| Previous changeset 0:a1d02d2e814a (2019-02-09) Next changeset 2:3bd767eee603 (2023-11-13) |
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Commit message:
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90" |
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modified:
wsi_extract_top_view.py wsi_extract_top_view.xml |
| b |
| diff -r a1d02d2e814a -r cfe88c6041e9 wsi_extract_top_view.py --- a/wsi_extract_top_view.py Sat Feb 09 14:49:03 2019 -0500 +++ b/wsi_extract_top_view.py Wed Dec 18 05:03:44 2019 -0500 |
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| @@ -4,7 +4,7 @@ import fnmatch import skimage.io import numpy as np - + def wsi_extract_top_view(input_path, out_path): img_raw = openslide.OpenSlide(input_path) top_size = img_raw.level_dimensions[len(img_raw.level_dimensions)-1] @@ -18,5 +18,5 @@ parser.add_argument('input_file', type=argparse.FileType('r'), help='input file') parser.add_argument('out_file', help='out file') args = parser.parse_args() - + wsi_extract_top_view(args.input_file.name, args.out_file) |
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| diff -r a1d02d2e814a -r cfe88c6041e9 wsi_extract_top_view.xml --- a/wsi_extract_top_view.xml Sat Feb 09 14:49:03 2019 -0500 +++ b/wsi_extract_top_view.xml Wed Dec 18 05:03:44 2019 -0500 |
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| @@ -1,12 +1,13 @@ -<tool id="ip_wsi_extract_top_view" name="Extract top view" version="0.1"> +<tool id="ip_wsi_extract_top_view" name="Extract top view" version="0.2"> <description>from whole-slice image</description> - <requirements> + <requirements> <requirement type="package" version="0.14.2">scikit-image</requirement> <requirement type="package" version="1.15.4">numpy</requirement> <requirement type="package" version="1.1.1">openslide-python</requirement> <requirement type="package" version="0.5">glob2</requirement> + <requirement type="package" version="0.15.1">tifffile</requirement> </requirements> - <command> + <command detect_errors="aggressive"> <![CDATA[ python '$__tool_directory__/wsi_extract_top_view.py' '$input' '$output' ]]> |