--- a/idr_download_by_ids.xml	Wed Nov 08 12:57:25 2023 +0000
+++ b/idr_download_by_ids.xml	Thu Sep 26 12:32:17 2024 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.44.1" profile="18.09">
+<tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.45" profile="18.09">
     <description></description>
     <macros>
         <xml name="region_spec" token_pos="upper-left corner">
@@ -19,8 +19,8 @@
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
     <requirements>
-        <requirement type="package" version="5.10.1">omero-py</requirement>
-        <requirement type="package" version="0.4.2">pylibtiff</requirement>
+        <requirement type="package" version="5.19.4">omero-py</requirement>
+        <requirement type="package" version="2024.9.20">tifffile</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         
@@ -51,6 +51,8 @@
         #end if
         #if $image_region.original == "original":
             --download-original
+        #elif $image_region.original == "full":
+            --download-full
         #else:
             #set $channel = str($image_region.channel).strip()
             #if $channel:
@@ -87,7 +89,7 @@
 }
         ]]></configfile>
     </configfiles>
-<inputs>
+    <inputs>
         <conditional name="omero_instance_type">
             <param name="omero_instance" type="select" label="Which OMERO instance to connect?"
                    help="By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you 
@@ -135,9 +137,11 @@
         <conditional name="image_region">
             <param name="original" type="select" label="Which images do you want to download?">
                 <option value="TIFF" selected="true">Exported TIFF (single channel, single stack)</option>
+                <option value="full">Whole TIFF (all channels, all frames, all stacks)</option>
                 <option value="original">Original file (file uploaded to omero, only available for private instances)</option>
             </param>
             <when value="original"/>
+            <when value="full"/>
             <when value="TIFF">
                 <param name="channel" type="text"
                     label="Name of the channel to download"
@@ -182,7 +186,7 @@
         </data> 
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -202,10 +206,10 @@
             </conditional>
             <param name="download_tar" value="false" />
             <output_collection name="output_file" type="list">
-                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff"/>
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff" compare="image_diff" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -225,10 +229,10 @@
             </conditional>
             <param name="download_tar" value="false" />
             <output_collection name="output_file" type="list">
-                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff"/>
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff" compare="image_diff"/>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -248,10 +252,10 @@
             </conditional>
             <param name="download_tar" value="false" />
             <output_collection name="output_file" type="list">
-                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test2.tiff"/>
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test2.tiff" compare="image_diff"/>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -270,7 +274,11 @@
             <output_collection name="output_file" type="list" count="3">
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="320.868" />
+                        <has_image_center_of_mass center_of_mass="541.664, 456.743" />
                     </assert_contents>
                 </element>
             </output_collection>
@@ -299,7 +307,7 @@
             </conditional>
             <param name="download_tar" value="false" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- Repeat test with non-existing image-ID 9036708999,
             but use skip-failed option -->
             <conditional name="omero_instance_type">
@@ -321,7 +329,11 @@
             <output_collection name="output_file" type="list" count="2">
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="320.868" />
+                        <has_image_center_of_mass center_of_mass="541.664, 456.743" />
                     </assert_contents>
                 </element>
             </output_collection>
@@ -333,7 +345,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -354,17 +366,25 @@
             </conditional>
             <output name="output_tar">
                     <assert_contents>
-                        <has_size value="1382400" />
+                        <has_size size="1382400" />
                         <has_archive_member path=".*/*__1828167__0__0__671__511.tiff" >
-                            <has_size value="685896" />
+                            <has_size size="685896" />
+                            <has_image_width width="671" />
+                            <has_image_height height="511" />
+                            <has_image_mean_intensity mean_intensity="388.711" />
+                            <has_image_center_of_mass center_of_mass="354.627, 267" />
                         </has_archive_member>
                         <has_archive_member path=".*/*__1828658__0__0__671__511.tiff" >
-                            <has_size value="685896" />
+                            <has_size size="685896" />
+                            <has_image_width width="671" />
+                            <has_image_height height="511" />
+                            <has_image_mean_intensity mean_intensity="397.507" />
+                            <has_image_center_of_mass center_of_mass="346.098, 250.652" />
                         </has_archive_member>
                     </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="priv" />
                  <param name="omero_host" value="idr.openmicroscopy.org" />
@@ -387,7 +407,7 @@
             </conditional>
             <param name="download_tar" value="false" />
             <output_collection name="output_file" type="list">
-                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff"/>
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff" compare="image_diff"/>
             </output_collection>
         </test>
         <test expect_failure="true">
@@ -415,7 +435,7 @@
                 <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" />
             </assert_stderr >
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -426,27 +446,43 @@
             <output_collection name="output_file" type="list" count="4">
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="145.310" />
+                        <has_image_center_of_mass center_of_mass="527.499, 480.704" />
                     </assert_contents>
                 </element>
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D__9036708__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="147.025" />
+                        <has_image_center_of_mass center_of_mass="528.977, 480.691" />
                     </assert_contents>
                 </element>
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D_zproj__9036710__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="210.787" />
+                        <has_image_center_of_mass center_of_mass="534.629, 473.267" />
                     </assert_contents>
                 </element>
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_REF__9036709__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="3816.051" />
+                        <has_image_center_of_mass center_of_mass="512.274, 503.186" />
                     </assert_contents>
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -462,6 +498,24 @@
             <output_collection name="output_file" type="list" count="0">
             </output_collection>
         </test>
+        <test expect_num_outputs="2">
+            <conditional name="omero_instance_type">
+                 <param name="omero_instance" value="idr" />
+            </conditional>
+            <param name="source" value="link" />
+            <param name="id_spec" value="1229801" />
+            <param name="download_tar" value="false" />
+            <conditional name="image_region">
+                <param name="original" value="full"/> 
+            </conditional>
+            <output_collection name="output_file" type="list" count="1">
+                <element name="JL_120731_S6A_[Well_A-1;_Field_#1]__1229801__full">
+                    <assert_contents>
+                        <has_size size="91592058" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 Download image data from the IDR_ (Image Data Resource) - a public repository