| Previous changeset 2:f3c05a734dd1 (2019-07-22) Next changeset 4:3179853faae9 (2024-04-04) |
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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d |
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modified:
scale_image.py scale_image.xml |
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| diff -r f3c05a734dd1 -r d09507d3fb0e scale_image.py --- a/scale_image.py Mon Jul 22 05:04:55 2019 -0400 +++ b/scale_image.py Fri Nov 10 14:23:33 2023 +0000 |
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| @@ -1,13 +1,14 @@ import argparse import sys + +import scipy.misc import skimage.io import skimage.transform -import scipy.misc from PIL import Image - + def scale_image(input_file, output_file, scale, order=1): - Image.MAX_IMAGE_PIXELS = 50000*50000 + Image.MAX_IMAGE_PIXELS = 50000 * 50000 img_in = skimage.io.imread(input_file) if order == 0: interp = 'nearest' @@ -29,8 +30,8 @@ if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') - parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (PNG)') - parser.add_argument('scale', type=str, help='fraction scaling factor(float), percentage scaling factor(int), output size(tuple(height,width))') # integer option not implemented in galaxy wrapper + parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (PNG)') + parser.add_argument('scale', type=str, help='fraction scaling factor(float), percentage scaling factor(int), output size(tuple(height,width))') # integer option not implemented in galaxy wrapper parser.add_argument('order', type=int, default=1, help='interpolation method') args = parser.parse_args() |
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| diff -r f3c05a734dd1 -r d09507d3fb0e scale_image.xml --- a/scale_image.xml Mon Jul 22 05:04:55 2019 -0400 +++ b/scale_image.xml Fri Nov 10 14:23:33 2023 +0000 |
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| @@ -1,5 +1,12 @@ -<tool id="ip_scale_image" name="Scale Image" version="0.4"> - <description>Scales image</description> +<tool id="ip_scale_image" name="Scale image" version="0.4-2"> + <description>with scikit-image</description> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">scikit-image</xref> + <xref type="biii">scikit-image</xref> + </xrefs> <requirements> <requirement type="package" version="6.1.0">pillow</requirement> <requirement type="package" version="0.14.2">scikit-image</requirement> @@ -46,9 +53,11 @@ <tests> <test> <param name="input" value="sample1.png"/> <!--continue here--> - <param name="use_scale_option.use_scale" value="false"/> - <param name="use_scale_option.scale_x" value="200"/> - <param name="use_scale_option.scale_y" value="150"/> + <conditional name="use_scale_option"> + <param name="use_scale" value="false"/> + <param name="scale_x" value="200"/> + <param name="scale_y" value="150"/> + </conditional> <param name="order" value="0"/> <output name="output" value="out2.png" ftype="png" compare="sim_size"/> </test> |