Mercurial > repos > imgteam > anisotropic_diffusion

changeset 3:097b803aeb5d draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:23:48 +0000
parents e6987afa0484
children 6ad5de2c5b7c
files anisotropic_diffusion.xml creators.xml tests.xml
diffstat 3 files changed, 138 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/anisotropic_diffusion.xml	Mon Nov 13 22:10:29 2023 +0000
+++ b/anisotropic_diffusion.xml	Thu Apr 04 15:23:48 2024 +0000
@@ -1,13 +1,21 @@
-<tool id="ip_anisotropic_diffusion" name="Apply anisotropic diffusion" version="0.2-2"> 
+<tool id="ip_anisotropic_diffusion" name="Apply anisotropic diffusion" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 
     <description>with MedPy</description>
+    <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+        <token name="@TOOL_VERSION@">0.4.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <creator>
+        <expand macro="creators/bmcv" />
+    </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
     <requirements>
-        <requirement type="package" version="0.14.2">scikit-image</requirement>
-        <requirement type="package" version="0.3.0">medpy</requirement>
-        <requirement type="package" version="1.15.4">numpy</requirement>
-        <requirement type="package" version="0.15.1">tifffile</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">medpy</requirement>
+        <requirement type="package" version="1.20">numpy</requirement>
+        <requirement type="package" version="0.18.1">scikit-image</requirement>
     </requirements> 
     <command detect_errors="aggressive">
         <![CDATA[
@@ -15,13 +23,13 @@
         ]]>
     </command>
     <inputs>
-        <param name="input" type="data" format="tiff" label="Image file"/>
+        <param name="input" type="data" format="tiff" label="Input image"/>
         <param label="Number of iterations" name="niter" optional="true" type="integer" value="50"/>
         <param label="Conduction coefficient" name="kappa" optional="true" type="integer" value="50"/>
         <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/>
-        <param name="eqoption" type="select" label="Diffusion Feature" help="Perona Malik diffusion equation">
-            <option value="1" selected="True">Favour high contrast edges</option>
-            <option value="2">Favour wide regions</option>
+        <param name="eqoption" type="select" label="Diffusion feature" help="Perona Malik diffusion equation">
+            <option value="1" selected="True">Favor high contrast edges</option>
+            <option value="2">Favor wide regions</option>
         </param>
     </inputs>
     <outputs>
@@ -34,13 +42,13 @@
             <param name="kappa" value="50" />
             <param name="gamma" value="0.1" />
             <param name="eqoption" value="1" />
-            <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="res.tif" ftype="tiff"/>
         </test>
     </tests>
     <help>
-    **What it does**
 
-    Edge-preserving, Anisotropic image diffusion
+        **Applies edge-preserving, anisotropic image diffusion.**
+
     </help>
     <citations>
         <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/creators.xml	Thu Apr 04 15:23:48 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests.xml	Thu Apr 04 15:23:48 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>