csv(args.rule_file, delimiter="\t") - - cols = [a for a in rules.columns if not 'Unnamed' in a] + + cols = [a for a in rules.columns if 'Unnamed' not in a] for a_c in cols: a_min = rules[rules.ix[:, 0] == 'min'][a_c] a_max = rules[rules.ix[:, 0] == 'max'][a_c]
--- a/2d_filter_segmentation_by_features.xml Mon Jul 22 05:00:03 2019 -0400 +++ b/2d_filter_segmentation_by_features.xml Mon Nov 13 22:10:21 2023 +0000 @@ -1,17 +1,23 @@ -<tool id="ip_2d_filter_segmentation_by_features" name="Filter segmentation" version="0.0.1"> - <description>Filter segmentation by rules</description> - <requirements> +<tool id="ip_2d_filter_segmentation_by_features" name="Filter label map by rules" version="0.0.1-2"> + <description></description> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">galaxy_image_analysis</xref> + </xrefs> + <requirements> <requirement type="package" version="0.14.2">scikit-image</requirement> <requirement type="package" version="5.3.0">pillow</requirement> <requirement type="package" version="0.23.4">pandas</requirement> <requirement type="package" version="0.15.1">tifffile</requirement> - </requirements> - <command detect_errors="aggressive"> - <![CDATA[ - python '$__tool_directory__/2d_filter_segmentation_by_features.py' '$input' '$output' '$feature_file' '$rule_file' - ]]> - </command> - <inputs> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + python '$__tool_directory__/2d_filter_segmentation_by_features.py' '$input' '$output' '$feature_file' '$rule_file' + ]]> + </command> + <inputs> <param name="input" type="data" format="tiff" label="Source file" /> <param name="feature_file" type="data" format="tabular" label="Feature file" /> <param name="rule_file" type="data" format="tabular" label="Rules file" />