diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 3e63ce24..ec993282 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -8,7 +8,7 @@ on: workflow_dispatch: env: GALAXY_FORK: galaxyproject - GALAXY_BRANCH: release_25.0 + GALAXY_BRANCH: release_26.0 MAX_CHUNKS: 40 jobs: setup: diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 1990956d..792bcddb 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -15,7 +15,7 @@ on: - '*' env: GALAXY_FORK: galaxyproject - GALAXY_BRANCH: release_25.0 + GALAXY_BRANCH: release_26.0 MAX_CHUNKS: 4 MAX_FILE_SIZE: 1M concurrency: diff --git a/tools/parse_image_metadata/.shed.yml b/tools/parse_image_metadata/.shed.yml new file mode 100644 index 00000000..5c96c62e --- /dev/null +++ b/tools/parse_image_metadata/.shed.yml @@ -0,0 +1,15 @@ +categories: +- Imaging + +description: Parse image metadata as parameter values (width, height, number of channels, etc.) + +long_description: | + This tool can be used in workflows to parse parameter values from image metadata. + +name: parse_image_metadata + +owner: imgteam +homepage_url: https://github.com/bmcv +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/parse_image_metadata/ + +type: unrestricted diff --git a/tools/parse_image_metadata/creators.xml b/tools/parse_image_metadata/creators.xml new file mode 120000 index 00000000..5d2b71e0 --- /dev/null +++ b/tools/parse_image_metadata/creators.xml @@ -0,0 +1 @@ +../../macros/creators.xml \ No newline at end of file diff --git a/tools/parse_image_metadata/parse_image_metadata.xml b/tools/parse_image_metadata/parse_image_metadata.xml new file mode 100644 index 00000000..29ae7247 --- /dev/null +++ b/tools/parse_image_metadata/parse_image_metadata.xml @@ -0,0 +1,128 @@ + + + + creators.xml + + + + + + + + operation_3443 + + + { + return { + 'width': parseInt($job.input1.metadata.width), + 'height': parseInt($job.input1.metadata.height), + 'channels': parseInt($job.input1.metadata.channels), + 'depth': parseInt($job.input1.metadata.depth), + 'frames': parseInt($job.input1.metadata.frames) + }; + } + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tools/parse_image_metadata/test-data/input_yxc.png b/tools/parse_image_metadata/test-data/input_yxc.png new file mode 100644 index 00000000..64b89e0d Binary files /dev/null and b/tools/parse_image_metadata/test-data/input_yxc.png differ diff --git a/tools/parse_image_metadata/test-data/input_yxt.tiff b/tools/parse_image_metadata/test-data/input_yxt.tiff new file mode 100644 index 00000000..eb29cf83 Binary files /dev/null and b/tools/parse_image_metadata/test-data/input_yxt.tiff differ diff --git a/tools/parse_image_metadata/test-data/input_yxz.tiff b/tools/parse_image_metadata/test-data/input_yxz.tiff new file mode 100644 index 00000000..13ce9100 Binary files /dev/null and b/tools/parse_image_metadata/test-data/input_yxz.tiff differ