Mercurial > repos > lldelisle > omero_hyperstack_to_gastruloid_measurements
diff omero_hyperstack_to_gastruloid_measurements.xml @ 1:bd5771ff6aa3 draft
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements commit aec2e2ead02236551c1e9c6d333034057daf0bca
| author | lldelisle |
|---|---|
| date | Wed, 20 Dec 2023 20:07:13 +0000 |
| parents | 5396ab665901 |
| children | 45375dc5dd8d |
line wrap: on
line diff
--- a/omero_hyperstack_to_gastruloid_measurements.xml Fri Mar 24 13:03:39 2023 +0000 +++ b/omero_hyperstack_to_gastruloid_measurements.xml Wed Dec 20 20:07:13 2023 +0000 @@ -1,6 +1,49 @@ <tool id="omero_hyperstack_to_gastruloid_measurements" name="Omero hyperstack to Gastruloid measurements" profile="20.01" version="@TOOL_VERSION@+galaxy0"> <macros> - <token name="@TOOL_VERSION@">20230324</token> + <token name="@TOOL_VERSION@">20231220</token> + <xml name="segmentation"> + <conditional name="use_ilastik"> + <param name="segmentation_method" type="select" label="Segmentation method"> + <option value="convert_to_mask">Simply convert to mask</option> + <option value="ilastik">Use an ilastik project</option> + </param> + <when value="ilastik"> + <param name="ilastik_project" type="data" format="h5" label="Ilastik project" /> + <param name="ilastik_project_type" type="select" label="Type of Ilastik project"> + <option value="Regular">Regular</option> + <option value="Auto-context">Auto-context</option> + </param> + <param name="ilastik_label_OI" type="integer" value="3" label="Index of label of interest in Ilastik project" /> + <param name="probability_threshold" type="float" min="0" max="1" value="0.4" label="Probability threshold for ilastik" /> + <conditional name="background"> + <param name="get_background" type="select" label="Get ROI with background" help="Can be useful to normalize fluo"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="ilastik_label_BG" type="integer" value="1" label="Index of label of background in Ilastik project" /> + <param name="probability_threshold_BG" type="float" min="0" max="1" value="0.8" label="Probability threshold for background in ilastik" /> + </when> + <when value="no"> + <param name="ilastik_label_BG" type="hidden" value="0"/> + <param name="probability_threshold_BG" type="hidden" value="0"/> + </when> + </conditional> + </when> + <when value="convert_to_mask"> + <param name="ilastik_project_type" type="hidden" value="Regular" /> + <param name="ilastik_label_OI" type="hidden" value="3" /> + <param name="probability_threshold" type="hidden" value="0" /> + <section name="background" title="" > + <param name="ilastik_label_BG" type="hidden" value="0"/> + <param name="probability_threshold_BG" type="hidden" value="0"/> + </section> + </when> + </conditional> + <param name="radius_median" type="float" value="20" label="Radius for median (=smooth the mask)" /> + <param name="min_size_particle" type="integer" min="0" value="5000" label="Minimum surface for Analyze Particle" /> + <param name="keep_only_largest" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Keep only one gastruloid per timepoint" /> + </xml> </macros> <requirements> <requirement type="package" version="20220414">fiji</requirement> @@ -20,16 +63,24 @@ echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 && exit 1 && #end if + #if str($mode.use_ilastik.segmentation_method) == "ilastik": + #set $ilastik_project_file = str($mode.use_ilastik.ilastik_project) + #set $ilastik_project_name = str($mode.use_ilastik.ilastik_project.name) + #else + #set $ilastik_project_file = "inexisting.ilp" + #set $ilastik_project_name = "inexisting.ilp" + #end if + mkdir output && ## Because ilastik wants to write to ${HOME}/.cache and ${HOME}/.config export HOME=`pwd` && ImageJ-ilastik --ij2 --headless --console --run '$__tool_directory__/'1-omero_timelapse_image_to_measurements_phase.groovy - 'USERNAME="",PASSWORD="",credentials="${credentials}",host="${omero_host}",port="${omero_port}",object_type="${omero_object.object_type}",id="${omero_object.omero_id}",ilastik_project="${ilastik_project}",ilastik_project_short_name="${ilastik_project.name}",ilastik_project_type="${ilastik_project_type}",ilastik_label_OI="${ilastik_label_OI}",probability_threshold="${probability_threshold}",radius_median="${radius_median}",min_size_particle="${min_size_particle}",get_spine="true",minimum_diameter="${minimum_diameter}",closeness_tolerance="${closeness_tolerance}",min_similarity="${min_similarity}",output_directory="output",debug="${debug}"' > output.log + 'USERNAME="",PASSWORD="",credentials="${credentials}",host="${omero_host}",port="${omero_port}",object_type="${omero_object.object_type}",id="${omero_object.omero_id}",segmentation_method="${mode.use_ilastik.segmentation_method}",use_existing="${mode.use_existing}",ilastik_project="$ilastik_project_file",ilastik_project_short_name="$ilastik_project_name",ilastik_project_type="${mode.use_ilastik.ilastik_project_type}",ilastik_label_OI="${mode.use_ilastik.ilastik_label_OI}",probability_threshold="${mode.use_ilastik.probability_threshold}",radius_median="${mode.radius_median}",min_size_particle="${mode.min_size_particle}",get_spine="true",minimum_diameter="${minimum_diameter}",closeness_tolerance="${closeness_tolerance}",min_similarity="${min_similarity}",output_directory="output",debug="${debug}",rescue="${mode.rescue}",ilastik_label_BG="${mode.use_ilastik.background.ilastik_label_BG}",probability_threshold_BG="${mode.use_ilastik.background.probability_threshold_BG}",keep_only_largest="${mode.keep_only_largest}"' > output.log ]]> </command> <configfiles> <configfile name="credentials"><![CDATA[#set $username = $__user__.extra_preferences.get('omero_account|username', "") - #set $password = $__user__.extra_preferences.get('omero_account|password', "") +#set $password = $__user__.extra_preferences.get('omero_account|password', "") $username $password ]]></configfile> @@ -60,15 +111,40 @@ <param name="omero_id" type="integer" value="" label="Dataset ID on omero" /> </when> </conditional> - <param name="ilastik_project" type="data" format="h5" label="Ilastik project" /> - <param name="ilastik_project_type" type="select" label="Type of Ilastik project"> - <option value="Regular">Regular</option> - <option value="Auto-context">Auto-context</option> - </param> - <param name="ilastik_label_OI" type="integer" value="3" label="Index of label of interest in Ilastik project" /> - <param name="probability_threshold" type="float" min="0" max="1" value="0.4" label="Probability threshold for ilastik" /> - <param name="radius_median" type="float" value="20" label="Radius for median (=smooth the mask)" /> - <param name="min_size_particle" type="integer" min="0" value="5000" label="Minimum surface for Analyze Particle" /> + <conditional name="mode"> + <param name="mode_select" type="select" label="Which mode do you want to use?" > + <option value="regular">Regular (from scratch)</option> + <option value="spine_only">Recompute only spine</option> + <option value="rescue">Rescue (if Regular did not go to the end)</option> + </param> + <when value="regular"> + <expand macro="segmentation"/> + <param name="rescue" type="hidden" value="false"/> + <param name="use_existing" type="hidden" value="false"/> + </when> + <when value="rescue"> + <expand macro="segmentation"/> + <param name="rescue" type="hidden" value="true"/> + <param name="use_existing" type="hidden" value="false"/> + </when> + <when value="spine_only"> + <section name="use_ilastik" title="" > + <param name="segmentation_method" type="hidden" value="convert_to_mask" /> + <param name="ilastik_project_type" type="hidden" value="Regular" /> + <param name="ilastik_label_OI" type="hidden" value="3" /> + <param name="probability_threshold" type="hidden" value="0" /> + <section name="background" title="" > + <param name="ilastik_label_BG" type="hidden" value="0"/> + <param name="probability_threshold_BG" type="hidden" value="0"/> + </section> + </section> + <param name="radius_median" type="hidden" value="20" /> + <param name="min_size_particle" type="hidden" value="5000" /> + <param name="keep_only_largest" type="hidden" value="true"/> + <param name="rescue" type="hidden" value="false"/> + <param name="use_existing" type="hidden" value="true"/> + </when> + </conditional> <param name="minimum_diameter" type="integer" min="0" value="20" label="Minimum diameter of inscribed circles" /> <param name="closeness_tolerance" type="integer" min="0" value="50" label="Closeness Tolerance for the spine" help="Maximum distance between circles along the spine"/> <param name="min_similarity" type="float" min="-1" max="1" value="0.1" label="Min similarity for the spine" help="Close to 0 values allow more U shapes while close to 1 values only allows I shapes" /> @@ -77,18 +153,18 @@ </inputs> <outputs> - <data name="logfile" format="txt" from_work_dir="output.log" label="${tool.name} on ID ${omero_object.omero_id} with ${ilastik_project.name}: logfile"> + <data name="logfile" format="txt" from_work_dir="output.log" label="${tool.name} on ${omero_object.object_type} ID ${omero_object.omero_id} with $getVar('mode.use_ilastik.ilastik_project.name', 'no ilastik'): logfile"> </data> - <collection name="tables" type="list" label="${tool.name} on ID ${omero_object.omero_id} with ${ilastik_project.name}: Tables"> + <collection name="tables" type="list" label="${tool.name} on ${omero_object.object_type} ID ${omero_object.omero_id} with $getVar('mode.use_ilastik.ilastik_project.name', 'no ilastik'): Tables"> <discover_datasets pattern="(?P<designation>.+)\.csv" directory="output" format="csv"/> <filter>keep_intermediate</filter> </collection> - <collection name="hyperstacks_with_overlay" type="list" label="${tool.name} on ID ${omero_object.omero_id} with ${ilastik_project.name}: Hyperstacks"> + <collection name="hyperstacks_with_overlay" type="list" label="${tool.name} on ${omero_object.object_type} ID ${omero_object.omero_id} with $getVar('mode.use_ilastik.ilastik_project.name', 'no ilastik'): Hyperstacks"> <discover_datasets pattern="(?P<designation>.+)\.tiff" directory="output" format="tiff"/> </collection> - <collection name="ilastik_results" type="list" label="${tool.name} on ID ${omero_object.omero_id} with ${ilastik_project.name}: Ilastik"> + <collection name="ilastik_results" type="list" label="${tool.name} on ${omero_object.object_type} ID ${omero_object.omero_id} with $getVar('mode.use_ilastik.ilastik_project.name', 'no ilastik'): Ilastik"> <discover_datasets pattern="(?P<designation>.+)\.tif$" directory="output" format="tiff"/> - <filter>keep_intermediate</filter> + <filter>keep_intermediate and mode['use_ilastik']['segmentation_method'] == "ilastik"</filter> </collection> </outputs> <help> @@ -106,12 +182,13 @@ // This macro was written by the BIOP (https://github.com/BIOP) // Romain Guiet and Rémy Dornier // Lucille Delisle modified to support headless + // And to be more robust to OMERO reboot // merge the analysis script with templates available at - // https://github.com/BIOP/OMERO-scripts/tree/main/Fiji + // https://github.com/BIOP/OMERO-scripts/tree/025047955b5c1265e1a93b259c1de4600d00f107/Fiji /* * = COPYRIGHT = - * © All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2022 + * © All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2023 * * Licensed under the BSD-3-Clause License: * Redistribution and use in source and binary forms, with or without modification, are permitted provided