diff --git a/tools/trackastra_galaxy/.shed.yml b/tools/trackastra_galaxy/.shed.yml new file mode 100644 index 00000000000..ced24f5b1ae --- /dev/null +++ b/tools/trackastra_galaxy/.shed.yml @@ -0,0 +1,14 @@ +name: trackastra_galaxy +owner: iuc +categories: + - Machine Learning + - Imaging +description: Track cell instances in time-lapse OME-Zarr datasets using Trackastra and Cellpose. +long_description: | + Trackastra-Galaxy is a wrapper around the Trackastra cell-tracking pipeline that supports + both segmentation+tracking and track-only workflows on time-lapse OME-Zarr datasets. + It can consume remote or local Zarr datasets and outputs a CTC track log plus per-frame mask images. +homepage_url: https://github.com/bioinfbrad/trackastra_galaxy +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/trackastra_galaxy +type: unrestricted + diff --git a/tools/trackastra_galaxy/macros.xml b/tools/trackastra_galaxy/macros.xml new file mode 100644 index 00000000000..fa1df07481f --- /dev/null +++ b/tools/trackastra_galaxy/macros.xml @@ -0,0 +1,85 @@ + + 1.0.1 + 25.1 + 0 + + + trackastra-galaxy + + + + + + + + + + + + + + + + + + + + + + + ^(https?|s3)://.+$ + + + + + + + + + + + trackastra-galaxy + cellpose + trackastra + numpy + scikit-image + ome-zarr + + + + + + + + + + + + + + + + ^\s*\d+(\s*[, ]\s*\d+)*\s*$ + + + + + + + + + @article{trackastra, + title={Trackastra: transformer-based cell tracking}, + author={Theis, F. J. and others}, + journal={Nature Methods}, + year={2024} +} + @article{cellpose, + title={Cellpose: a generalist algorithm for cellular segmentation}, + author={Stringer, C. and Wang, T. and others}, + journal={Nature Methods}, + year={2021} +} + + + diff --git a/tools/trackastra_galaxy/test-data/segment_and_track/man_track.tsv b/tools/trackastra_galaxy/test-data/segment_and_track/man_track.tsv new file mode 100644 index 00000000000..cd0a56730a3 --- /dev/null +++ b/tools/trackastra_galaxy/test-data/segment_and_track/man_track.tsv @@ -0,0 +1 @@ +1 1 2 0 diff --git a/tools/trackastra_galaxy/test-data/segment_and_track/man_track0000.tiff b/tools/trackastra_galaxy/test-data/segment_and_track/man_track0000.tiff new file mode 100644 index 00000000000..fa84b861a7b Binary files /dev/null and b/tools/trackastra_galaxy/test-data/segment_and_track/man_track0000.tiff differ diff --git a/tools/trackastra_galaxy/test-data/segment_and_track/man_track0001.tiff b/tools/trackastra_galaxy/test-data/segment_and_track/man_track0001.tiff new file mode 100644 index 00000000000..e2db3973000 Binary files /dev/null and b/tools/trackastra_galaxy/test-data/segment_and_track/man_track0001.tiff differ diff --git a/tools/trackastra_galaxy/test-data/segment_and_track/man_track0002.tiff b/tools/trackastra_galaxy/test-data/segment_and_track/man_track0002.tiff new file mode 100644 index 00000000000..2de9b9b515f Binary files /dev/null and b/tools/trackastra_galaxy/test-data/segment_and_track/man_track0002.tiff differ diff --git a/tools/trackastra_galaxy/test-data/track_only/man_track.tsv b/tools/trackastra_galaxy/test-data/track_only/man_track.tsv new file mode 100644 index 00000000000..d7dd582ef60 --- /dev/null +++ b/tools/trackastra_galaxy/test-data/track_only/man_track.tsv @@ -0,0 +1,30 @@ +1 0 2 0 +2 0 2 0 +3 0 1 0 +4 0 1 0 +5 0 2 0 +6 0 1 0 +7 0 2 0 +8 0 1 0 +9 1 2 0 +10 1 2 0 +11 1 2 0 +12 1 2 0 +13 1 2 0 +14 1 2 0 +15 1 2 0 +16 1 1 0 +17 1 2 0 +18 1 2 0 +19 1 1 0 +20 1 2 0 +21 1 2 0 +22 1 2 0 +23 1 2 0 +24 1 2 0 +25 1 2 0 +26 1 2 0 +27 2 2 16 +28 2 2 16 +29 2 2 19 +30 2 2 19 diff --git a/tools/trackastra_galaxy/test-data/track_only/man_track0000.tiff b/tools/trackastra_galaxy/test-data/track_only/man_track0000.tiff new file mode 100644 index 00000000000..1709875955a Binary files /dev/null and b/tools/trackastra_galaxy/test-data/track_only/man_track0000.tiff differ diff --git a/tools/trackastra_galaxy/test-data/track_only/man_track0001.tiff b/tools/trackastra_galaxy/test-data/track_only/man_track0001.tiff new file mode 100644 index 00000000000..86bb55af422 Binary files /dev/null and b/tools/trackastra_galaxy/test-data/track_only/man_track0001.tiff differ diff --git a/tools/trackastra_galaxy/test-data/track_only/man_track0002.tiff b/tools/trackastra_galaxy/test-data/track_only/man_track0002.tiff new file mode 100644 index 00000000000..b2a76f89cad Binary files /dev/null and b/tools/trackastra_galaxy/test-data/track_only/man_track0002.tiff differ diff --git a/tools/trackastra_galaxy/trackastra_galaxy.xml b/tools/trackastra_galaxy/trackastra_galaxy.xml new file mode 100644 index 00000000000..69d28d7c963 --- /dev/null +++ b/tools/trackastra_galaxy/trackastra_galaxy.xml @@ -0,0 +1,170 @@ + + with Trackastra Galaxy pipeline + + macros.xml + + + + result_directory/man_track.tsv +&& +#raw +find result_directory -name 'man_track*.tif' -exec sh -c 'mv "$1" "${1%.tif}.tiff"' _ {} \; || true +#end raw + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + ^\s*\d+(\s*[, ]\s*\d+)*\s*$ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +