Mercurial > repos > bgruening > cp_track_objects

annotate track_objects.xml @ 0:644e5e32a83c 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 10:03:00 +0000
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children 1fd453cd757b
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644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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1 <tool id="cp_track_objects" name="TrackObjects" version="@CP_VERSION@" python_template_version="3.5">
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2 <description> tracking objects throughout sequential frames of a series of images</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="common">
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6 <conditional name="con_filter_by_lifetime">
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7 <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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8 <option value="Yes">Yes</option>
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9 <option value="No">No</option>
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10 </param>
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11 <when value="Yes">
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12 <conditional name="con_use_min">
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13 <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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14 <option value="Yes">Yes</option>
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15 <option value="No">No</option>
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16 </param>
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17 <when value="Yes">
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18 <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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19 </when>
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20 <when value="No">
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21 </when>
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22 </conditional>
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23 <conditional name="con_use_max">
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24 <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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25 <option value="Yes">Yes</option>
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26 <option value="No">No</option>
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27 </param>
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28 <when value="Yes">
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29 <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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30 </when>
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31 <when value="No">
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32 </when>
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33 </conditional>
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34 </when>
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35 <when value="No">
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36 </when>
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37 </conditional>
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38 <param name="display_option" type="select" label="Select display option">
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39 <option value="Color and Number">Color and Number</option>
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40 <option value="Color only">Color only</option>
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41 </param>
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42 <conditional name="con_save_coded_img">
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43 <param name="save_coded_img" type="select" label="Save color-coded image?">
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44 <option value="Yes">Yes</option>
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45 <option value="No">No</option>
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46 </param>
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47 <when value="Yes">
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48 <param name="name_output_img" type="text" label="Name the output image"/>
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49 </when>
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50 <when value="No">
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51 </when>
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52 </conditional>
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53 </xml>
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54
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55 <xml name="overlap_distance">
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56 <param name="max_distance" type="integer" value="50" label="Maximum pixel distance to consider matches">
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57 <help>
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58 <![CDATA[
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59 Objects in the subsequent frame will be considered potential matches if they are within this distance.
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60 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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61 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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62 ]]>
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63 </help>
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64 </param>
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65 </xml>
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66
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67 <xml name="lap">
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68 <param name="movement_method" type="select" label="Select the movement model">
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69 <option value="Random">Random</option>
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70 <option value="Velocity">Velocity</option>
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71 <option value="Both">Both</option>
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72 </param>
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73 <param name="no_std_radius" type="float" value="3.0" label="Number of standard deviations for search radius" />
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74 <param name="min_radius" type="float" value="2.0" label="Minimum search radius in pixel units" />
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75 <param name="max_radius" type="float" value="10.0" label="Maximum search radius in pixel units" />
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76
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77 <conditional name="con_second_lap">
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78 <param name="second_lap" type="select" label="Run the second phase of the LAP algorithm?">
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79 <option value="Yes">Yes</option>
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80 <option value="No">No</option>
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81 </param>
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82 <when value="Yes">
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83 <param name="gap_closing" type="integer" value="50" label="Gap closing cost" />
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84 <param name="split_alt" type="integer" value="50" label="Split alternative cost" />
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85 <param name="merge_alt" type="integer" value="50" label="Merge alternative cost" />
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86 <param name="mitosis_alt" type="integer" value="50" label="Mitosis alternative cost" />
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87 <param name="max_gap_displacement" type="integer" value="50" label="Maximum gap displacement, in pixel units" />
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88 <param name="max_split" type="integer" value="50" label="Maximum split score" />
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89 <param name="max_merge" type="integer" value="50" label="Maximum merge score" />
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90 <param name="max_temporal" type="integer" value="50" label="Maximum temporal gap, in frames" />
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91 <param name="max_mitosis_distance" type="integer" value="50" label="Maximum mitosis distance, in pixel units" />
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92 </when>
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93 <when value="No">
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94 </when>
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95 </conditional>
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96 </xml>
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97
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98 <xml name="measurements">
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99 <conditional name="con_measurement_category">
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100 <param name="measurement_category" type="select" label="Select object measurement category to use for tracking">
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101 <option value="AreaShape">AreaShape</option>
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102 <option value="Intensity">Intensity</option>
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103 <option value="Location">Location</option>
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104 <option value="Number">Number</option>
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105 </param>
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106 <when value="AreaShape">
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107 <param name="measurement" type="select" label="Select object measurement to use for tracking">
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108 <option value="Area">Area</option>
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109 <option value="Center_X">Center_X</option>
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110 <option value="Center_Y">Center_Y</option>
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111 <option value="Center_Z">Center_Z</option>
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112 <option value="Compactness">Compactness</option>
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113 <option value="Eccentricity">Eccentricity</option>
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114 <option value="EulerNumber">EulerNumber</option>
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115 <option value="Extent">Extent</option>
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116 <option value="FormFactor">FormFactor</option>
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117 <option value="MajorAxisLength">MajorAxisLength</option>
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118 <option value="MaxFeretDiameter">MaxFeretDiameter</option>
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119 <option value="MaximumRadius">MaximumRadius</option>
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120 <option value="MeanRadius">MeanRadius</option>
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121 <option value="MedianRadius">MedianRadius</option>
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122 <option value="MinFeretDiameter">MinFeretDiameter</option>
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123 <option value="MinorAxisLength">MinorAxisLength</option>
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124 <option value="Orientation">Orientation</option>
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125 <option value="Perimeter">Perimeter</option>
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126 <option value="Solidity">Solidity</option>
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127 </param>
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128 </when>
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129 <when value="Intensity">
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130 <param name="measurement" type="select" label="Select object measurement to use for tracking">
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131 <option value="IntegratedIntensity">IntegratedIntensity</option>
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132 <option value="IntegratedIntensityEdge">IntegratedIntensityEdge</option>
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133 <option value="LowerQuartileIntensity">LowerQuartileIntensity</option>
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134 <option value="MADIntensity">MADIntensity</option>
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135 <option value="MassDisplacement">MassDisplacement</option>
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136 <option value="MaxIntensity">MaxIntensity</option>
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137 <option value="MaxIntensityEdge">MaxIntensityEdge</option>
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138 <option value="MeanIntensity">MeanIntensity</option>
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139 <option value="MeanIntensityEdge">MeanIntensityEdge</option>
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140 <option value="MedianIntensity">MedianIntensity</option>
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141 <option value="MinIntensity">MinIntensity</option>
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142 <option value="MinIntensityEdge">MinIntensityEdge</option>
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143 <option value="StdIntensity">StdIntensity</option>
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144 <option value="StdIntensityEdge">StdIntensityEdge</option>
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145 <option value="UpperQuartileIntensity">UpperQuartileIntensity</option>
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146 </param>
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147 <param name="img_measure" type="text" label="Image"/>
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148 </when>
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149 <when value="Location">
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150 <param name="measurement" type="select" label="Select object measurement to use for tracking">
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151 <option value="CenterMassIntensity_X">CenterMassIntensity_X</option>
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152 <option value="CenterMassIntensity_Y">CenterMassIntensity_Y</option>
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153 <option value="CenterMassIntensity_Z">CenterMassIntensity_Z</option>
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154 <option value="Center_X">Center_X</option>
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155 <option value="Center_Y">Center_Y</option>
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156 <option value="Center_Z">Center_Z</option>
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157 <option value="MaxIntensity_X">MaxIntensity_X</option>
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158 <option value="MaxIntensity_Y">MaxIntensity_Y</option>
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159 <option value="MaxIntensity_Z">MaxIntensity_Z</option>
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160 </param>
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161 <param name="img_measure" type="text" label="Image"/>
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162 </when>
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163 <when value="Number">
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164 <param name="measurement" type="select" label="Select object measurement to use for tracking">
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165 <option value="ObjectNumber">ObjectNumber</option>
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166 </param>
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167 </when>
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168 </conditional>
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169 <param name="max_distance" type="integer" value="50" label="Maximum pixel distance to consider matches" >
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170 <help>
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171 <![CDATA[
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172 Objects in the subsequent frame will be considered potential matches if they are within this distance.
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173 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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174 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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175 ]]>
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176 </help>
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177 </param>
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178 </xml>
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179
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180 <xml name="follow_neighbors">
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181 <param name="max_distance" type="integer" value="50" label="Maximum pixel distance to consider matches">
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182 <help>
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183 <![CDATA[
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184 Objects in the subsequent frame will be considered potential matches if they are within this distance.
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185 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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186 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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187 ]]>
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188 </help>
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189 </param>
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190 <param name="avg_diameter" type="float" value="35.0" label="Average cell diameter in pixels">
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191 <help>
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192 <![CDATA[
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193 The average cell diameter is used to scale many Follow Neighbors algorithm parameters.
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194 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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195 ]]>
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196 </help>
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197 </param>
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198
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199 <conditional name="con_adv_parameter">
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200 <param name="adv_parameter" type="select" label="Use advanced configuration parameters">
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201 <option value="Yes">Yes</option>
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202 <option value="No">No</option>
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203 </param>
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204 <when value="Yes">
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205 <param name="cost" type="float" value="15.0" label="Cost of cell to empty matching" />
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206 <param name="weight" type="float" value="25.0" label="Weight of area difference in function matching cost" />
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207 </when>
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208 <when value="No">
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209 </when>
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210 </conditional>
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211
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212 </xml>
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213 </macros>
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214 <expand macro="py_requirements"/>
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215 <command detect_errors="exit_code">
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216 <![CDATA[
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217 python '$__tool_directory__/track_objects.py' -p '$input_pipeline' -i '$input_json'
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218 ]]>
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219 </command>
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220 <configfiles>
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221 <inputs name="input_json"/>
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222 </configfiles>
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223 <inputs>
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224 <expand macro="input_pipeline_param"/>
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225 <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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226 <conditional name="con_tracking_method">
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227 <param name="tracking_method" type="select" label="Choose a tracking method">
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228 <help>
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229 <![CDATA[
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230 <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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231 <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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232 <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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233 <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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234 <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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235 ]]>
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236 </help>
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237 <option value="Overlap">Overlap</option>
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238 <option value="Distance">Distance</option>
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239 <option value="Measurements">Measurements</option>
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240 <option value="LAP">LAP</option>
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241 <option value="Follow Neighbors">Follow Neighbors</option>
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242 </param>
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243 <when value="Overlap">
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244 <expand macro="overlap_distance" />
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245 <expand macro="common" />
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246 </when>
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247 <when value="Distance">
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248 <expand macro="overlap_distance" />
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249 <expand macro="common" />
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250 </when>
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251 <when value="Measurements">
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252 <expand macro="measurements" />
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253 <expand macro="common" />
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254 </when>
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255 <when value="LAP">
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256 <expand macro="lap" />
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257 <expand macro="common" />
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258 </when>
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259 <when value="Follow Neighbors">
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260 <expand macro="follow_neighbors" />
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261 <expand macro="common" />
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262 </when>
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263 </conditional>
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264 </inputs>
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265 <outputs>
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266 <expand macro="output_pipeline_param" />
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267 </outputs>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
268 <tests>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
269 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
270 <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
271 <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
272 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
273 <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
274 <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
275 <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
276 <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
277 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
278 <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
279 <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
280 <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
281 <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
282 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
283 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
284 <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
285 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
286 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
287 <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
288 <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
289 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
290 <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
291 <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
292 <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
293 <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
294 <conditional name="con_use_min">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
295 <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
296 <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
297 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
298 <conditional name="con_use_max">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
299 <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
300 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
301 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
302 <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
303 <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
304 <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
305 <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
306 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
307 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
308 <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
309 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
310 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
311 <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
312 <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
313 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
314 <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
315 <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
316 <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
317 <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
318 <conditional name="con_use_min">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
319 <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
320 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
321 <conditional name="con_use_max">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
322 <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
323 <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
324 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
325 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
326 <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
327 <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
328 <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
329 <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
330 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
331 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
332 <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
333 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
334 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
335 <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
336 <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
337 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
338 <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
339 <conditional name="con_measurement_category">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
340 <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
341 <param name="measurement" value = "MADIntensity"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
342 <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
343 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
344 <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
345 <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
346 <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
347 <conditional name="con_use_min">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
348 <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
349 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
350 <conditional name="con_use_max">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
351 <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
352 <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
353 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
354 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
355 <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
356 <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
357 <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
358 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
359 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
360 <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
361 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
362 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
363 <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
364 <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
365 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
366 <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
367 <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
368 <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
369 <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
370 <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
371 <conditional name="con_second_lap">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
372 <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
373 <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
374 <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
375 <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
376 <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
377 <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
378 <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
379 <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
380 <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
381 <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
382 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
383 <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
384 <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
385 <conditional name="con_use_min">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
386 <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
387 <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
388 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
389 <conditional name="con_use_max">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
390 <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
391 <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
392 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
393 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
394 <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
395 <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
396 <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
397 <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
398 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
399 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
400 <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
401 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
402 <test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
403 <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
404 <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
405 <conditional name="con_tracking_method">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
406 <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
407 <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
408 <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
409 <conditional name="con_adv_parameter">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
410 <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
411 <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
412 <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
413 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
414 <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
415 <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
416 <conditional name="con_use_min">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
417 <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
418 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
419 <conditional name="con_use_max">
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
420 <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
421 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
422 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
423 <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
424 <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
425 <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
426 <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
427 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
428 </conditional>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
429 <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
430 </test>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
431 </tests>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
432
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
433 <help>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
434 <![CDATA[
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
435
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
436 .. class:: infomark
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
437
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
438 **What it does**
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
439
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
440 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
441
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
442 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"
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 @COMMON_HELP@
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 </help>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
447 <expand macro="citations"/>
644e5e32a83c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
448 </tool>