Mercurial > repos > bgruening > cp_image_math

annotate image_math.xml @ 3:6100a22bf4f2 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 14:06:51 +0000
parents 6d3851ac885f
children ff1a86a87364
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3
6100a22bf4f2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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1 <tool id="cp_image_math" name="ImageMath" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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2 <description>perform simple mathematical operations on images</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@">0</token>
0
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6 <xml name="image_without_multiplier" token_order="first">
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7 <conditional name="image_or_measurement_@ORDER@">
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8 <param name="image_or_measurement_@ORDER@" type="select" label="Image or measurement?" help="You can perform math operations or you can use a measurement for one of the operands.">
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9 <option value="Image">Image</option>
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10 <option value="Measurement">Measurement</option>
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11 </param>
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12 <when value="Image">
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13 <param name="select_the_@ORDER@_image" type="text" label="Enter the name of the @ORDER@ image">
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14 <expand macro="text_validator"/>
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15 </param>
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16 </when>
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17 <when value="Measurement">
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18 <conditional name="category_@ORDER@">
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19 <param name="category_@ORDER@" type="select" label="Category" help="Select a measurement made on the @ORDER@ image. The value of the measurement is used for the operand for all of the pixels of the other operand's image.">
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20 <option value="FileName">FileName</option>
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21 <option value="Frame">Frame</option>
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22 <option value="Height">Height</option>
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23 <option value="MD5digest">MD5Digest</option>
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24 <option value="PathName">PathName</option>
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25 <option value="Scaling">Scaling</option>
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26 <option value="Series">Series</option>
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27 <option value="URL">URL</option>
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28 <option value="Width">Width</option>
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29 </param>
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30 <when value="FileName">
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31 <param name="measurement_@ORDER@" type="text" label="Measurement">
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32 <expand macro="text_validator"/>
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33 </param>
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34 </when>
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35 <when value="Frame">
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36 <param name="measurement_@ORDER@" type="text" label="Measurement">
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37 <expand macro="text_validator"/>
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38 </param>
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39 </when>
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40 <when value="Height">
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41 <param name="measurement_@ORDER@" type="text" label="Measurement">
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42 <expand macro="text_validator"/>
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43 </param>
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44 </when>
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45 <when value="MD5digest">
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46 <param name="measurement_@ORDER@" type="text" label="Measurement">
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47 <expand macro="text_validator"/>
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48 </param>
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49 </when>
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50 <when value="PathName">
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51 <param name="measurement_@ORDER@" type="text" label="Measurement">
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52 <expand macro="text_validator"/>
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53 </param>
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54 </when>
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55 <when value="Scaling">
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56 <param name="measurement_@ORDER@" type="text" label="Measurement">
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57 <expand macro="text_validator"/>
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58 </param>
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59 </when>
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60 <when value="Series">
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61 <param name="measurement_@ORDER@" type="text" label="Measurement">
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62 <expand macro="text_validator"/>
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63 </param>
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64 </when>
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65 <when value="URL">
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66 <param name="measurement_@ORDER@" type="text" label="Measurement">
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67 <expand macro="text_validator"/>
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68 </param>
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69 </when>
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70 <when value="Width">
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71 <param name="measurement_@ORDER@" type="text" label="Measurement">
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72 <expand macro="text_validator"/>
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73 </param>
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74 </when>
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75 </conditional>
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76 </when>
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77 </conditional>
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78 </xml>
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79
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80
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81 <xml name="section_image_with_multiplier" token_title="First Image" token_order="first">
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82 <section name="@ORDER@_image" title="@TITLE@" expanded="true">
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83 <expand macro="image_without_multiplier" order="@ORDER@"/>
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84 <param name="multiply_the_@ORDER@_image_by" type="float" value="1.0" label="Enter the number that you would like to multiply the @ORDER@ image by"/>
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85 </section>
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86 </xml>
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87
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88
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89 <xml name="section_image_without_multiplier" token_title="First Image" token_order="first">
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90 <section name="@ORDER@_image" title="@TITLE@" expanded="true">
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91 <expand macro="image_without_multiplier" order="@ORDER@"/>
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92 </section>
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93 </xml>
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94
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95
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96 <xml name="section_ops_result">
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97 <section name="op_results" title="OPERATIONS ON THE RESULTS" expanded="false">
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98 <param name="raise_the_power_of_the_result_by" type="float" value="1.0" label="Enter an exponent to raise the result to after the chosen operation"/>
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99 <param name="multiply_the_result_by" type="float" value="1.0" label="Enter the number that you would like to multiply the above image by"/>
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100 <param name="add_to_result" type="float" value="0.0" label="Enter a number to add to the result after the chosen operation"/>
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101 <param name="set_values_less_than_0_equal_to_0" type="select" display="radio" label="Set the values less than 0 equal to 0?" help="Values outside the range 0 to 1 might not be handled well by other CellProfiler tools.">
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102 <option value="Yes">Yes</option>
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103 <option value="No">No</option>
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104 </param>
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105 <param name="set_values_greater_than_1_equal_to_1" type="select" display="radio" label="Set the values greater than 1 equal to 1?" help="Values outside the range 0 to 1 might not be handled well by other CellProfiler tools.">
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106 <option value="Yes">Yes</option>
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107 <option value="No">No</option>
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108 </param>
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109 </section>
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110 </xml>
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111 </macros>
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112 <expand macro="py_requirements"/>
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113 <command detect_errors="exit_code">
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114 <![CDATA[
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115 python '$__tool_directory__/image_math.py' -p '$input_pipeline' -i '$input_json'
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116 ]]>
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117 </command>
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118 <configfiles>
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119 <inputs name="input_json"/>
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120 </configfiles>
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121 <inputs>
1
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122 <expand macro="input_pipeline_param"/>
0
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123 <param name="name_output_image" type="text" label="Enter a name for the resulting image">
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124 <expand macro="text_validator"/>
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125 </param>
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126 <conditional name="operation">
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127 <param name="operation" type="select" label="Operation" help="You can select operations for single images (Invert, Log transform base 2, Log transform legacy) or between pairs of images (Add, Subtract, Absolute Difference, Multiply, Divide, Average, Minimum, Maximum). Some operations produce binary images (And, Or, Not, Equals).">
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128 <option value="add">Add</option>
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129 <option value="subtract">Subtract</option>
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130 <option value="multiply">Multiply</option>
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131 <option value="divide">Divide</option>
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132 <option value="average">Average</option>
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133 <option value="minimum">Minimum</option>
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134 <option value="maximum">Maximum</option>
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135 <option value="invert">Invert</option>
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136 <option value="log_2">Log transform (base 2)</option>
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137 <option value="log_legacy">Log transform (legacy)</option>
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138 <option value="and">And</option>
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139 <option value="or">Or</option>
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140 <option value="not">Not</option>
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141 <option value="equals">Equals</option>
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142 </param>
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143 <when value="add">
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144 <expand macro="section_image_with_multiplier" title="First Image" order="first"/>
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145 <expand macro="section_image_with_multiplier" title="Second Image" order="second"/>
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146 <expand macro="section_ops_result"/>
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147 </when>
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148 <when value="subtract">
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149 <expand macro="section_image_with_multiplier" title="First Image" order="first"/>
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150 <expand macro="section_image_with_multiplier" title="Second Image" order="second"/>
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151 <expand macro="section_ops_result"/>
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152 </when>
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153 <when value="multiply">
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154 <expand macro="section_image_with_multiplier" title="First Image" order="first"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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155 <expand macro="section_image_with_multiplier" title="Second Image" order="second"/>
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156 <expand macro="section_ops_result"/>
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157 </when>
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158 <when value="divide">
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159 <expand macro="section_image_with_multiplier" title="First Image" order="first"/>
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160 <expand macro="section_image_with_multiplier" title="Second Image" order="second"/>
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161 <expand macro="section_ops_result"/>
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162 </when>
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163 <when value="average">
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164 <expand macro="section_image_with_multiplier" title="First Image" order="first"/>
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165 <expand macro="section_image_with_multiplier" title="Second Image" order="second"/>
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166 <expand macro="section_ops_result"/>
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167 </when>
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168 <when value="minimum">
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169 <expand macro="section_image_with_multiplier" title="First Image" order="first"/>
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170 <expand macro="section_image_with_multiplier" title="Second Image" order="second"/>
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171 <expand macro="section_ops_result"/>
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172 </when>
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173 <when value="maximum">
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174 <expand macro="section_image_with_multiplier" title="First Image" order="first"/>
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175 <expand macro="section_image_with_multiplier" title="Second Image" order="second"/>
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176 <expand macro="section_ops_result"/>
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177 </when>
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178 <when value="invert">
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179 <param name="select_the_image" type="text" label="Select the image">
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180 <expand macro="text_validator"/>
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181 </param>
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182 <param name="multiply_the_image_by" type="float" value="1.0" label="Enter the number that you would like to multiply the above image by"/>
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183 <expand macro="section_ops_result"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
184 </when>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
185 <when value="log_2">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
186 <param name="select_the_image" type="text" label="Select the image">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
187 <expand macro="text_validator"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
188 </param>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
189 <param name="multiply_the_image_by" type="float" value="1.0" label="Enter the number that you would like to multiply the above image by"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
190 <expand macro="section_ops_result"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
191 </when>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
192 <when value="log_legacy">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
193 <param name="select_the_image" type="text" label="Select the image">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
194 <expand macro="text_validator"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
195 </param>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
196 <param name="multiply_the_image_by" type="float" value="1.0" label="Enter the number that you would like to multiply the above image by"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
197 <expand macro="section_ops_result"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
198 </when>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
199 <when value="and">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
200 <expand macro="section_image_without_multiplier" title="First Image" order="first"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
201 <expand macro="section_image_without_multiplier" title="Second Image" order="second"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
202 </when>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
203 <when value="or">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
204 <expand macro="section_image_without_multiplier" title="First Image" order="first"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
205 <expand macro="section_image_without_multiplier" title="Second Image" order="second"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
206 </when>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
207 <when value="not">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
208 <section name="first_image" title="Image" expanded="true">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
209 <conditional name="image_or_measurement_first">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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diff changeset
210 <param name="image_or_measurement_first" type="select" label="Image or measurement?">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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diff changeset
211 <option value="Image">Image</option>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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diff changeset
212 </param>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
213 <when value="Image">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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diff changeset
214 <param name="select_the_first_image" type="text" label="Enter the name of the image">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
215 <expand macro="text_validator"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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diff changeset
216 </param>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
217 </when>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
218 </conditional>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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diff changeset
219 </section>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
220 </when>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
221 <when value="equals">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
222 <expand macro="section_image_without_multiplier" title="First Image" order="first"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
223 <expand macro="section_image_without_multiplier" title="Second Image" order="second"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
224 </when>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
225 </conditional>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
226 <param name="ignore_the_image_masks" type="select" display="radio" label="Ignore the image masks?" help="Select Yes to set equal to zero all previously masked pixels and operate on the masked images as if no mask had been applied. Otherwise, the smallest image mask is applied after image math has been completed.">
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
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diff changeset
227 <option value="Yes">Yes</option>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
228 <option value="No">No</option>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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parents:
diff changeset
229 </param>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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diff changeset
230 </inputs>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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diff changeset
231 <outputs>
1
6d3851ac885f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 0
diff changeset
232 <expand macro="output_pipeline_param" />
0
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
233 </outputs>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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diff changeset
234 <tests>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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parents:
diff changeset
235 <test>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
236 <param name="input_pipeline" value="common_image_math.cppipe"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
237 <param name="operation" value="add"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
238 <param name="raise_the_power_of_the_result_by" value="1.0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
239 <param name="multiply_the_result_by" value="1.0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
240 <param name="add_to_result" value="0.0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
241 <param name="set_values_less_than_0_equal_to_0" value="Yes"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
242 <param name="set_values_greater_than_1_equal_to_1" value="Yes"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
243 <param name="ignore_the_image_masks" value="No"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
244 <param name="name_output_image" value="ImageAfterMath"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
245 <param name="image_or_measurement_first" value="Image"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
246 <param name="select_the_first_image" value="DNA"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
247 <param name="multiply_the_first_image_by" value="1.0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
248 <param name="image_or_measurement_second" value="Image"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
249 <param name="select_the_second_image" value="CellImage"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
250 <param name="multiply_the_second_image_by" value="2.0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
251 <output name="output_pipeline" ftype="txt" file="image_math_1.cppipe" lines_diff="0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
252 </test>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
253 <test>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
254 <param name="input_pipeline" value="common_image_math.cppipe"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
255 <param name="operation" value="subtract"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
256 <param name="raise_the_power_of_the_result_by" value="1.0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
257 <param name="multiply_the_result_by" value="1.0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
258 <param name="add_to_result" value="0.0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
259 <param name="set_values_less_than_0_equal_to_0" value="Yes"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
260 <param name="set_values_greater_than_1_equal_to_1" value="No"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
261 <param name="ignore_the_image_masks" value="No"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
262 <param name="name_output_image" value="ImageAfterMath"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
263 <param name="image_or_measurement_first" value="Image"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
264 <param name="select_the_first_image" value="DNA"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
265 <param name="multiply_the_first_image_by" value="1.0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
266 <param name="image_or_measurement_second" value="Measurement"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
267 <param name="multiply_the_second_image_by" value="5.0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
268 <param name="category_second" value="FileName"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
269 <param name="measurement_second" value="DNA"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
270 <output name="output_pipeline" ftype="txt" file="image_math_2.cppipe" lines_diff="0"/>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
271 </test>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
272 <test>
2005f8058036 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
273 <param name="input_pipeline" value="common_image_math.cppipe"/>
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274 <param name="operation" value="not"/>
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275 <param name="name_output_image" value="ImageAfterMath"/>
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276 <param name="select_the_first_image" value="DNA"/>
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277 <param name="ignore_the_image_masks" value="No"/>
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278 <output name="output_pipeline" ftype="txt" file="image_math_3.cppipe" lines_diff="0"/>
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279 </test>
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280 </tests>
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281 <help>
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282 <![CDATA[
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283
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284 .. class:: infomark
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285
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286 **What it does**
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287
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288 This module can perform addition, subtraction, multiplication, division, or averaging of two or more image intensities, as well as inversion, log transform, or scaling by a constant for individual image intensities.
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289
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290 Keep in mind that after the requested operations are carried out, the final image may have a substantially different range of pixel intensities than the original. CellProfiler assumes that the image is scaled from 0 – 1 for object identification and display purposes, so additional rescaling may be needed. Please see the RescaleIntensity module for more scaling options.
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291
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292 @COMMON_HELP@
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293 ]]>
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294 </help>
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295 <expand macro="citations"/>
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296 </tool>