[skip-ci]

* fix remote repo urls

* Leave the correct ones as is

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/

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/

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/

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/

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/

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/

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/

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/

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/

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/

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/

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/

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/

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/

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

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/

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/

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/

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/

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/

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/

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/

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

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/

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/

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/

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/

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/

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/

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/

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/

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/

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/

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/

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

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/