fetch all tools bot - step filter

results/imaging/tools_filtered_by_ts_categories.tsv

@@ -0,0 +1,19 @@
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on ANASTASIA	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CorGAT	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on Protologger	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	False		
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.8	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	178	4614	False		
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update		Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.6					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	8	43	False		
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.43	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	43	2605	False		
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2				Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	26	1537	False		
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.2.1	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	5	59	False		
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	67	False		
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False