applies the new conventions for imaging tools agreed at BioHackEU23 (#…

…1346) * updates first batch of tools Updated tools: - Adapt an elastic transformation - Add or remove noise - Add shadow effect - Adjust threshold - Align two images - Analyze particles - Analyze skeleton * updats more tools * fixes linter issues (planemo lint) * updates more tools * updates remaining ImageJ2 tools * updates cellprofiler tools * updats "Convert image format" tool * fixes tests for cellprofiler_v4 * fixes tests for cellprofiler_v4
bgruening · Nov 3, 2023 · 4b35e4e · 4b35e4e
1 parent 1570f3a
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diff --git a/tools/cellprofiler/cellprofiler.xml b/tools/cellprofiler/cellprofiler.xml
@@ -1,14 +1,21 @@
-<tool id="cp_cellprofiler" name="CellProfiler" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>run a CellProfiler pipeline</description>
+<tool id="cp_cellprofiler" name="Run CellProfiler pipeline" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>with CellProfiler 3</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <xml name="test_assert_content" token_n="291">
             <assert_contents>
                 <has_n_lines n="@N@" />
             </assert_contents>
         </xml>
     </macros>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
     <expand macro="cp_requirements" />
     <command detect_errors="aggressive"><![CDATA[
         bash '$script_file' &&

diff --git a/tools/cellprofiler/color_to_gray.xml b/tools/cellprofiler/color_to_gray.xml
@@ -1,8 +1,8 @@
 <tool id="cp_color_to_gray" name="ColorToGray" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
-    <description> converts color and channel-stacked images to grayscale</description>
+    <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <xml name="combine_weight">
             <param name="weight_red_channel" value="1.0" min = "0.0" max = "1.0" type="float" label="Relative weight of the red channel" />
             <param name="weight_green_channel" value="1.0" min = "0.0" max = "1.0" type="float" label="Relative weight of the green channel" />
@@ -127,6 +127,13 @@
         </xml>
 
     </macros>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
     <expand macro="py_requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
@@ -287,4 +294,4 @@
             ]]>
     </help>
     <expand macro="citations"/>
-</tool>
+</tool>
diff --git a/tools/cellprofiler/convert_objects_to_image.xml b/tools/cellprofiler/convert_objects_to_image.xml
@@ -1,9 +1,16 @@
 <tool id="cp_convert_objects_to_image" name="ConvertObjectsToImage" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>convert the identified objects into an image</description>
+    <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
     <configfiles>

diff --git a/tools/cellprofiler/display_data_on_image.xml b/tools/cellprofiler/display_data_on_image.xml
@@ -1,8 +1,8 @@
 <tool id="cp_display_data_on_image" name="DisplayDataOnImage" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>produce an image with data on top of identified objects</description>
+    <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <xml name="display_object">
             <param name="select_input_obj" label="Enter the name of the input objects" type="text" help="Enter the name of the objects identified by some other tool used upstream in the workflow (such as IdentifyPrimaryObjects or IdentifySecondaryObjects)." />
 
@@ -93,6 +93,14 @@
         </xml>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
 

diff --git a/tools/cellprofiler/enhance_or_suppress_features.xml b/tools/cellprofiler/enhance_or_suppress_features.xml
@@ -1,9 +1,9 @@
 <tool id="cp_enhance_or_suppress_features" name="EnhanceOrSuppressFeatures" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>to improve subsequent identification of objects</description>
+    <description>with CellProfiler</description>
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <xml name="feature_speckles">
             <param name="speckles_feature_size" label="Feature size" type="integer" value="10" help="Enter the diameter of the largest speckle, the width of the circle, or the width of the neurites to be enhanced or suppressed, which will be used to calculate an appropriate filter size." />
             <param name="speed_accuracy" label="Speed and accuracy" type="select">
@@ -56,6 +56,14 @@
         </xml>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
 

diff --git a/tools/cellprofiler/export_to_spreadsheet.xml b/tools/cellprofiler/export_to_spreadsheet.xml
@@ -1,8 +1,8 @@
 <tool id="cp_export_to_spreadsheet" name="ExportToSpreadsheet" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>export measurements into one or more files</description>
+    <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
         <xml name="metadata_sample_row" >
             <param name="metadata_category" type="select" label="Select the metadata to use as the identifier">
                 <option value="FileName">File name</option>
@@ -26,6 +26,14 @@
         </xml>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
 

diff --git a/tools/cellprofiler/gray_to_color.xml b/tools/cellprofiler/gray_to_color.xml
@@ -1,8 +1,8 @@
 <tool id="cp_gray_to_color" name="GrayToColor" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>take grayscale images and produces a color image from them</description>
+    <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <xml name="rgb">
             <param name="rgb_red" label="Enter the name of the image to be colored red" value="Leave this black" type="text"/>
             <param name="rgb_red_weight" label="Relative weight for the red image" optional="true" type="float" min="0.0" max="1.0" value="1.0" />
@@ -44,6 +44,14 @@
         </xml>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
 

diff --git a/tools/cellprofiler/identify_primary_objects.xml b/tools/cellprofiler/identify_primary_objects.xml
@@ -1,9 +1,9 @@
 <tool id="cp_identify_primary_objects" name="IdentifyPrimaryObjects" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>identify biological objects of interest</description>
+    <description>with CellProfiler</description>
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
         <xml name="ipo_common">
             <param name="input_from_nat" type="text" label="Enter the name of the input image (from NamesAndTypes)">
                 <expand macro="text_validator" />
@@ -192,6 +192,14 @@
         </xml>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
     <configfiles>

diff --git a/tools/cellprofiler/image_math.xml b/tools/cellprofiler/image_math.xml
@@ -1,8 +1,8 @@
 <tool id="cp_image_math" name="ImageMath" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
-    <description>perform simple mathematical operations on images</description>
+    <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <xml name="image_without_multiplier" token_order="first">
             <conditional name="image_or_measurement_@ORDER@">
                 <param name="image_or_measurement_@ORDER@" type="select" label="Image or measurement?" help="You can perform math operations or you can use a measurement for one of the operands.">
@@ -109,6 +109,13 @@
             </section>
         </xml>
     </macros>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
     <expand macro="py_requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
@@ -293,4 +300,4 @@
             ]]>
     </help>
     <expand macro="citations"/>
-</tool>
+</tool>
diff --git a/tools/cellprofiler/mask_image.xml b/tools/cellprofiler/mask_image.xml
@@ -1,11 +1,19 @@
 <tool id="cp_mask_image" name="MaskImage" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>hide portions of an image based on previously identified objects</description>
+    <description>with CellProfiler</description>
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" /> 
 

diff --git a/tools/cellprofiler/measure_granularity.xml b/tools/cellprofiler/measure_granularity.xml
@@ -1,11 +1,19 @@
 <tool id="cp_measure_granularity" name="MeasureGranularity" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>output spectra of size measurements of the textures</description>
+    <description>with CellProfiler</description>
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
 

diff --git a/tools/cellprofiler/measure_image_area_occupied.xml b/tools/cellprofiler/measure_image_area_occupied.xml
@@ -1,11 +1,19 @@
 <tool id="cp_measure_image_area_occupied" name="MeasureImageAreaOccupied" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>measure the area in an image occupied by objects</description>
+    <description>with CellProfiler</description>
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
 

diff --git a/tools/cellprofiler/measure_image_intensity.xml b/tools/cellprofiler/measure_image_intensity.xml
@@ -1,11 +1,19 @@
 <tool id="cp_measure_image_intensity" name="MeasureImageIntensity" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>measure several intensity features across an entire image</description>
+    <description>with CellProfiler</description>
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
 

diff --git a/tools/cellprofiler/measure_image_quality.xml b/tools/cellprofiler/measure_image_quality.xml
@@ -1,9 +1,9 @@
 <tool id="cp_measure_image_quality" name="MeasureImageQuality" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>measure features that indicate image quality</description>
+    <description>with CellProfiler</description>
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <xml name="macro_calc_threshold">
             <conditional name="con_use_all_methods">
                 <param name="use_all_methods" type="select" display="radio" label="Use all thresholding methods?">
@@ -84,6 +84,14 @@
         </xml>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
 

diff --git a/tools/cellprofiler/measure_object_intensity.xml b/tools/cellprofiler/measure_object_intensity.xml
@@ -1,11 +1,19 @@
 <tool id="cp_measure_object_intensity" name="MeasureObjectIntensity" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>measure several intensity features for identified objects</description>
+    <description>with CellProfiler</description>
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />
 

diff --git a/tools/cellprofiler/measure_object_size_shape.xml b/tools/cellprofiler/measure_object_size_shape.xml
@@ -1,11 +1,19 @@
 <tool id="cp_measure_object_size_shape" name="MeasureObjectSizeShape" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>measure area and shape features of identified objects</description>
+    <description>with CellProfiler</description>
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">CellProfiler</xref>
+        <xref type="biii">cellprofiler</xref>
+    </xrefs>
+
     <expand macro="py_requirements"/>
     <expand macro="cmd_modules" />