diff --git a/tools/2d_auto_threshold/.shed.yml b/tools/2d_auto_threshold/.shed.yml index 49a2a20c..45e98def 100644 --- a/tools/2d_auto_threshold/.shed.yml +++ b/tools/2d_auto_threshold/.shed.yml @@ -5,4 +5,4 @@ long_description: Applying a standard thresholding method to an image. name: 2d_auto_threshold owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ diff --git a/tools/2d_feature_extraction/.shed.yml b/tools/2d_feature_extraction/.shed.yml index bca086b1..3e02b15a 100644 --- a/tools/2d_feature_extraction/.shed.yml +++ b/tools/2d_feature_extraction/.shed.yml @@ -5,4 +5,4 @@ long_description: Extraction of various features in 2D. name: 2d_feature_extraction owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ diff --git a/tools/2d_filter_segmentation_by_features/.shed.yml b/tools/2d_filter_segmentation_by_features/.shed.yml index cf229f95..f1c72c46 100644 --- a/tools/2d_filter_segmentation_by_features/.shed.yml +++ b/tools/2d_filter_segmentation_by_features/.shed.yml @@ -5,4 +5,4 @@ long_description: Filter segmentation by features name: 2d_filter_segmentation_by_features owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/2d_filter_segmentation_by_features/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ diff --git a/tools/2d_histogram_equalization/.shed.yml b/tools/2d_histogram_equalization/.shed.yml index 164f64a6..834aca1d 100644 --- a/tools/2d_histogram_equalization/.shed.yml +++ b/tools/2d_histogram_equalization/.shed.yml @@ -5,4 +5,4 @@ long_description: Automatic histogram equalization in 2D name: 2d_histogram_equalization owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ diff --git a/tools/2d_simple_filter/.shed.yml b/tools/2d_simple_filter/.shed.yml index dd04756a..1de2f8cd 100644 --- a/tools/2d_simple_filter/.shed.yml +++ b/tools/2d_simple_filter/.shed.yml @@ -5,4 +5,4 @@ long_description: Simple filter in 2D name: 2d_simple_filter owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ diff --git a/tools/2d_split_binaryimage_by_watershed/.shed.yml b/tools/2d_split_binaryimage_by_watershed/.shed.yml index b2dd0a08..5169850d 100644 --- a/tools/2d_split_binaryimage_by_watershed/.shed.yml +++ b/tools/2d_split_binaryimage_by_watershed/.shed.yml @@ -5,4 +5,4 @@ long_description: Split binary image by using distance transform and watershed name: 2d_split_binaryimage_by_watershed owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_split_binaryimage_by_watershed/ diff --git a/tools/anisotropic_diffusion/.shed.yml b/tools/anisotropic_diffusion/.shed.yml index 8067f6ca..76e8a7a7 100644 --- a/tools/anisotropic_diffusion/.shed.yml +++ b/tools/anisotropic_diffusion/.shed.yml @@ -5,4 +5,4 @@ long_description: Edge-preserving, Anisotropic image diffusion. name: anisotropic_diffusion owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ diff --git a/tools/bfconvert/.shed.yml b/tools/bfconvert/.shed.yml index 727603bb..ff880d38 100644 --- a/tools/bfconvert/.shed.yml +++ b/tools/bfconvert/.shed.yml @@ -6,4 +6,4 @@ long_description: Convert image using biotools name: bfconvert owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ diff --git a/tools/binary2labelimage/.shed.yml b/tools/binary2labelimage/.shed.yml index 5b90399c..5e96937f 100644 --- a/tools/binary2labelimage/.shed.yml +++ b/tools/binary2labelimage/.shed.yml @@ -5,4 +5,4 @@ long_description: This tools converts a binary image to a label image (every obj name: binary2labelimage owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ diff --git a/tools/binaryimage2points/.shed.yml b/tools/binaryimage2points/.shed.yml index 1c962fc0..67c2058f 100644 --- a/tools/binaryimage2points/.shed.yml +++ b/tools/binaryimage2points/.shed.yml @@ -6,4 +6,4 @@ long_description: This tool calculates the center of mass of a binary image. name: binaryimage2points owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ diff --git a/tools/color-deconvolution/.shed.yml b/tools/color-deconvolution/.shed.yml index 85f410b1..246850dc 100644 --- a/tools/color-deconvolution/.shed.yml +++ b/tools/color-deconvolution/.shed.yml @@ -5,4 +5,4 @@ long_description: This tools does color space transformation using preset transf name: color_deconvolution owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/ diff --git a/tools/concat_channels/.shed.yml b/tools/concat_channels/.shed.yml index 84561355..49c974a2 100644 --- a/tools/concat_channels/.shed.yml +++ b/tools/concat_channels/.shed.yml @@ -5,4 +5,4 @@ long_description: This tool concatenates images. name: concat_channels owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/concat_channels/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ diff --git a/tools/coordinates_of_roi/.shed.yml b/tools/coordinates_of_roi/.shed.yml index 7fb3aaca..71adb047 100644 --- a/tools/coordinates_of_roi/.shed.yml +++ b/tools/coordinates_of_roi/.shed.yml @@ -5,4 +5,4 @@ long_description: Obtains the coordinates regions of interest on an image name: coordinates_of_roi owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ diff --git a/tools/count_objects/.shed.yml b/tools/count_objects/.shed.yml index d909bfc3..cafcaf29 100644 --- a/tools/count_objects/.shed.yml +++ b/tools/count_objects/.shed.yml @@ -5,4 +5,4 @@ long_description: Count objects in an image name: count_objects owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ diff --git a/tools/curl_post/.shed.yml b/tools/curl_post/.shed.yml index d3c47303..34d88097 100644 --- a/tools/curl_post/.shed.yml +++ b/tools/curl_post/.shed.yml @@ -6,4 +6,4 @@ long_description: This tool uses cURL to send a file via POST. name: curl_post owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/curl_post +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post diff --git a/tools/detection_viz/.shed.yml b/tools/detection_viz/.shed.yml index 0975220e..9f4743db 100644 --- a/tools/detection_viz/.shed.yml +++ b/tools/detection_viz/.shed.yml @@ -5,4 +5,4 @@ long_description: This tool visualizes detection. name: detection_viz owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ diff --git a/tools/image_info/.shed.yml b/tools/image_info/.shed.yml index 5633a2ef..78b0e92d 100644 --- a/tools/image_info/.shed.yml +++ b/tools/image_info/.shed.yml @@ -5,4 +5,4 @@ long_description: This tool extracts metadata from an image. name: image_info owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/image_info/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/ diff --git a/tools/image_registration_affine/.shed.yml b/tools/image_registration_affine/.shed.yml index 8635e0f4..15e3816e 100644 --- a/tools/image_registration_affine/.shed.yml +++ b/tools/image_registration_affine/.shed.yml @@ -6,4 +6,4 @@ description: Intensity-based Image Registration long_description: | This tool estimates the (affine) transformation matrix for registration of two images based on intensity information. homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/image_registration_affine/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/ diff --git a/tools/imagecoordinates_flipaxis/.shed.yml b/tools/imagecoordinates_flipaxis/.shed.yml index f29adc68..8a77b905 100644 --- a/tools/imagecoordinates_flipaxis/.shed.yml +++ b/tools/imagecoordinates_flipaxis/.shed.yml @@ -5,4 +5,4 @@ long_description: Makes x the horizontal axis (left to right) and y the vertical name: imagecoordinates_flipaxis owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/ diff --git a/tools/labelimage2points/.shed.yml b/tools/labelimage2points/.shed.yml index 71567faa..c0b7f689 100644 --- a/tools/labelimage2points/.shed.yml +++ b/tools/labelimage2points/.shed.yml @@ -5,4 +5,4 @@ long_description: This tool converts a label image to points. name: labelimage2points owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ diff --git a/tools/landmark_registration/.shed.yml b/tools/landmark_registration/.shed.yml index e14e49a5..8f028923 100644 --- a/tools/landmark_registration/.shed.yml +++ b/tools/landmark_registration/.shed.yml @@ -6,4 +6,4 @@ long_description: | name: landmark_registration owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/landmark_registration/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/ diff --git a/tools/mahotas-features/.shed.yml b/tools/mahotas-features/.shed.yml index 845cdacf..16dc6864 100644 --- a/tools/mahotas-features/.shed.yml +++ b/tools/mahotas-features/.shed.yml @@ -5,4 +5,4 @@ long_description: Mahotas is a computer vision and image processing library for name: mahotas_features owner: imgteam homepage_url: https://github.com/luispedro/mahotas -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ diff --git a/tools/mergeneighboursinlabelimage/.shed.yml b/tools/mergeneighboursinlabelimage/.shed.yml index 2cc304fc..39326489 100644 --- a/tools/mergeneighboursinlabelimage/.shed.yml +++ b/tools/mergeneighboursinlabelimage/.shed.yml @@ -5,4 +5,4 @@ long_description: This tools merges nearby objects in a label image using the mi name: mergeneighboursinlabelimage owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage diff --git a/tools/permutate_axis/.shed.yml b/tools/permutate_axis/.shed.yml index 7550f8d3..3596ac78 100644 --- a/tools/permutate_axis/.shed.yml +++ b/tools/permutate_axis/.shed.yml @@ -5,4 +5,4 @@ long_description: Edge-preserving, Anisotropic image diffusion. name: permutate_axis owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ diff --git a/tools/points2binaryimage/.shed.yml b/tools/points2binaryimage/.shed.yml index 3fc23a44..36991557 100644 --- a/tools/points2binaryimage/.shed.yml +++ b/tools/points2binaryimage/.shed.yml @@ -5,4 +5,4 @@ long_description: Converts points to binary image. name: points2binaryimage owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ diff --git a/tools/points2labelimage/.shed.yml b/tools/points2labelimage/.shed.yml index 6214cfa9..1b52f957 100644 --- a/tools/points2labelimage/.shed.yml +++ b/tools/points2labelimage/.shed.yml @@ -5,4 +5,4 @@ long_description: Converts points to label image name: points2labelimage owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ diff --git a/tools/projective_transformation/.shed.yml b/tools/projective_transformation/.shed.yml index cf990e5c..36d870c3 100644 --- a/tools/projective_transformation/.shed.yml +++ b/tools/projective_transformation/.shed.yml @@ -5,4 +5,4 @@ long_description: This tool performs a projective transformation of the input (m name: projective_transformation owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ diff --git a/tools/projective_transformation_points/.shed.yml b/tools/projective_transformation_points/.shed.yml index a32c8e44..6ec166ce 100644 --- a/tools/projective_transformation_points/.shed.yml +++ b/tools/projective_transformation_points/.shed.yml @@ -5,4 +5,4 @@ long_description: This tool performs a projective transformation of regions of i name: projective_transformation_points owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ diff --git a/tools/scale_image/.shed.yml b/tools/scale_image/.shed.yml index 8d68791b..e848bff5 100644 --- a/tools/scale_image/.shed.yml +++ b/tools/scale_image/.shed.yml @@ -5,4 +5,4 @@ long_description: Scales image by a certain factor using nearest, bilinear or bi name: scale_image owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ diff --git a/tools/segmetrics/.shed.yml b/tools/segmetrics/.shed.yml index f79ed9dd..85162aab 100644 --- a/tools/segmetrics/.shed.yml +++ b/tools/segmetrics/.shed.yml @@ -5,4 +5,4 @@ long_description: Image segmentation and object detection performance measures f name: segmetrics owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ diff --git a/tools/slice_image/.shed.yml b/tools/slice_image/.shed.yml index 653a6f4d..c667857c 100644 --- a/tools/slice_image/.shed.yml +++ b/tools/slice_image/.shed.yml @@ -5,4 +5,4 @@ long_description: Slices original image into several smaller patches name: slice_image owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ diff --git a/tools/split_labelmap/.shed.yml b/tools/split_labelmap/.shed.yml index 6f59e020..22da1a14 100644 --- a/tools/split_labelmap/.shed.yml +++ b/tools/split_labelmap/.shed.yml @@ -5,4 +5,4 @@ long_description: Separates different labels in the same image by creating a new name: split_labelmap owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/split_labelmaps/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ diff --git a/tools/superdsm/.shed.yml b/tools/superdsm/.shed.yml index 25079efc..2b7005cb 100644 --- a/tools/superdsm/.shed.yml +++ b/tools/superdsm/.shed.yml @@ -5,4 +5,4 @@ long_description: Globally optimal segmentation method based on superadditivity name: superdsm owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ diff --git a/tools/unzip/.shed.yml b/tools/unzip/.shed.yml index 2128db45..bb1e8a96 100644 --- a/tools/unzip/.shed.yml +++ b/tools/unzip/.shed.yml @@ -5,4 +5,4 @@ long_description: Unzip file to collection name: unzip owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ diff --git a/tools/visceral-evaluatesegmentation/.shed.yml b/tools/visceral-evaluatesegmentation/.shed.yml index 583895b3..af89765e 100644 --- a/tools/visceral-evaluatesegmentation/.shed.yml +++ b/tools/visceral-evaluatesegmentation/.shed.yml @@ -5,4 +5,4 @@ long_description: This tools calculates several measures to evaluate image segme name: visceral_evaluatesegmentation owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/visceral-evaluatesegmentation +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation diff --git a/tools/wsi_extract_top_view/.shed.yml b/tools/wsi_extract_top_view/.shed.yml index 004bfdf1..0e800efc 100644 --- a/tools/wsi_extract_top_view/.shed.yml +++ b/tools/wsi_extract_top_view/.shed.yml @@ -5,4 +5,4 @@ long_description: Extracts the top view of a whole-slide image (=virtual slide). name: wsi_extract_top_view owner: imgteam homepage_url: https://github.com/bmcv -remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/