Mercurial > repos > imgteam > color_deconvolution
changeset 1:0976b373a321 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ commit b2acc1845a25828181597fe5b6982fe116a7796d
| author | imgteam |
|---|---|
| date | Mon, 22 Jul 2019 05:02:00 -0400 |
| parents | 8aa6e767f737 |
| children | 612aa1478fe1 |
| files | color-deconvolution.xml color_deconvolution.py |
| diffstat | 2 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/color-deconvolution.xml Sat Feb 09 14:32:37 2019 -0500 +++ b/color-deconvolution.xml Mon Jul 22 05:02:00 2019 -0400 @@ -1,13 +1,14 @@ -<tool id="ip_color_deconvolution" name="Color Deconvolution" version="0.7"> +<tool id="ip_color_deconvolution" name="Color Deconvolution" version="0.8"> <description>Color deconvolution</description> <requirements> <requirement type="package" version="0.14.2">scikit-image</requirement> <requirement type="package" version="4.0.0">pillow</requirement> <requirement type="package" version="0.18.1">scikit-learn</requirement> <requirement type="package" version="1.12">numpy</requirement> + <requirement type="package" version="0.15.1">tifffile</requirement> </requirements> - <command> - <![CDATA[ + <command detect_errors="aggressive"> + <![CDATA[ python '$__tool_directory__/color_deconvolution.py' '$input' '$output' '$convtype' ]]> </command>
--- a/color_deconvolution.py Sat Feb 09 14:32:37 2019 -0500 +++ b/color_deconvolution.py Mon Jul 22 05:02:00 2019 -0400 @@ -74,7 +74,7 @@ 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 (TIFF)') parser.add_argument('conv_type', choices=convOptions.keys(), help='conversion type') -args = parser.parse_args() +args = parser.parse_args() img_in = skimage.io.imread(args.input_file.name)[:,:,0:3] res = convOptions[args.conv_type](img_in)