Feat: Add two additional cellprofiler modules

tools/cellprofiler/.shed.yml

@@ -3,6 +3,10 @@ owner: bgruening
 categories:
   - Imaging
 description: cellProfiler wrapper
+homepage_url: https://github.com/CellProfiler
+long_description: |
+  CellProfiler is a free open-source software designed to enable biologists without training in computer 
+  vision or programming to quantitatively measure phenotypes from thousands of images automatically.
 remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools
 type: unrestricted
 auto_tool_repositories:

tools/cellprofiler/cellprofiler.xml

@@ -2,7 +2,7 @@
     <description>with CellProfiler 3</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
         <xml name="test_assert_content" token_n="291">
             <assert_contents>
                 <has_n_lines n="@N@" />

tools/cellprofiler/color_to_gray.xml

@@ -2,7 +2,7 @@
     <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</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" />

tools/cellprofiler/convert_objects_to_image.xml

@@ -2,7 +2,7 @@
     <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>

tools/cellprofiler/display_data_on_image.xml

@@ -2,7 +2,7 @@
     <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</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)." />
 

tools/cellprofiler/enhance_or_suppress_features.xml

@@ -3,7 +3,7 @@
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</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">

tools/cellprofiler/gray_to_color.xml

@@ -2,7 +2,7 @@
     <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</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" />

tools/cellprofiler/identify_tertiary_objects.xml

@@ -0,0 +1,109 @@
+<tool id="cp_identify_tertiary_objects" name="IdentifyTertiarxObjects" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>with CellProfiler</description>
+
+    <macros>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">2</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>
+        <inputs name="inputs" />
+        <configfile name="script_file">
+import json
+import sys
+import os
+
+FOURSPACES=@SPACES@
+
+input_json_path = sys.argv[1]
+input_pipeline= sys.argv[2]
+
+params = json.load(open(input_json_path, "r"))
+
+def writemoi():
+    _str = "\nIdentifyTertiaryObjects:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:3|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
+
+    _str += FOURSPACES + "Select the larger identified objects:%s\n" % params['larger_identify_object']
+    _str += FOURSPACES + "Select the smaller identified objects:%s\n" % params['smaller_identify_object']
+    _str += FOURSPACES + "Name the tertiary objects to be identified:%s\n" % params['tertiary_object']
+    _str += FOURSPACES + "Shrink smaller object prior to subtraction?%s\n" % params['shrink_objects']
+
+    return _str
+
+
+with open(input_pipeline) as fin:
+    lines = fin.readlines()
+
+    k, v = lines[4].strip().split(':')
+
+    module_count = int(v)
+    new_count = module_count + 1
+    lines[4] = k + ":%d\n" % new_count
+    with open("output.cppipe", "w") as f:
+        f.writelines(lines)
+        f.write(writemoi())
+
+    f.close()
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <expand macro="input_pipeline_param" />
+            <param name="larger_identify_object" label="Select the larger identified objects" type="text">
+                <expand macro="text_validator" />
+            </param>
+            <param name="smaller_identify_object" label="Select the smaller identified objects" type="text">
+                <expand macro="text_validator" />
+            </param>
+            <param name="tertiary_object" label="Name the tertiary objects to be identified" type="text">
+                <expand macro="text_validator" />
+            </param>
+            <param name="shrink_objects" label=" Shrink smaller object prior to subtraction?" type="select">
+                <option value="Yes">Yes</option>
+                <option value="No">No</option>
+            </param>
+    </inputs>
+
+    <outputs>
+        <expand macro="output_pipeline_param" />
+    </outputs>
+
+    <tests>
+        <test>
+            <expand macro="test_input_pipeline_param" />
+            <param name="larger_identify_object" value="Cells" />
+            <param name="smaller_identify_object" value="Nuclei" />
+            <param name="tertiary_object" value="Cytoplasm" />
+            <param name="shrink_objects" value="Yes" />
+            <expand macro="test_out_file" file="measure_object_intensity.cppipe" />
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+
+            .. class:: infomark
+
+            **What it does**
+
+           identifies tertiary objects (e.g., cytoplasm) by removing smaller primary objects (e.g. nuclei) from larger secondary objects (e.g., cells), leaving a ring shape. 
+
+            ]]>
+    </help>
+
+
+
+    <expand macro="citations" />
+
+</tool>

tools/cellprofiler/image_math.xml

@@ -2,7 +2,7 @@
     <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</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.">

tools/cellprofiler/mask_image.xml

@@ -3,7 +3,7 @@
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
 
     <edam_operations>

tools/cellprofiler/measure_granularity.xml

@@ -3,7 +3,7 @@
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
 
     <edam_operations>

tools/cellprofiler/measure_image_area_occupied.xml

@@ -3,7 +3,7 @@
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
 
     <edam_operations>

tools/cellprofiler/measure_image_intensity.xml

@@ -3,7 +3,7 @@
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
 
     <edam_operations>

tools/cellprofiler/measure_image_quality.xml

@@ -3,7 +3,7 @@
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</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?">

tools/cellprofiler/measure_object_intensity.xml

@@ -3,7 +3,7 @@
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
 
     <edam_operations>

tools/cellprofiler/measure_object_size_shape.xml

@@ -3,7 +3,7 @@
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
 
     <edam_operations>

tools/cellprofiler/measure_texture.xml

@@ -3,7 +3,7 @@
 
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
         <xml name="measureImgObj">
             <repeat name="rpt_obj_to_measure" title="new object" min="1">
 

tools/cellprofiler/overlay_outlines.xml

@@ -2,7 +2,7 @@
     <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
         <xml name="non_blank">
             <param name="image_to_outline" type="text" label="Enter the name of image on which to display outlines" >
                 <help>

tools/cellprofiler/relate_objects.xml

@@ -2,7 +2,7 @@
     <description>with CellProfiler</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
         <xml name="distToOtherParents">
             <conditional name="con_other_parent_dist">
                 <param name="calc_dist_to_others" label="Calculate distances to other parents?" display="radio" type="select">

tools/cellprofiler/test-data/identify_secondary_objects_adv_adaptive_otsu.cppipe

@@ -0,0 +1,82 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifySecondaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify whole cells from a cytoplasm/membrane image using nuclei as seeds.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input objects:Nuclei
+    Name the objects to be identified:Cells
+    Select the method to identify the secondary objects:Propagation
+    Select the input image:Cytoplasm
+    Number of pixels by which to expand the primary objects:10
+    Regularization factor:0.0800
+    Discard secondary objects touching the border of the image?:Yes
+    Discard the associated primary objects?:Yes
+    Name the objects to be identified:TestName
+    Fill holes in identified objects?:Yes
+    Threshold settings version:10
+    Threshold strategy:Adaptive
+    Thresholding method:Otsu
+    Threshold smoothing scale:1.5000
+    Threshold correction factor:1.000
+    Lower and upper bounds on threshold:0.0000,1.0000
+    Manual threshold:0.0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Three classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Otsu