Mercurial > repos > lldelisle > max_projections_stack_and_upload_omero

changeset 3:24004ccd992e draft default tip

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planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero commit 3c3c4d7009b9ca03d1e88142f090ea70d136f2e8
author lldelisle
date Fri, 13 Dec 2024 09:55:12 +0000
parents 3fd95c753cff
children
files CHANGELOG.md max_projections_stack_and_upload_omero.xml stack_max_projs.groovy
diffstat 3 files changed, 10 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/CHANGELOG.md	Fri Dec 13 09:33:54 2024 +0000
+++ b/CHANGELOG.md	Fri Dec 13 09:55:12 2024 +0000
@@ -1,5 +1,10 @@
 # CHANGELOG
 
+## 20241213.2
+
+- Fixed a variable definition in the groovy
+- Do not ask for the Project ID when the Dataset exists
+
 ## 20241213.1
 
 - Fixed a forgotten nT
--- a/max_projections_stack_and_upload_omero.xml	Fri Dec 13 09:33:54 2024 +0000
+++ b/max_projections_stack_and_upload_omero.xml	Fri Dec 13 09:55:12 2024 +0000
@@ -1,7 +1,7 @@
 <tool id="max_projections_stack_and_upload_omero" name="Stack MaxProj" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="BSD-3">
     <description>And upload to omero</description>
     <macros>
-        <token name="@TOOL_VERSION@">20241213.1</token>
+        <token name="@TOOL_VERSION@">20241213.2</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
@@ -79,7 +79,7 @@
                         <param name="dataset_name_or_id" type="text" value="MyNewDataset" label="Name of the dataset (on omero)" />
                     </when>
                     <when value="none">
-                        <param name="project_name_or_id" type="integer" min="1" value="12" label="ID of the project (on omero)" />
+                        <param name="project_name_or_id" type="hidden" value="none"/>
                         <param name="dataset_name_or_id" type="integer" min="1" value="56" label="ID of the dataset (on omero)" />
                     </when>
                 </conditional>
--- a/stack_max_projs.groovy	Fri Dec 13 09:33:54 2024 +0000
+++ b/stack_max_projs.groovy	Fri Dec 13 09:55:12 2024 +0000
@@ -29,7 +29,7 @@
  */
 
 // Version number = date of last modif
-VERSION = "20241213.1"
+VERSION = "20241213.2"
 
 /**
  * *****************************************************************************************************************
@@ -116,6 +116,7 @@
 
 	// Explore the HashMap and save to tiff
 	for(String unique_identifier : samplesMap.keySet()){
+		println "Merging " + unique_identifier
 		// get the channel map
 		Map<String, ImagePlus> channelsMap = samplesMap.get(unique_identifier)
 		ArrayList<String> channels = []
@@ -135,11 +136,11 @@
 			}
 		}
 		
+		ImagePlus final_imp
 		if (all_compatibles) {
 			// Merge all
 			ImagePlus merged_imps = Concatenator.run(current_images as ImagePlus[])
 			// Re-order to make a multi-channel, time-lapse image
-			ImagePlus final_imp
 			if (channels.size() == 1 && ref_nT == 1) {
 				final_imp = merged_imps
 			} else {