Fix omero plate (#82)

* fix omero dataset to plate * fixes it tests
Helmholtz-UFZ · Dec 19, 2024 · 3d98eed · 3d98eed
1 parent 66c6acf
commit 3d98eed
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Showing 2 changed files with 19 additions and 13 deletions.
diff --git a/tools/omero/omero_dataset_to_plate.xml b/tools/omero/omero_dataset_to_plate.xml
@@ -22,7 +22,7 @@
    </configfiles>
    <inputs>
        <expand macro="host_port"/>
-       <param name="dataset_id" type="integer" optional="false" min = "1" label="Dataset ID to convert to a plate"/>
+       <param name="dataset_id" type="integer" optional="false" min="1" value="" label="Dataset ID to convert to a plate"/>
        <param name="mapping" type="data" format= "tabular" optional="false" label="Mapping file"/>
        <param name="delete_dataset" type="boolean" truevalue="--delete_dataset" falsevalue="" checked="false" label="Delete Dataset" help="Delete dataset after import"/>
    </inputs>

diff --git a/tools/omero/omero_metadata_import.xml b/tools/omero/omero_metadata_import.xml
@@ -35,14 +35,14 @@
             <option value="image">Image</option>
         </param>
         <conditional name="object_id">
-        <param name="object_id_selection" type="select" label="Selection" help="Create a new OMERO object or target an existing one">
-            <option value="new_object">Create new object</option>
-            <option value="existing_object">Target an existing object</option>
-        </param>
-        <when value="new_object"/>
-        <when value="existing_object">
-            <param name="did" type="integer" min = "1" optional="false" label="Object ID"/>
-        </when>
+            <param name="object_id_selection" type="select" label="Selection" help="Create a new OMERO object or target an existing one">
+                <option value="new_object">Create new object</option>
+                <option value="existing_object">Target an existing object</option>
+            </param>
+            <when value="new_object"/>
+            <when value="existing_object">
+                <param name="did" type="integer" min = "1" optional="false" label="Object ID"/>
+            </when>
         </conditional>
         <param argument="ann_type" type="select" optional="false" label="Annotation type" help="Select annotation format">
             <option value="table">Table</option>
@@ -60,7 +60,9 @@
             <param name="omero_port" value="6064"/>
             <param name="obj_type" value="project"/>
             <param name="ann_type" value="table"/>
-            <param name="object_id_selection" value="new_object"/>
+            <conditional name="object_id">
+                <param name="object_id_selection" value="new_object"/>
+            </conditional>
             <param name="ann_file" value="metadata.tsv"/>
             <param name="an_name" value="Table_Test"/>
             <param name="test_username" value="root"/>
@@ -76,7 +78,9 @@
             <param name="omero_port" value="6064"/>
             <param name="obj_type" value="dataset"/>
             <param name="ann_type" value="KV"/>
-            <param name="object_id_selection" value="new_object"/>
+            <conditional name="object_id">
+                <param name="object_id_selection" value="new_object"/>
+            </conditional>
             <param name="ann_file" value="metadata.tsv"/>
             <param name="an_name" value="KV_Test"/>
             <param name="test_username" value="root"/>
@@ -92,8 +96,10 @@
             <param name="omero_port" value="6064"/>
             <param name="obj_type" value="dataset"/>
             <param name="ann_type" value="KV"/>
-            <param name="object_id_selection" value="existing_object"/>
-            <param name="did" value="1"/>
+            <conditional name="object_id">
+                <param name="object_id_selection" value="existing_object"/>
+                <param name="did" value="1"/>
+            </conditional>
             <param name="ann_file" value="metadata.tsv"/>
             <param name="an_name" value="Additional_KV_Values"/>
             <param name="test_username" value="root"/>