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changeset 5:9b4830300f3a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:26:50 +0000
parents dc5f72f6b1e9
children 79ec3263686a
files creators.xml superdsm.xml tests.xml
diffstat 3 files changed, 140 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/creators.xml	Thu Apr 04 15:26:50 2024 +0000
@@ -0,0 +1,23 @@
+<macros>
+
+    <xml name="creators/bmcv">
+        <organization name="Biomedical Computer Vision Group, Heidelberg Universtiy" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" />
+        <yield />
+    </xml>
+
+    <xml name="creators/alliecreason">
+        <person givenName="Allison" familyName="Creason"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/bugraoezdemir">
+        <person givenName="Bugra" familyName="Oezdemir"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/thawn">
+        <person givenName="Till" familyName="Korten"/>
+        <yield/>
+    </xml>
+    
+</macros>
--- a/superdsm.xml	Mon Feb 12 14:58:45 2024 +0000
+++ b/superdsm.xml	Thu Apr 04 15:26:50 2024 +0000
@@ -1,9 +1,14 @@
 <tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>with SuperDSM</description>
     <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
         <token name="@TOOL_VERSION@">0.2.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
+    <creator>
+        <expand macro="creators/bmcv"/>
+    </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
@@ -13,7 +18,7 @@
     </xrefs>
     <requirements>
 
-        <requirement type="package" version="0.2.0">superdsm</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">superdsm</requirement>
 
         <!--
         Pin the dependencies to specific versions for reproducibility:
@@ -159,8 +164,18 @@
             <param name="dataset" value="BBBC033_C2_z28.png" />
             <param name="global_energy_minimization_pruning" value="exact" />
             <param name="outputs" value="overlay,masks,cfg" />
-            <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
+            <expand macro="tests/intensity_image_diff" name="overlay" value="overlay.png" ftype="png"/>
             <output name="cfg" value="cfg-full.tsv" ftype="tsv" compare="diff" />
+            <output name="masks" ftype="png">
+                <assert_contents>
+
+                    <has_image_width width="1024"/>
+                    <has_image_height height="1344"/>
+                    <has_image_channels channels="1"/>
+                    <has_image_n_labels n="16"/><!-- 15 objects plus the background -->
+
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <param name="dataset" value="BBBC033_C2_z28.png" />
@@ -170,9 +185,13 @@
         </test>
     </tests>
     <help>
-        This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images.
+
+        **Performs segmentation of 2-D fluorescence microscopy images using deformable shape models and superadditivity.**
+
+        SuperDSM is a globally optimal method for cell nuclei segmentation using deformable shape models and their inherent law of superadditivity.
 
         You can either use an individual input image (PNG, TIF) or a collection of such images.
+
     </help>
     <citations>
         <citation type="bibtex">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests.xml	Thu Apr 04 15:26:50 2024 +0000
@@ -0,0 +1,95 @@
+<macros>
+
+    <!-- Macros for verification of image outputs -->
+
+    <xml
+        name="tests/binary_image_diff"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="mae"
+        token_eps="0.01">
+
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0">
+            <assert_contents>
+                <has_image_n_labels n="2"/>
+                <yield/>
+            </assert_contents>
+        </output>
+
+    </xml>
+
+    <xml
+        name="tests/label_image_diff"
+        tokens="name,value,ftype,metric,eps,pin_labels"
+        token_metric="iou"
+        token_eps="0.01"
+        token_pin_labels="0">
+
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </output>
+
+    </xml>
+
+    <xml
+        name="tests/intensity_image_diff"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="rms"
+        token_eps="0.01">
+
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </output>
+
+    </xml>
+
+    <!-- Variants of the above for verification of collection elements -->
+
+    <xml
+        name="tests/binary_image_diff/element"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="mae"
+        token_eps="0.01">
+
+        <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0">
+            <assert_contents>
+                <has_image_n_labels n="2"/>
+                <yield/>
+            </assert_contents>
+        </element>
+
+    </xml>
+
+    <xml
+        name="tests/label_image_diff/element"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="iou"
+        token_eps="0.01"
+        token_pin_labels="0">
+
+        <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </element>
+
+    </xml>
+
+    <xml
+        name="tests/intensity_image_diff/element"
+        tokens="name,value,ftype,metric,eps"
+        token_metric="rms"
+        token_eps="0.01">
+
+        <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </element>
+
+    </xml>
+
+</macros>