Mercurial > repos > bgruening > cp_identify_primary_objects

annotate identify_primary_objects.xml @ 4:993faa34333b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author bgruening
date Sat, 06 Feb 2021 09:57:35 +0000
parents 52c01fb29b2a
children b6eec6087271
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1 <tool id="cp_identify_primary_objects" name="IdentifyPrimaryObjects" version="@CP_VERSION@">
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2 <description>identify biological objects of interest</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <xml name="ipo_common">
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7 <param name="input_from_nat" type="text" label="Enter the name of the input image (from NamesAndTypes)">
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8 <expand macro="text_validator" />
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9 </param>
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10 <param name="name_to_be_identified" type="text" label="Enter the name of the primary objects to be identified">
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11 <expand macro="text_validator" />
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12 </param>
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13 <param name="min_diameter" type="integer" label="Typical minimum diameter of objects, in pixel units (Min)" value="10" min="0">
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14 <help>
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15 <![CDATA[
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16 The min and max diameters are crucial for two reasons: first, the module uses it to calculate certain automatic settings in order to identify your objects of interest properly (see below). Second, when used in conjunction with the 'Discard objects outside the diameter range?' setting below, you can choose to remove objects outside the size range you provide here.
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17 ]]>
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18 </help>
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19 </param>
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20 <param name="max_diameter" type="integer" label="Typical maximum diameter of objects, in pixel units (Max)" value="40" min="0" />
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21 <param name="discard_outside_border" type="select" display="radio" label="Discard objects outside the diameter range?">
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22 <option value="Yes">Yes</option>
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23 <option value="No">No</option>
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24 </param>
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25 <param name="discard_touching_border" type="select" display="radio" label="Discard objects touching the border of the image?">
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26 <option value="Yes">Yes</option>
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27 <option value="No">No</option>
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28 </param>
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29 </xml>
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31 <xml name="clumped_objects_params">
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32 <conditional name="con_smoothing_filter">
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33 <param name="smoothing_filter" type="select" label="Automatically calculate size of smoothing filter for declumping?">
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34 <help>
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35 <![CDATA[
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36 Select 'Yes' to automatically calculate the amount of smoothing applied to the image to assist in declumping. Select "No" to manually enter the smoothing filter size.
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37 This setting, along with the Minimum allowed distance between local maxima setting, affects whether objects close to each other are considered a single object or multiple objects. It does not affect the dividing lines between an object and the background.
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38 Please note that this smoothing setting is applied after thresholding, and is therefore distinct from the threshold smoothing method setting above, which is applied before thresholding.
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39 The size of the smoothing filter is automatically calculated based on the Typical diameter of objects, in pixel units (Min,Max) setting above. If you see too many objects merged that ought to be separate or too many objects split up that ought to be merged, you may want to override the automatically calculated value.
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40 ]]>
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41 </help>
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42 <option value="Yes">Yes</option>
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43 <option value="No">No</option>
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44 </param>
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45 <when value="No">
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46 <param name="size_smoothing_filter" type="integer" label="Size of smoothing filter" min="0" max="1" value="1">
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47 <help>
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48 <![CDATA[
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49 If you see too many objects merged that ought to be separated (under-segmentation), this value should be lower. If you see too many objects split up that ought to be merged (over-segmentation), the value should be higher.
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50 Note that splitting and merging is also affected by your choice of settings for the setting, Automatically calculate minimum allowed distance between local maxima? It is an art to balance these two settings; read the help carefully for both.
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51 Reducing the texture of objects by increasing the smoothing increases the chance that each real, distinct object has only one peak of intensity but also increases the chance that two distinct objects will be recognized as only one object. Note that increasing the size of the smoothing filter increases the processing time exponentially.
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52 Enter 0 to prevent any image smoothing in certain cases; for example, for low resolution images with small objects ( < ~5 pixels in diameter).
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53 ]]>
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54 </help>
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55 </param>
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56 </when>
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57 <when value="Yes" />
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58 </conditional>
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59 <conditional name="con_min_distance">
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60 <param name="min_distance" type="select" label="Automatically calculate minimum allowed distance between local maxima?">
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61 <help>
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62 <![CDATA[
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63 Select "Yes" to automatically calculate the distance between intensity maxima to assist in declumping. Select "No" to manually enter the permissible maxima distance.
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64 This setting, along with the Size of smoothing filter setting, affects whether objects close to each other are considered a single object or multiple objects. It does not affect the dividing lines between an object and the background. Local maxima that are closer together than the minimum allowed distance will be suppressed (the local intensity histogram is smoothed to remove the peaks within that distance).
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65 The distance can be automatically calculated based on the minimum entered for the Typical diameter of objects, in pixel units (Min,Max) setting above, but if you see too many objects merged that ought to be separate, or too many objects split up that ought to be merged, you may want to override the automatically calculated value.
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66 ]]>
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67 </help>
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68 <option value="Yes">Yes</option>
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69 <option value="No">No</option>
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70 </param>
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71 <when value="No">
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72 <param name="min_allowed_distance" type="integer" label="Supress local maxima that are closer than this minimum allowed distance" value="7">
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73 <help>
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74 <![CDATA[
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75 Enter a positive integer, in pixel units. If you see too many objects merged that ought to be separated (under-segmentation), the value should be lower. If you see too many objects split up that ought to be merged (over-segmentation), the value should be higher.
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76 The maxima suppression distance should be set to be roughly equivalent to the radius of the smallest object of interest that you would expect to see in the experiment.
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77 Any distinct 'objects' that are found but are within two times this distance from each other will be assumed to be actually two lumpy parts of the same object, and they will be merged.
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78 Note that splitting and merging is also affected by your choice of settings for the setting 'Size of smoothing filter'.
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79 ]]>
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80 </help>
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81 </param>
0
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82 </when>
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83 <when value="Yes" />
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84 </conditional>
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85 <param name="speed_up" type="select" display="radio" label="Speed up by using lower-resolution image to find local maxima?">
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86 <help>
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87 <![CDATA[
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88 Select 'Yes' to down-sample the image for declumping. This can be helpful for saving processing time on large images.
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89 Note that if you have entered a minimum object diameter of 10 or less, checking this box will have no effect.
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90 ]]>
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91 </help>
0
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92 <option value="Yes">Yes</option>
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93 <option value="No">No</option>
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94 </param>
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95 </xml>
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96
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97 <xml name="clumped_objects">
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98 <conditional name="con_dividing_lines">
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99 <param name="dividing_lines" type="select" label="Method to draw dividing lines between clumped objects">
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100 <help>
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101 <![CDATA[
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102 This setting allows you to choose the method that is used to draw the line between segmented objects, provided that you have chosen to declump the objects. To decide between these methods, you can run Test mode to see the results of each.
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103 <br> - Intensity: Works best where the dividing lines between clumped objects are dimmer than the remainder of the objects.
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104 <br> - Technical description: Using the previously identified local maxima as seeds, this method is a watershed (Vincent and Soille, 1991) on the intensity image.
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105 <br> - Shape: Dividing lines between clumped objects are based on the shape of the clump. For example, when a clump contains two objects, the dividing line will be placed where indentations occur between the two objects. The intensity patterns in the original image are largely irrelevant: the cells need not be dimmer along the lines between clumped objects. Technical description: Using the previously identified local maxima as seeds, this method is a watershed on the distance-transformed thresholded image.
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106 <br> - Propagate: This method uses a propagation algorithm instead of a watershed. The image is ignored and the pixels are assigned to the objects by repeatedly adding unassigned pixels to the objects that are immediately adjacent to them. This method is suited in cases such as objects with branching extensions, for instance neurites, where the goal is to trace outward from the cell body along the branch, assigning pixels in the branch along the way. See the help for the IdentifySecondaryObjects module for more details on this method.
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107 <br> - None: If objects are well separated and bright relative to the background, it may be unnecessary to attempt to separate clumped objects. Using the very fast None option, a simple threshold will be used to identify objects.
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108 ]]>
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109 </help>
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110 <option value="Intensity">Intensity</option>
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111 <option value="Shape">Shape</option>
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112 <option value="Propagate">Propagate</option>
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113 <option value="None">None</option>
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114 </param>
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115 <when value="Shape">
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116 <expand macro="clumped_objects_params"/>
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117 </when>
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118 <when value="Intensity">
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119 <expand macro="clumped_objects_params"/>
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120 </when>
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121 <when value="Propagate"/>
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122 <when value="None"/>
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123 </conditional>
3
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124 </xml>
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125 <xml name="otsu_threshold_category">
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126
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127 <conditional name="con_threshold_class">
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128 <param name="threshold_class" type="select" label="Two-class or three-class thresholding?">
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129 <help>
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130 <![CDATA[
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131 - Two classes: Select this option if the grayscale levels are readily distinguishable into only two classes: foreground (i.e., regions of interest) and background.
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132 <br> - Three classes: Choose this option if the grayscale levels fall instead into three classes: foreground, background and a middle intensity between the two. You will then be asked whether the middle intensity class should be added to the foreground or background class in order to generate the final two-class output.
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133 ]]>
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134 </help>
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135 <option value="Two classes">Two classes</option>
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136 <option value="Three classes">Three classes</option>
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137 </param>
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138 <when value="Three classes">
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139 <param name="assign_pixel" type="select" label="Assign pixels in the middle intensity class to the foreground or the background?" help="Choose whether you want the pixels with middle grayscale intensities to be assigned to the foreground class or the background class.">
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140 <option value="Foreground">Foreground</option>
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141 <option value="Background">Background</option>
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142 </param>
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143 </when>
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144 <when value="Two classes" />
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145 </conditional>
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146 </xml>
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147 <xml name="threshold_values">
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148 <param name="threshold_correction_factor" type="float" value="1.0" min="0.0" label="Threshold correction factor">
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149 <help>
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150 <![CDATA[
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151 The value entered here adjusts the threshold either upwards or downwards, by multiplying it by this value.
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152 A value of 1 means no adjustment, 0 to 1 makes the threshold more lenient and greater than 1 makes the threshold more stringent.
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153 ]]>
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154 </help>
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155 </param>
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156 <param name="threshold_lower" type="float" value="0.0" min="0.0" max="1.0" label="Lower bound on threshold">
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157 <help>
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158 <![CDATA[
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159 This is helpful as a safety precaution: when the threshold as calculated automatically is clearly outside a reasonable range, the min/max allowable threshold will override the automatic threshold.
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160 ]]>
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161 </help>
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162 </param>
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163 <param name="threshold_upper" type="float" value="1.0" min="0.0" max="1.0" label="Upper bound on threshold"/>
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164 </xml>
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165 <xml name="threshold_smoothing_scale">
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166 <param name="threshold_smoothing_scale" type="float" value="1.3488" label="Threshold smoothing scale">
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167 <help>
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168 <![CDATA[
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169 This setting controls the scale used to smooth the input image before the threshold is applied.
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170 The input image can be optionally smoothed before being thresholded.
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171 Smoothing can improve the uniformity of the resulting objects, by removing holes and jagged edges caused by noise in the acquired image.
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172 Smoothing is most likely not appropriate if the input image is binary, if it has already been smoothed or if it is an output of a pixel-based classifier.
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173 The scale should be approximately the size of the artifacts to be eliminated by smoothing.
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174 A Gaussian is used with a sigma adjusted so that 1/2 of the Gaussian’s distribution falls within the diameter given by the scale (sigma = scale / 0.674) Use a value of 0 for no smoothing.
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175 Use a value of 1.3488 for smoothing with a sigma of 1.
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176 ]]>
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177 </help>
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178 </param>
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179 </xml>
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180 <xml name="threshold_method_help">
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181 <help>
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182 <![CDATA[
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183 The intensity threshold affects the decision of whether each pixel will be considered foreground (region(s) of interest) or background.
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184 A higher threshold value will result in only the brightest regions being identified, whereas a lower threshold value will include dim regions.
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185 When using the strategy "Global", you can have the threshold automatically calculated from a choice of several methods, however, when you choose "Adaptive" as the thresholding strategy, your only option is Otsu automatic thresholding.
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186 The threshold that is used for each image is recorded as a per-image measurement, so if you are surprised by unusual measurements from one of your images, you might check whether the automatically calculated threshold was unusually high or low compared to the other images. See the FlagImage module if you would like to flag an image based on the threshold value.
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187
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188 <br> - Otsu: This approach calculates the threshold separating the two classes of pixels (foreground and background) by minimizing the variance within the each class.
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189 ]]>
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190 </help>
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191 </xml>
0
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192 </macros>
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193
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194 <expand macro="py_requirements"/>
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195 <expand macro="cmd_modules" />
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196 <configfiles>
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197 <inputs name="inputs" />
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198
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199 <configfile name="script_file">
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200 import json
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201 import sys
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202 import os
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203
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204 FOURSPACES=@SPACES@
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205
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206 input_json_path = sys.argv[1]
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207 input_pipeline= sys.argv[2]
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208
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209 params = json.load(open(input_json_path, "r"))
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210
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211 ipo = params['con_advanced']
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212
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213 adv = params['con_advanced']['advanced']
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214
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215
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216 def write_ipo():
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217 _str = "\nIdentifyPrimaryObjects:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:13|show_window:True|notes:\\x5B\\'Identify the nuclei from the DNA channel.\\', \\'PARAMS\\x3A\\', \\'- Typical diameter of objects (Min,Max)\\', \\'- Method to distinguish clumped objects\\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
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218
3
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219 _str += FOURSPACES + "Select the input image:%s\n" % ipo['input_from_nat']
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220 _str += FOURSPACES + "Name the primary objects to be identified:%s\n" % ipo['name_to_be_identified']
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221 _str += FOURSPACES + "Typical diameter of objects, in pixel units (Min,Max):%d,%d\n" % (ipo['min_diameter'], ipo['max_diameter'])
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222 _str += FOURSPACES + "Discard objects outside the diameter range?:%s\n" % ipo['discard_outside_border']
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223 _str += FOURSPACES + "Discard objects touching the border of the image?:%s\n" % ipo['discard_touching_border']
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224
0
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225
3
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226 # default values when adv=no;required in the cppipe file
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227 distinguish_clumped_objects = "Intensity"
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228 dividing_lines = "Intensity"
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229 size_smoothing_filter = 1
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230 min_allowed_distance = 7
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231 speed_up = "Yes"
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232 fill_hole = "After both thresholding and declumping"
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233 calc_size_smoothing_filter = "Yes"
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234 calc_min_disance = "Yes"
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235 excessive_handling = "Continue"
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236 max_obj = 500
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237 thre_setting_version = 10
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238 threshold_strategy = "Global"
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239 threshold_method = "Minimum cross entropy"
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240 threshold_smoothing_scale = 1.3488
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241 threshold_correction_factor = 1.0
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242 threshold_lower = 0.0
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243 threshold_upper = 1.0
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244 manual_threshold = 0.0
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245 threshold_measurement = "None"
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246 threshold_class = "Two classes"
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247 assign_pixel = "Foreground"
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248 adaptive_window = 50
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249 lower_outlier_fraction = 0.05
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250 upper_outlier_fraction = 0.05
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251 avg_method = "Mean"
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252 variance_method = "Standard deviation"
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253 no_of_deviation = 2.0
0
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254
3
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255 if adv == "Yes":
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256 distinguish_clumped_objects = ipo['con_distinguish_clumped_objects'][
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257 'distinguish_clumped_objects']
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258 if "con_dividing_lines" in ipo['con_distinguish_clumped_objects']:
3
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259 smoothing = ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_smoothing_filter']['smoothing_filter']
0
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260 supress = ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_min_distance']['min_distance']
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261 dividing_lines = ipo['con_distinguish_clumped_objects']['con_dividing_lines']['dividing_lines']
0
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262
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263 if smoothing == "Yes":
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
264 size_smoothing_filter= 0
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
265 else:
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
266 size_smoothing_filter = ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_smoothing_filter'][
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
267 'size_smoothing_filter']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
268
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
269 if supress == "No":
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
270 min_allowed_distance = ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_min_distance'][
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
271 'min_allowed_distance']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
272
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
273 speed_up = ipo['con_distinguish_clumped_objects']['con_dividing_lines']['speed_up']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
274
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
275 calc_size_smoothing_filter = ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_smoothing_filter'][
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
276 'smoothing_filter']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
277 calc_min_disance = ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_min_distance']['min_distance']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
278
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
279 fill_hole = ipo['fill_hole']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
280
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
281 if "con_handling_excessive" in ipo:
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
282 excessive_handling = ipo['con_handling_excessive']['excessive_handling']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
283 if excessive_handling == "Continue":
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
284 max_obj = 500
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
285 else:
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
286 max_obj = ipo['con_handling_excessive']['max_obj']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
287
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
288 threshold_strategy=ipo['con_threshold_strategy']['threshold_strategy']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
289 threshold_method = ipo['con_threshold_strategy']['con_threshold_method']['threshold_method']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
290
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
291 if threshold_strategy =="Adaptive":
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
292 adaptive_window =ipo['con_threshold_strategy']['adaptive_window']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
293 threshold_smoothing_scale = ipo['con_threshold_strategy']['threshold_smoothing_scale']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
294 threshold_class = ipo['con_threshold_strategy']['con_threshold_method']['con_threshold_class'][
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
295 'threshold_class']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
296 if threshold_class == "Three classes":
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
297 assing_pixel = ipo['con_threshold_strategy']['con_threshold_method']['con_threshold_class']['assign_pixel']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
298 else:
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
299 if threshold_method == "Manual":
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
300 manual_threshold = ipo['con_threshold_strategy']['con_threshold_method']['manual_threshold']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
301 else:
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
302 if threshold_method == "Measurement":
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
303 threshold_measurement = ipo['con_threshold_strategy']['con_threshold_method']['global_measurement_threshold_cat'] +"_" +ipo['con_threshold_strategy']['con_threshold_method']['global_measurement_threshold_measurement']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
304
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
305 if threshold_method == "Otsu":
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
306 threshold_class = ipo['con_threshold_strategy']['con_threshold_method']['con_threshold_class'][
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
307 'threshold_class']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
308 if threshold_class == "Three classes":
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
309 assign_pixel=ipo['con_threshold_strategy']['con_threshold_method']['con_threshold_class']['assign_pixel']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
310
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
311 threshold_smoothing_scale = ipo['con_threshold_strategy']['con_threshold_method']['threshold_smoothing_scale']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
312
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
313 if threshold_method == "Minimum cross entropy":
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
314 threshold_smoothing_scale = ipo['con_threshold_strategy']['con_threshold_method']['threshold_smoothing_scale']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
315
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
316 if threshold_method == "RobustBackground":
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
317 threshold_smoothing_scale = ipo['con_threshold_strategy']['con_threshold_method']['threshold_smoothing_scale']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
318 lower_outlier_fraction = ipo['con_threshold_strategy']['con_threshold_method']['lower_outlier_fraction']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
319 upper_outlier_fraction =ipo['con_threshold_strategy']['con_threshold_method']['upper_outlier_fraction']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
320 avg_method = ipo['con_threshold_strategy']['con_threshold_method']['avg_method']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
321 variance_method = ipo['con_threshold_strategy']['con_threshold_method'] ['variance_method']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
322 no_of_deviation = ipo['con_threshold_strategy']['con_threshold_method']['no_of_deviations']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
323
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
324 threshold_correction_factor = ipo['con_threshold_strategy']['con_threshold_method'][
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
325 'threshold_correction_factor']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
326 threshold_lower = ipo['con_threshold_strategy']['con_threshold_method']['threshold_lower']
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
327 threshold_upper = ipo['con_threshold_strategy']['con_threshold_method']['threshold_upper']
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
328
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
329 _str += FOURSPACES + "Method to distinguish clumped objects:%s\n" % distinguish_clumped_objects
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
330 _str += FOURSPACES + "Method to draw dividing lines between clumped objects:%s\n" % dividing_lines
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
331 _str += FOURSPACES + "Size of smoothing filter:%d\n" % size_smoothing_filter
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
332 _str += FOURSPACES + "Suppress local maxima that are closer than this minimum allowed distance:%d\n" % min_allowed_distance
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
333 _str += FOURSPACES + "Speed up by using lower-resolution image to find local maxima?:%s\n" % speed_up
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
334 _str += FOURSPACES + "Fill holes in identified objects?:%s\n" % fill_hole
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
335 _str += FOURSPACES + "Automatically calculate size of smoothing filter for declumping?:%s\n" % calc_size_smoothing_filter
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
336 _str += FOURSPACES + "Automatically calculate minimum allowed distance between local maxima?:%s\n" % calc_min_disance
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
337 _str += FOURSPACES + "Handling of objects if excessive number of objects identified:%s\n" % excessive_handling
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
338 _str += FOURSPACES + "Maximum number of objects:%d\n" % max_obj
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
339
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
340 _str += FOURSPACES + "Use advanced settings?:%s\n" % adv
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
341 _str += FOURSPACES + "Threshold settings version:10\n"
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
342 _str += FOURSPACES + "Threshold strategy:%s\n" % threshold_strategy
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
343 _str += FOURSPACES + "Thresholding method:%s\n" % threshold_method
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
344 _str += FOURSPACES + "Threshold smoothing scale:%.4f\n" % threshold_smoothing_scale
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
345 _str += FOURSPACES + "Threshold correction factor:%.1f\n" % threshold_correction_factor
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
346 _str += FOURSPACES + "Lower and upper bounds on threshold:%.1f,%.1f\n" % (threshold_lower, threshold_upper)
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
347 _str += FOURSPACES + "Manual threshold:%d\n" % manual_threshold
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
348 _str += FOURSPACES + "Select the measurement to threshold with:%s\n" % threshold_measurement
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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349 _str += FOURSPACES + "Two-class or three-class thresholding?:%s\n" % threshold_class
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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350 _str += FOURSPACES + "Assign pixels in the middle intensity class to the foreground or the background?:%s\n" % assign_pixel
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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351 _str += FOURSPACES + "Size of adaptive window:%d\n" % adaptive_window
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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352 _str += FOURSPACES + "Lower outlier fraction:%.2f\n" % lower_outlier_fraction
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
353 _str += FOURSPACES + "Upper outlier fraction:%.2f\n" % upper_outlier_fraction
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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354 _str += FOURSPACES + "Averaging method:%s\n" % avg_method
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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355 _str += FOURSPACES + "Variance method:%s\n" % variance_method
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
356 _str += FOURSPACES + "# of deviations:%.2f\n" % no_of_deviation
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
357
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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358 _str += FOURSPACES + "Thresholding method:%s\n" % threshold_method # This is a repeated entry, but needed for pipeline file
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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359
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360 return _str
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361
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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362
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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363 with open(input_pipeline) as fin:
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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364 lines = fin.readlines()
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parents:
diff changeset
365
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
366 k, v = lines[4].strip().split(':')
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367
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
368 module_count = int(v)
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369 new_count = module_count + 1
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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370 lines[4] = k + ":%d\n" % new_count
3
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371 with open("output.cppipe", "w") as f:
0
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diff changeset
372 f.writelines(lines)
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373 f.write(write_ipo())
3
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diff changeset
374 f.close()
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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diff changeset
375 </configfile>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
376 </configfiles>
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377
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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378 <inputs>
3
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diff changeset
379 <expand macro="input_pipeline_param" />
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
380 <conditional name="con_advanced">
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
381 <param name="advanced" type="select" label="Use advanced settings?">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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382 <option value="No">No, use basic settings</option>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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383 <option value="Yes">Yes, use advanced settings</option>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
384 </param>
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385 <when value="No">
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
386 <expand macro="ipo_common" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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parents:
diff changeset
387 </when>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
388 <when value="Yes">
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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diff changeset
389 <expand macro="ipo_common" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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diff changeset
390 <conditional name="con_threshold_strategy">
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
391 <param name="threshold_strategy" type="select" label="Threshold strategy">
3
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diff changeset
392 <help>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
393 <![CDATA[
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
394 The thresholding strategy determines the type of input that is used to calculate the threshold. These options allow you to calculate a threshold based on the whole image or based on image sub-regions.
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
395 The choices for the threshold strategy are:
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
396
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
397 <br> - Global: Calculates a single threshold value based on the unmasked pixels of the input image and use that value to classify pixels above the threshold as foreground and below as background.
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
398 image0 This strategy is fast and robust, especially if the background is relatively uniform (for example, after illumination correction).
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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399
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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400 <br> - Adaptive: Calculates a different threshold for each pixel, thus adapting to changes in foreground/background intensities across the image. For each pixel, the threshold is calculated based on the pixels within a given neighborhood (or window) surrounding that pixel.
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
401 image1 This method is slower but can produce better results for non-uniform backgrounds. However, for significant illumination variation, using the CorrectIllumination modules is preferable.
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
402 ]]>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
403 </help>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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diff changeset
404 <option value="Global">Global</option>
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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diff changeset
405 <option value="Adaptive" selected="true">Adaptive</option>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
406 </param>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
407 <when value="Adaptive">
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
408 <conditional name="con_threshold_method">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
409 <param name="threshold_method" type="select" label="Thresholding method">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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diff changeset
410 <expand macro="threshold_method_help"/>
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411 <option value="Otsu" selected="True">Otsu</option>
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diff changeset
412 </param>
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diff changeset
413 <when value="Otsu">
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diff changeset
414 <expand macro="otsu_threshold_category" />
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diff changeset
415
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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416 </when>
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diff changeset
417 </conditional>
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418 <param name="adaptive_window" type="integer" label="Size of the adaptive window" value="50" help="Often a good choice is some multiple of the largest expected object size." />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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diff changeset
419 <expand macro="threshold_smoothing_scale" />
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420 <expand macro="threshold_values" />
0
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diff changeset
421 </when>
3
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diff changeset
422 <when value="Global">
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diff changeset
423 <conditional name="con_threshold_method">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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diff changeset
424 <param name="threshold_method" type="select" label="Thresholding method">
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425 <expand macro="threshold_method_help"/>
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426 <option value="Manual">Manual</option>
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427 <option value="Measurement">Measurement</option>
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428 <option value="Minimum cross entropy">Minimum cross entropy</option>
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429 <option value="Otsu" selected="True">Otsu</option>
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430 <option value="RobustBackground">Robust background</option>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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431 </param>
3
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432 <when value="Otsu">
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433 <expand macro="otsu_threshold_category" />
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diff changeset
434
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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diff changeset
435 <expand macro="threshold_smoothing_scale" />
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436 <expand macro="threshold_values" />
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437 </when>
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438 <when value="Manual">
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439 <param name="manual_threshold" type="float" label="Enter the value that will act as an absolute threshold for the images" min="0" max="1" value="0" />
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440 </when>
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441 <when value="RobustBackground">
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442 <param name="lower_outlier_fraction" type="float" value="0.05" min="0.0" max="1.0" label="Lower outlier fraction" />
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443 <param name="upper_outlier_fraction" type="float" value="0.05" min="0.0" max="1.0" label="Upper outlier fraction" />
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444 <param name="avg_method" type="select" label="Averaging method">
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445 <option value="Mean">Mean</option>
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446 <option value="Median">Median</option>
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447 <option value="Mode">Mode</option>
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448 </param>
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449 <param name="variance_method" type="select" label="Variance">
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450 <option value="Standard deviation">Standard deviation</option>
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451 <option value="Median absolute deviation">Median absolute deviation</option>
0
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452 </param>
3
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453 <param name="no_of_deviations" type="float" value="2.0" label="# of deviations">
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454 <help>
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455 <![CDATA[
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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456 Robust background calculates the variance, multiplies it by the value given by this setting and adds it to the average.
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457 Adding several deviations raises the threshold well above the average. Use a larger number to be more stringent about identifying foreground pixels.
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458 Use a smaller number to be less stringent. It’s even possible to use a negative number if you want the threshold to be lower than the average (e.g., for images that are densely covered by foreground).
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459 ]]>
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460 </help>
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461 </param>
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462 <expand macro="threshold_smoothing_scale" />
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463 <expand macro="threshold_values" />
0
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464 </when>
3
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465 <when value="Measurement">
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466 <param name="global_measurement_threshold_cat" type="select" label="Select the measurement category to threshold with">
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467 <option value="FileName">File Name</option>
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468 <option value="Frame">Frame</option>
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469 <option value="Height">Height</option>
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470 <option value="MD5Digest">MD5Digest</option>
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471 <option value="PathName">Path Name</option>
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472 <option value="Scaling">Scaling</option>
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473 <option value="Series">Series</option>
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474 <option value="URL">URL</option>
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475 <option value="Width">Width</option>
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476 </param>
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477 <param name="global_measurement_threshold_measurement" type="text" label="Select the measurement to threshold with">
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478 <help>
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479 Measurement corresponds to the names in Starting modules.
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480 </help>
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481 </param>
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482 <expand macro="threshold_values" />
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483 </when>
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484 <when value="Minimum cross entropy">
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485 <expand macro="threshold_smoothing_scale" />
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486 <expand macro="threshold_values" />
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487 </when>
0
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488 </conditional>
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489 </when>
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490 </conditional>
3
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491
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492
0
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493 <conditional name="con_distinguish_clumped_objects">
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494 <param name="distinguish_clumped_objects" type="select" label="Method to distinguish clumped objects">
3
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495 <help>
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496 <![CDATA[
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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497 This setting allows you to choose the method that is used to distinguish between individual objects that are touching each other (and not properly delineated as two objects by thresholding alone). In other words, this setting allows you to “declump” a large, merged object into individual objects of interest. To decide between these methods, you can run Test mode to see the results of each.
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498 <br> - Intensity: For objects that tend to have only a single peak of brightness (e.g., objects that are brighter towards their interiors and dimmer towards their edges), this option counts each intensity peak as a separate object. The objects can be any shape, so they need not be round and uniform in size as would be required for the Shape option.
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499 <br> - Shape: For cases when there are definite indentations separating objects. The image is converted to black and white (binary) and the shape determines whether clumped objects will be distinguished. The declumping results of this method are affected by the thresholding method you choose.
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500 <br> - None: If objects are well separated and bright relative to the background, it may be unnecessary to attempt to separate clumped objects. Using the very fast None option, a simple threshold will be used to identify objects.
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501 ]]>
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502 </help>
0
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503 <option value="Shape">Shape</option>
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504 <option value="Intensity" selected="True">Intensity</option>
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505 <option value="None">None</option>
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506 </param>
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507 <when value="Shape">
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508 <expand macro="clumped_objects"/>
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509 </when>
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510 <when value="Intensity">
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511 <expand macro="clumped_objects"/>
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512 </when>
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513 <when value="None"/>
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514 </conditional>
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515 <param name="fill_hole" type="select" label="Fill holes in identified objects">
3
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516 <help>
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517 <![CDATA[
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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518 This option controls how holes (regions of background surrounded by one or more objects) are filled in:
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519 <br> - After both thresholding and declumping: Fill in holes that are smaller than the maximum object size prior to declumping and to fill in any holes after declumping.
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520 <br> - After declumping only: Fill in holes located within identified objects after declumping.
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521 <br> - Never: Leave holes within objects. Please note that if an object is located within a hole and this option is enabled, the object will be lost when the hole is filled in.
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522 ]]>
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523 </help>
0
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524 <option value="Never">Never</option>
3
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525 <option value="After both thresholding and declumping" selected="True">After both thresholding and declumping</option>
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526 <option value="After declumping only">After declumping only</option>
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527 </param>
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528
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
529 <conditional name="con_handling_excessive">
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
530 <param name="excessive_handling" type="select" label="Handling of objects if excessive number of objects identified">
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
531 <help>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
532 <![CDATA[
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
533 This setting deals with images that are segmented into an unreasonable number of objects. This might happen if the module calculates a low threshold or if the image has unusual artifacts. IdentifyPrimaryObjects can handle this condition in one of three ways:
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
534 <br> - Continue: Continue processing regardless if large numbers of objects are found.
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
535 <br> - Erase: Erase all objects if the number of objects exceeds the maximum. This results in an image with no primary objects. This option is a good choice if a large number of objects indicates that the image should not be processed; it can save a lot of time in subsequent Measure modules.
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
536 ]]>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
537 </help>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
538 <option value="Continue">Continue</option>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
539 <option value="Erase">Erase</option>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
540 </param>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
541 <when value="Erase">
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
542 <param name="max_obj" type="integer" value="500" label="Maximum number of objects" help="This setting limits the number of objects in the image." />
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
543 </when>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
544 <when value="Continue" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
545 </conditional>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
546 </when>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
547 </conditional>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
548 </inputs>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
549
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
550 <outputs>
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
551 <expand macro="output_pipeline_param" />
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
552 </outputs>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
553
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
554 <tests>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
555 <test>
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
556 <!-- no advanced setting -->
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
557 <expand macro="test_input_pipeline_param" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
558 <conditional name="con_advanced">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
559 <param name="advanced" value="No" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
560 <param name="input_from_nat" value="DNA" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
561 <param name="name_to_be_identified" value="Nuclei" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
562 <param name="min_diameter" value="15" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
563 <param name="max_diameter" value="200" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
564 <param name="discard_outside_border" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
565 <param name="discard_touching_border" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
566 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
567 <expand macro="test_out_file" file="identify_primary_objects_noadv.cppipe" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
568 </test>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
569 <test>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
570 <!-- advanced setting, adaptive threshold strategy, otsu method -->
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
571 <expand macro="test_input_pipeline_param" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
572 <conditional name="con_advanced">
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
573 <param name="advanced" value="Yes" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
574 <param name="input_from_nat" value="DNA" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
575 <param name="name_to_be_identified" value="Nuclei" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
576 <param name="min_diameter" value="15" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
577 <param name="max_diameter" value="200" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
578 <param name="discard_outside_border" value="Yes" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
579 <param name="discard_touching_border" value="Yes" />
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
580
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
581 <conditional name="con_threshold_strategy">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
582 <param name="threshold_strategy" value="Adaptive" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
583 <conditional name="con_threshold_method">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
584 <param name="threshold_method" value="Otsu" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
585 <conditional name="con_threshold_class">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
586 <param name="threshold_class" value="Three classes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
587 <param name="assign_pixel" value="Foreground" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
588 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
589 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
590 <param name="adaptive_window" value="50" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
591 <param name="threshold_smoothing_scale" value="1.5" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
592 <param name="threshold_correction_factor" value="1" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
593 <param name="threshold_lower" value="0.0" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
594 <param name="threshold_upper" value="1.0" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
595 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
596 <conditional name="con_distinguish_clumped_objects">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
597 <param name="distinguish_clumped_objects" value="Shape" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
598 <conditional name="con_dividing_lines" >
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
599 <param name="dividing_lines" value="Shape" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
600 <conditional name="con_smoothing_filter">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
601 <param name="smoothing_filter" value="No"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
602 <param name="size_smoothing_filter" value="1" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
603 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
604 <conditional name="con_min_distance">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
605 <param name="min_distance" value="No"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
606 <param name="min_allowed_distance" value="1"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
607 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
608 <param name="speed_up" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
609 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
610 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
611 <param name="fill_hole" value="After both thresholding and declumping" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
612 <conditional name="con_handling_excessive">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
613 <param name="excessive_handling" value="Continue"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
614 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
615 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
616 <expand macro="test_out_file" file="identify_primary_objects_adv_adaptive_otsu.cppipe" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
617 </test>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
618
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
619 <test>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
620 <!-- advanced setting, global threshold strategy, manual method -->
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
621 <expand macro="test_input_pipeline_param" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
622 <conditional name="con_advanced">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
623 <param name="advanced" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
624 <param name="input_from_nat" value="DNA" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
625 <param name="name_to_be_identified" value="Nuclei" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
626 <param name="min_diameter" value="5" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
627 <param name="max_diameter" value="20" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
628 <param name="discard_outside_border" value="No" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
629 <param name="discard_touching_border" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
630
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
631 <conditional name="con_threshold_strategy">
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
632 <param name="threshold_strategy" value="Global" />
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
633 <conditional name="con_threshold_method">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
634 <param name="threshold_method" value="Manual" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
635 <param name="manual_threshold" value="1" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
636 </conditional>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
637 </conditional>
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
638 <conditional name="con_distinguish_clumped_objects">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
639 <param name="distinguish_clumped_objects" value="Shape" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
640 <conditional name="con_dividing_lines" >
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
641 <param name="dividing_lines" value="Shape" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
642 <conditional name="con_smoothing_filter">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
643 <param name="smoothing_filter" value="No"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
644 <param name="size_smoothing_filter" value="1" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
645 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
646 <conditional name="con_min_distance">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
647 <param name="min_distance" value="No"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
648 <param name="min_allowed_distance" value="1"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
649 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
650 <param name="speed_up" value="Yes" />
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
651 </conditional>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
652 </conditional>
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
653 <param name="fill_hole" value="After both thresholding and declumping" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
654 <conditional name="con_handling_excessive">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
655 <param name="excessive_handling" value="Erase"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
656 <param name="max_obj" value="499" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
657 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
658 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
659 <expand macro="test_out_file" file="identify_primary_objects_adv_global_manual.cppipe" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
660 </test>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
661 <test>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
662 <!-- advanced setting, global threshold strategy, measurement method -->
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
663 <expand macro="test_input_pipeline_param" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
664 <conditional name="con_advanced">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
665 <param name="advanced" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
666 <param name="input_from_nat" value="DNA" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
667 <param name="name_to_be_identified" value="Nuclei" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
668 <param name="min_diameter" value="5" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
669 <param name="max_diameter" value="20" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
670 <param name="discard_outside_border" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
671 <param name="discard_touching_border" value="No" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
672
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
673 <conditional name="con_threshold_strategy">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
674 <param name="threshold_strategy" value="Global" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
675 <conditional name="con_threshold_method">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
676 <param name="threshold_method" value="Measurement" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
677 <param name="global_measurement_threshold_cat" value="FileName" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
678 <param name="global_measurement_threshold_measurement" value="DNA" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
679 <param name="threshold_correction_factor" value="1" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
680 <param name="threshold_lower" value="0.1" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
681 <param name="threshold_upper" value="0.4" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
682 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
683 </conditional>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
684 <conditional name="con_distinguish_clumped_objects">
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
685 <param name="distinguish_clumped_objects" value="Intensity" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
686 <conditional name="con_dividing_lines" >
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
687 <param name="dividing_lines" value="Shape" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
688 <conditional name="con_smoothing_filter">
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
689 <param name="smoothing_filter" value="Yes"/>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
690 </conditional>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
691 <conditional name="con_min_distance">
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
692 <param name="min_distance" value="No"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
693 <param name="min_allowed_distance" value="6"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
694 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
695 <param name="speed_up" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
696 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
697 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
698 <param name="fill_hole" value="After both thresholding and declumping" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
699 <conditional name="con_handling_excessive">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
700 <param name="excessive_handling" value="Continue"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
701 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
702 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
703 <expand macro="test_out_file" file="identify_primary_objects_adv_global_measurement.cppipe" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
704 </test>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
705
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
706 <test>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
707 <!-- advanced setting, global threshold strategy, minimum cross entropy method -->
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
708 <expand macro="test_input_pipeline_param" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
709 <conditional name="con_advanced">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
710 <param name="advanced" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
711 <param name="input_from_nat" value="DNA" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
712 <param name="name_to_be_identified" value="Nuclei" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
713 <param name="min_diameter" value="15" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
714 <param name="max_diameter" value="40" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
715 <param name="discard_outside_border" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
716 <param name="discard_touching_border" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
717
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
718 <conditional name="con_threshold_strategy">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
719 <param name="threshold_strategy" value="Global" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
720 <conditional name="con_threshold_method">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
721 <param name="threshold_method" value="Minimum cross entropy" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
722 <param name="threshold_smoothing_scale" value="1.5" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
723 <param name="threshold_correction_factor" value="1" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
724 <param name="threshold_lower" value="0.0" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
725 <param name="threshold_upper" value="1.0" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
726 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
727 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
728 <conditional name="con_distinguish_clumped_objects">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
729 <param name="distinguish_clumped_objects" value="Shape" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
730 <conditional name="con_dividing_lines" >
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
731 <param name="dividing_lines" value="Shape" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
732 <conditional name="con_smoothing_filter">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
733 <param name="smoothing_filter" value="No"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
734 <param name="size_smoothing_filter" value="1" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
735 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
736 <conditional name="con_min_distance">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
737 <param name="min_distance" value="No"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
738 <param name="min_allowed_distance" value="7"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
739 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
740 <param name="speed_up" value="Yes" />
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
741 </conditional>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
742 </conditional>
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
743 <param name="fill_hole" value="After both thresholding and declumping" />
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
744 <conditional name="con_handling_excessive">
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
745 <param name="excessive_handling" value="Continue"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
746 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
747 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
748 <expand macro="test_out_file" file="identify_primary_objects_adv_global_mce.cppipe" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
749 </test>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
750
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
751 <test>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
752 <!-- advanced setting, global threshold strategy, robustbackground method -->
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
753 <expand macro="test_input_pipeline_param" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
754 <conditional name="con_advanced">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
755 <param name="advanced" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
756 <param name="input_from_nat" value="DNA" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
757 <param name="name_to_be_identified" value="Nuclei" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
758 <param name="min_diameter" value="10" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
759 <param name="max_diameter" value="40" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
760 <param name="discard_outside_border" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
761 <param name="discard_touching_border" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
762
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
763 <conditional name="con_threshold_strategy">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
764 <param name="threshold_strategy" value="Global" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
765 <conditional name="con_threshold_method">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
766 <param name="threshold_method" value="RobustBackground" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
767 <param name="lower_outlier_fraction" value="0.06" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
768 <param name="upper_outlier_fraction" value="0.07" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
769 <param name="avg_method" value="Median"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
770 <param name="variance_method" value="Median absolute deviation"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
771 <param name="no_of_deviations" value="3.0" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
772 <param name="threshold_smoothing_scale" value="1.4" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
773 <param name="threshold_correction_factor" value="1" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
774 <param name="threshold_lower" value="0.0" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
775 <param name="threshold_upper" value="1.0" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
776 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
777 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
778 <conditional name="con_distinguish_clumped_objects">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
779 <param name="distinguish_clumped_objects" value="Shape" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
780 <conditional name="con_dividing_lines" >
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
781 <param name="dividing_lines" value="Shape" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
782 <conditional name="con_smoothing_filter">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
783 <param name="smoothing_filter" value="No"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
784 <param name="size_smoothing_filter" value="1" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
785 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
786 <conditional name="con_min_distance">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
787 <param name="min_distance" value="No"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
788 <param name="min_allowed_distance" value="7"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
789 </conditional>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
790 <param name="speed_up" value="Yes" />
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
791 </conditional>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
792 </conditional>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
793 <param name="fill_hole" value="After both thresholding and declumping" />
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
794 <conditional name="con_handling_excessive">
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
795 <param name="excessive_handling" value="Continue"/>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
796 </conditional>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
797 </conditional>
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
798 <expand macro="test_out_file" file="identify_primary_objects_adv_global_rb.cppipe" />
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
799 </test>
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
800
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
801 </tests>
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
802
3
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
803 <help>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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804 <![CDATA[
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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805 .. class:: infomark
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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806
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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807 **What it does**
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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808
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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809 This tool identifies biological objects of interest. It requires grayscale images containing bright objects on a dark background. Incoming images must be 2D (including 2D slices of 3D images); please use the Watershed module for identification of objects in 3D.
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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810
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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811 @COMMON_HELP@
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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812 ]]>
52c01fb29b2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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813 </help>
0
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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814
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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815 <expand macro="citations" />
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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816
99e493b2e951 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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817 </tool>