Mercurial > repos > imgteam > overlay_segmentation_mask
changeset 2:22e573b7dcb1 draft default tip
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 0500f513ee291ae0f6fad32a0b4fad05cd59cb71"
| author | imgteam |
|---|---|
| date | Sat, 26 Feb 2022 17:14:53 +0000 |
| parents | 8ad39f493587 |
| children | |
| files | overlay_segmentation_mask.py overlay_segmentation_mask.xml test-data/outt.png |
| diffstat | 3 files changed, 11 insertions(+), 15 deletions(-) [+] |
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--- a/overlay_segmentation_mask.py Mon Jul 22 05:03:51 2019 -0400 +++ b/overlay_segmentation_mask.py Sat Feb 26 17:14:53 2022 +0000 @@ -1,20 +1,17 @@ import argparse -import sys -import os import matplotlib -matplotlib.use('Agg') import matplotlib.pyplot as plt +import skimage.io +import skimage.measure -#TODO make importable by python script - -import skimage.io -import skimage.measure +matplotlib.use('Agg') +# TODO make importable by python script parser = argparse.ArgumentParser() parser.add_argument('input_file', type=argparse.FileType('r'), help='input file') parser.add_argument('mask_file', type=argparse.FileType('r'), help='mask file') -parser.add_argument('out_file', type=str, help='out file (PNG)') # file would be created immediately with argparse.FileType('w') s.t. file cannot be renamed on galaxy +parser.add_argument('out_file', type=str, help='out file (PNG)') # file would be created immediately with argparse.FileType('w') s.t. file cannot be renamed on galaxy parser.add_argument('--grey', dest='greyscale', action='store_true', help='image is greyscale') parser.add_argument('--label', dest='label', action='store_true', help='plot label') parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='label color')
--- a/overlay_segmentation_mask.xml Mon Jul 22 05:03:51 2019 -0400 +++ b/overlay_segmentation_mask.xml Sat Feb 26 17:14:53 2022 +0000 @@ -1,11 +1,9 @@ -<tool id="ip_overlay_segmentation" name="Overlay Segmentation Mask" version="0.0.6"> +<tool id="ip_overlay_segmentation" name="Overlay Segmentation Mask" version="0.0.7" profile="20.05"> <description>Overlay Segmentation Mask</description> <requirements> - <requirement type="package" version="0.14.2">scikit-image</requirement> - <requirement type="package" version="3.0.2">matplotlib</requirement> - <requirement type="package" version="5.3.0">pillow</requirement> - <requirement type="package" version="0.15.1">tifffile</requirement> - <requirement type="package" version="1.16.0">numpy</requirement> + <requirement type="package" version="0.18.1">scikit-image</requirement> + <requirement type="package" version="3.3.4">matplotlib</requirement> + <requirement type="package" version="1.20.2">numpy</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ python '$__tool_directory__/overlay_segmentation_mask.py' @@ -53,8 +51,9 @@ **What it does** This tool overlays a segmentation mask over an image. + + Note: This tool is deprecated and may not be supported in future. Please use the tool "Overlay Images" instead. </help> <citations> - <citation type="doi">10.7717/peerj.453</citation> </citations> </tool>