Mercurial > repos > bgruening > cp_track_objects

annotate track_objects.xml @ 2:972d2c365739 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:31:44 +0000
parents 1fd453cd757b
children
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1 <tool id="cp_track_objects" name="TrackObjects" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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2 <description>with CellProfiler</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 <xml name="common">
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7 <conditional name="con_filter_by_lifetime">
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8 <param name="filter_by_lifetime" type="select" label="Filter objects by lifetime?" help = "Select Yes if you want objects to be filtered by their lifetime, i.e., total duration in frames. This is useful for marking objects which transiently appear and disappear, such as the results of a mis-segmentation.">
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9 <option value="Yes">Yes</option>
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10 <option value="No">No</option>
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11 </param>
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12 <when value="Yes">
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13 <conditional name="con_use_min">
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14 <param name="use_min" type="select" label="Filter using a minimum lifetime?" help = "Select Yes to filter the object on the basis of a minimum number of frames. ">
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15 <option value="Yes">Yes</option>
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16 <option value="No">No</option>
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17 </param>
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18 <when value="Yes">
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19 <param name="min_lifetime" type="integer" value="1" label="Minimum lifetime" help = " Enter the minimum number of frames an object is permitted to persist. Objects which last this number of frames or lower are filtered out."/>
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20 </when>
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21 <when value="No">
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22 </when>
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23 </conditional>
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24 <conditional name="con_use_max">
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25 <param name="use_max" type="select" label="Filter using a maximum lifetime?" help = "Select Yes to filter the object on the basis of a maximum number of frames.">
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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 <when value="Yes">
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30 <param name="max_lifetime" type="integer" value="100" label="Maximum lifetime" help = "Enter the maximum number of frames an object is permitted to persist. Objects which last this number of frames or more are filtered out"/>
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31 </when>
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32 <when value="No">
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33 </when>
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34 </conditional>
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35 </when>
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36 <when value="No">
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37 </when>
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38 </conditional>
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39 <param name="display_option" type="select" label="Select display option">
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40 <option value="Color and Number">Color and Number</option>
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41 <option value="Color only">Color only</option>
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42 </param>
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43 <conditional name="con_save_coded_img">
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44 <param name="save_coded_img" type="select" label="Save color-coded image?">
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45 <option value="Yes">Yes</option>
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46 <option value="No">No</option>
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47 </param>
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48 <when value="Yes">
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49 <param name="name_output_img" type="text" label="Name the output image"/>
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50 </when>
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51 <when value="No">
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52 </when>
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53 </conditional>
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54 </xml>
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55
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56 <xml name="overlap_distance">
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57 <param name="max_distance" type="integer" value="50" label="Maximum pixel distance to consider matches">
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58 <help>
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59 <![CDATA[
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60 Objects in the subsequent frame will be considered potential matches if they are within this distance.
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61 To determine a suitable pixel distance, you can look at the axis increments on each image (shown in pixel units) or use the distance measurement tool.
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62 To measure distances in an open image, use the “Measure length” tool under Tools in the display window menu bar. If you click on an image and drag, a line will appear between the two endpoints, and the distance between them will be shown at the right-most portion of the bottom panel.
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63 ]]>
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64 </help>
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65 </param>
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66 </xml>
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67
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68 <xml name="lap">
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69 <param name="movement_method" type="select" label="Select the movement model">
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70 <option value="Random">Random</option>
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71 <option value="Velocity">Velocity</option>
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72 <option value="Both">Both</option>
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73 </param>
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74 <param name="no_std_radius" type="float" value="3.0" label="Number of standard deviations for search radius" />
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75 <param name="min_radius" type="float" value="2.0" label="Minimum search radius in pixel units" />
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76 <param name="max_radius" type="float" value="10.0" label="Maximum search radius in pixel units" />
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77
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78 <conditional name="con_second_lap">
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79 <param name="second_lap" type="select" label="Run the second phase of the LAP algorithm?">
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80 <option value="Yes">Yes</option>
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81 <option value="No">No</option>
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82 </param>
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83 <when value="Yes">
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84 <param name="gap_closing" type="integer" value="50" label="Gap closing cost" />
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85 <param name="split_alt" type="integer" value="50" label="Split alternative cost" />
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86 <param name="merge_alt" type="integer" value="50" label="Merge alternative cost" />
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87 <param name="mitosis_alt" type="integer" value="50" label="Mitosis alternative cost" />
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88 <param name="max_gap_displacement" type="integer" value="50" label="Maximum gap displacement, in pixel units" />
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89 <param name="max_split" type="integer" value="50" label="Maximum split score" />
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90 <param name="max_merge" type="integer" value="50" label="Maximum merge score" />
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91 <param name="max_temporal" type="integer" value="50" label="Maximum temporal gap, in frames" />
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92 <param name="max_mitosis_distance" type="integer" value="50" label="Maximum mitosis distance, in pixel units" />
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93 </when>
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94 <when value="No">
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95 </when>
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96 </conditional>
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97 </xml>
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98
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99 <xml name="measurements">
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100 <conditional name="con_measurement_category">
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101 <param name="measurement_category" type="select" label="Select object measurement category to use for tracking">
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102 <option value="AreaShape">AreaShape</option>
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103 <option value="Intensity">Intensity</option>
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104 <option value="Location">Location</option>
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105 <option value="Number">Number</option>
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106 </param>
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107 <when value="AreaShape">
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108 <param name="measurement" type="select" label="Select object measurement to use for tracking">
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109 <option value="Area">Area</option>
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110 <option value="Center_X">Center_X</option>
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111 <option value="Center_Y">Center_Y</option>
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112 <option value="Center_Z">Center_Z</option>
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113 <option value="Compactness">Compactness</option>
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114 <option value="Eccentricity">Eccentricity</option>
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115 <option value="EulerNumber">EulerNumber</option>
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116 <option value="Extent">Extent</option>
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117 <option value="FormFactor">FormFactor</option>
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118 <option value="MajorAxisLength">MajorAxisLength</option>
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119 <option value="MaxFeretDiameter">MaxFeretDiameter</option>
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120 <option value="MaximumRadius">MaximumRadius</option>
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121 <option value="MeanRadius">MeanRadius</option>
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122 <option value="MedianRadius">MedianRadius</option>
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123 <option value="MinFeretDiameter">MinFeretDiameter</option>
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124 <option value="MinorAxisLength">MinorAxisLength</option>
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125 <option value="Orientation">Orientation</option>
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126 <option value="Perimeter">Perimeter</option>
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127 <option value="Solidity">Solidity</option>
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128 </param>
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129 </when>
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130 <when value="Intensity">
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131 <param name="measurement" type="select" label="Select object measurement to use for tracking">
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132 <option value="IntegratedIntensity">IntegratedIntensity</option>
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133 <option value="IntegratedIntensityEdge">IntegratedIntensityEdge</option>
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134 <option value="LowerQuartileIntensity">LowerQuartileIntensity</option>
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135 <option value="MADIntensity">MADIntensity</option>
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136 <option value="MassDisplacement">MassDisplacement</option>
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137 <option value="MaxIntensity">MaxIntensity</option>
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138 <option value="MaxIntensityEdge">MaxIntensityEdge</option>
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139 <option value="MeanIntensity">MeanIntensity</option>
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140 <option value="MeanIntensityEdge">MeanIntensityEdge</option>
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141 <option value="MedianIntensity">MedianIntensity</option>
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142 <option value="MinIntensity">MinIntensity</option>
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143 <option value="MinIntensityEdge">MinIntensityEdge</option>
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144 <option value="StdIntensity">StdIntensity</option>
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145 <option value="StdIntensityEdge">StdIntensityEdge</option>
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146 <option value="UpperQuartileIntensity">UpperQuartileIntensity</option>
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147 </param>
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148 <param name="img_measure" type="text" label="Image"/>
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149 </when>
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150 <when value="Location">
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151 <param name="measurement" type="select" label="Select object measurement to use for tracking">
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152 <option value="CenterMassIntensity_X">CenterMassIntensity_X</option>
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153 <option value="CenterMassIntensity_Y">CenterMassIntensity_Y</option>
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154 <option value="CenterMassIntensity_Z">CenterMassIntensity_Z</option>
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155 <option value="Center_X">Center_X</option>
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156 <option value="Center_Y">Center_Y</option>
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157 <option value="Center_Z">Center_Z</option>
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158 <option value="MaxIntensity_X">MaxIntensity_X</option>
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159 <option value="MaxIntensity_Y">MaxIntensity_Y</option>
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160 <option value="MaxIntensity_Z">MaxIntensity_Z</option>
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161 </param>
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162 <param name="img_measure" type="text" label="Image"/>
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163 </when>
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164 <when value="Number">
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165 <param name="measurement" type="select" label="Select object measurement to use for tracking">
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166 <option value="ObjectNumber">ObjectNumber</option>
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167 </param>
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168 </when>
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169 </conditional>
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170 <param name="max_distance" type="integer" value="50" label="Maximum pixel distance to consider matches" >
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171 <help>
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172 <![CDATA[
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173 Objects in the subsequent frame will be considered potential matches if they are within this distance.
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174 To determine a suitable pixel distance, you can look at the axis increments on each image (shown in pixel units) or use the distance measurement tool.
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175 To measure distances in an open image, use the “Measure length” tool under Tools in the display window menu bar. If you click on an image and drag, a line will appear between the two endpoints, and the distance between them will be shown at the right-most portion of the bottom panel. "
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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
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181 <xml name="follow_neighbors">
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182 <param name="max_distance" type="integer" value="50" label="Maximum pixel distance to consider matches">
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183 <help>
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184 <![CDATA[
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185 Objects in the subsequent frame will be considered potential matches if they are within this distance.
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186 To determine a suitable pixel distance, you can look at the axis increments on each image (shown in pixel units) or use the distance measurement tool.
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187 To measure distances in an open image, use the “Measure length” tool under Tools in the display window menu bar. If you click on an image and drag, a line will appear between the two endpoints, and the distance between them will be shown at the right-most portion of the bottom panel.
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188 ]]>
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189 </help>
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190 </param>
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191 <param name="avg_diameter" type="float" value="35.0" label="Average cell diameter in pixels">
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192 <help>
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193 <![CDATA[
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194 The average cell diameter is used to scale many Follow Neighbors algorithm parameters.
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195 To measure distances in an open image, use the “Measure length” tool under Tools in the display window menu bar. If you click on an image and drag, a line will appear between the two endpoints, and the distance between them will be shown at the right-most portion of the bottom panel.
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196 ]]>
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197 </help>
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198 </param>
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199
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200 <conditional name="con_adv_parameter">
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201 <param name="adv_parameter" type="select" label="Use advanced configuration parameters">
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202 <option value="Yes">Yes</option>
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203 <option value="No">No</option>
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204 </param>
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205 <when value="Yes">
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206 <param name="cost" type="float" value="15.0" label="Cost of cell to empty matching" />
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207 <param name="weight" type="float" value="25.0" label="Weight of area difference in function matching cost" />
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208 </when>
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209 <when value="No">
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210 </when>
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211 </conditional>
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212
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213 </xml>
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214 </macros>
2
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215 <edam_operations>
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216 <edam_operation>operation_3443</edam_operation>
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217 </edam_operations>
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218 <xrefs>
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219 <xref type="bio.tools">CellProfiler</xref>
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220 <xref type="biii">cellprofiler</xref>
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221 </xrefs>
0
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222 <expand macro="py_requirements"/>
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223 <command detect_errors="exit_code">
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224 <![CDATA[
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225 python '$__tool_directory__/track_objects.py' -p '$input_pipeline' -i '$input_json'
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226 ]]>
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227 </command>
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228 <configfiles>
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229 <inputs name="input_json"/>
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230 </configfiles>
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231 <inputs>
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232 <expand macro="input_pipeline_param"/>
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233 <param name="object_to_track" type="text" label="Enter the name of the objects to track" help="The object to track from previous IdentifyPrimaryObjects module" />
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234 <conditional name="con_tracking_method">
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235 <param name="tracking_method" type="select" label="Choose a tracking method">
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236 <help>
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237 <![CDATA[
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238 <i>Overlap:</i> Compares the amount of spatial overlap between identified objects in the previous frame with those in the current frame. The object with the greatest amount of spatial overlap will be assigned the same number.
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239 <i>Distance:</i> Compares the distance between each identified object in the previous frame with that of the current frame. The closest objects to each other will be assigned the same number (label). Distances are measured from the perimeter of each object.
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240 <i>Measurements:</i> Compares each object in the current frame with objects in the previous frame based on a particular feature you have measured for the objects. This approach assumes objects move in a coordinated way (contrary to LAP). An object's movement direction is more likely to be in agreement with the movement directions of its neighbors. The problem is formulated as an optimization problem and solved using LAP algorithm (same as in LAP method).
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241 <i>LAP:</i> Uses the linear assignment problem (LAP) framework. The linear assignment problem (LAP) algorithm (Jaqaman et al., 2008) addresses the challenges of high object density, motion heterogeneity, temporary disappearances, and object merging and splitting.
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242 <i>Follow Neighbors:</i> Uses the multiobject tracking approach described by Delgado-Gonzalo et al., 2010. This approach assumes objects move in a coordinated way (contrary to LAP). An object's movement direction is more likely to be in agreement with the movement directions of its "neighbor" The problem is formulated as an optimization problem and solved using LAP algorithm (same as in LAP method)."
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243 ]]>
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244 </help>
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245 <option value="Overlap">Overlap</option>
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246 <option value="Distance">Distance</option>
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247 <option value="Measurements">Measurements</option>
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248 <option value="LAP">LAP</option>
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249 <option value="Follow Neighbors">Follow Neighbors</option>
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250 </param>
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251 <when value="Overlap">
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252 <expand macro="overlap_distance" />
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253 <expand macro="common" />
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254 </when>
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255 <when value="Distance">
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256 <expand macro="overlap_distance" />
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257 <expand macro="common" />
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258 </when>
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259 <when value="Measurements">
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260 <expand macro="measurements" />
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261 <expand macro="common" />
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262 </when>
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263 <when value="LAP">
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264 <expand macro="lap" />
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265 <expand macro="common" />
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266 </when>
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267 <when value="Follow Neighbors">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
268 <expand macro="follow_neighbors" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
269 <expand macro="common" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
270 </when>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
271 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
272 </inputs>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
273 <outputs>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
274 <expand macro="output_pipeline_param" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
275 </outputs>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
276 <tests>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
277 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
278 <param name="input_pipeline" value="common.cppipe"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
279 <param name="object_to_track" value="Embryos" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
280 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
281 <param name="tracking_method" value="Overlap" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
282 <param name="max_distance" value="50" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
283 <conditional name="con_filter_by_lifetime">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
284 <param name="filter_by_lifetime" value="No" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
285 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
286 <param name="display_option" value="Color and Number" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
287 <conditional name="con_save_coded_img">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
288 <param name="save_coded_img" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
289 <param name="name_output_img" value="TrackedCells"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
290 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
291 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
292 <expand macro="test_out_file" file="track_object.cppipe" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
293 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
294 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
295 <param name="input_pipeline" value="common.cppipe"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
296 <param name="object_to_track" value="DNA" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
297 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
298 <param name="tracking_method" value="Overlap" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
299 <param name="max_distance" value="40" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
300 <conditional name="con_filter_by_lifetime">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
301 <param name="filter_by_lifetime" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
302 <conditional name="con_use_min">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
303 <param name="use_min" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
304 <param name="min_lifetime" value= "2"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
305 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
306 <conditional name="con_use_max">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
307 <param name="use_max" value = "No" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
308 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
309 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
310 <param name="display_option" value="Color only" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
311 <conditional name="con_save_coded_img">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
312 <param name="save_coded_img" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
313 <param name="name_output_img" value="ColorCodedImage"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
314 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
315 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
316 <expand macro="test_out_file" file="track_object_overlap_no_filter_max.cppipe" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
317 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
318 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
319 <param name="input_pipeline" value="common.cppipe"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
320 <param name="object_to_track" value="DNA" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
321 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
322 <param name="tracking_method" value="Distance" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
323 <param name="max_distance" value="50" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
324 <conditional name="con_filter_by_lifetime">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
325 <param name="filter_by_lifetime" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
326 <conditional name="con_use_min">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
327 <param name="use_min" value="No" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
328 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
329 <conditional name="con_use_max">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
330 <param name="use_max" value = "Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
331 <param name="max_lifetime" value= "80"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
332 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
333 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
334 <param name="display_option" value="Color and Number" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
335 <conditional name="con_save_coded_img">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
336 <param name="save_coded_img" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
337 <param name="name_output_img" value="OutputImage"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
338 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
339 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
340 <expand macro="test_out_file" file="track_object_distance_no_filter_min.cppipe" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
341 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
342 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
343 <param name="input_pipeline" value="common.cppipe"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
344 <param name="object_to_track" value="DNA" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
345 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
346 <param name="tracking_method" value="Measurements" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
347 <conditional name="con_measurement_category">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
348 <param name="measurement_category" value = "Intensity" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
349 <param name="measurement" value = "MADIntensity"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
350 <param name="img_measure" value = "Image1"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
351 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
352 <param name="max_distance" value= "40" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
353 <conditional name="con_filter_by_lifetime">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
354 <param name="filter_by_lifetime" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
355 <conditional name="con_use_min">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
356 <param name="use_min" value="No" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
357 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
358 <conditional name="con_use_max">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
359 <param name="use_max" value = "Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
360 <param name="max_lifetime" value= "120"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
361 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
362 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
363 <param name="display_option" value="Color only" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
364 <conditional name="con_save_coded_img">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
365 <param name="save_coded_img" value="No" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
366 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
367 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
368 <expand macro="test_out_file" file="track_object_measurement_intensity.cppipe" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
369 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
370 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
371 <param name="input_pipeline" value="common.cppipe"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
372 <param name="object_to_track" value="DNA" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
373 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
374 <param name="tracking_method" value="LAP" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
375 <param name="movement_method" value="Velocity" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
376 <param name="no_std_radius" value="4.0" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
377 <param name="min_radius" value="5.0"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
378 <param name="max_radius" value="11.0"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
379 <conditional name="con_second_lap">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
380 <param name="second_lap" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
381 <param name="gap_closing" value = "6"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
382 <param name="split_alt" value = "6" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
383 <param name="merge_alt" value = "6"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
384 <param name="mitosis_alt" value = "6" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
385 <param name="max_gap_displacement" value = "6"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
386 <param name="max_split" value = "6" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
387 <param name="max_merge" value = "6" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
388 <param name="max_temporal" value = "6" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
389 <param name="max_mitosis_distance" value = "6" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
390 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
391 <conditional name="con_filter_by_lifetime">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
392 <param name="filter_by_lifetime" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
393 <conditional name="con_use_min">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
394 <param name="use_min" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
395 <param name="min_lifetime" value= "1"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
396 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
397 <conditional name="con_use_max">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
398 <param name="use_max" value = "Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
399 <param name="max_lifetime" value= "100"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
400 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
401 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
402 <param name="display_option" value="Color and Number" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
403 <conditional name="con_save_coded_img">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
404 <param name="save_coded_img" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
405 <param name="name_output_img" value="OutputImage"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
406 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
407 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
408 <expand macro="test_out_file" file="track_object_lap_velocity.cppipe" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
409 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
410 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
411 <param name="input_pipeline" value="common.cppipe"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
412 <param name="object_to_track" value="DNA" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
413 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
414 <param name="tracking_method" value = "Follow Neighbors" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
415 <param name="max_distance" value = "60" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
416 <param name="avg_diameter" value = "36.0" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
417 <conditional name="con_adv_parameter">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
418 <param name="adv_parameter" value = "Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
419 <param name="cost" value = "11.0" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
420 <param name="weight" value = "20.0" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
421 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
422 <conditional name="con_filter_by_lifetime">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
423 <param name="filter_by_lifetime" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
424 <conditional name="con_use_min">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
425 <param name="use_min" value="No" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
426 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
427 <conditional name="con_use_max">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
428 <param name="use_max" value = "No" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
429 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
430 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
431 <param name="display_option" value="Color only" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
432 <conditional name="con_save_coded_img">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
433 <param name="save_coded_img" value="Yes" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
434 <param name="name_output_img" value="OutputImage"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
435 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
436 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
437 <expand macro="test_out_file" file="track_object_follow_neighbors.cppipe" />
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
438 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
439 </tests>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
440
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
441 <help>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
442 <![CDATA[
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
443
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
444 .. class:: infomark
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
445
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
446 **What it does**
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
447
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
448 This module allows tracking objects throughout sequential frames of a series of images, so that from frame to frame each object maintains a unique identity in the output measurements.
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
449
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
450 This module must be placed downstream of a module that identifies objects (e.g., IdentifyPrimaryObjects). TrackObjects will associate each object with the same object in the frames before and after. This allows the study of objects' lineages and the timing and characteristics of dynamic events in movies.
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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451
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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452 @COMMON_HELP@
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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453 ]]>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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454 </help>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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455 <expand macro="citations"/>
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972d2c365739 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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456 </tool>