Mercurial > repos > bgruening > cp_overlay_outlines

annotate overlay_outlines.xml @ 1:91560258e972 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 14:15:35 +0000
parents 39006f6fd6bf
children b44b081bcf37
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1 <tool id="cp_overlay_outlines" name="OverlayOutlines" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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2 <description> places outlines of objects over a desired image. </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>
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6 <xml name="non_blank">
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7 <param name="image_to_outline" type="text" label="Enter the name of image on which to display outlines" >
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8 <help>
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9 <![CDATA[
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10 Choose the image to serve as the background for the outlines. You can choose from images that were loaded or created by modules previous to this one.
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11 ]]>
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12 </help>
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13 </param>
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14 <conditional name="con_display_mode">
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15 <param name="display_mode" type="select" label="Outline display mode">
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16 <help>
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17 <![CDATA[
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18 Specify how to display the outline contours around your objects.
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19 <i>Color:</i> outlines produce a clearer display for images where the cell borders have a high intensity, but take up more space in memory.
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20 <i>Grayscale:</i> outlines are displayed with either the highest possible intensity or the same intensity as the brightest pixel in the image.
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21 ]]>
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22 </help>
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23 <option value="Color">Color</option>
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24 <option value="Grayscale">Grayscale</option>
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25 </param>
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26 <when value="Color">
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27 <repeat name="rpt_obj_to_display" title="Outline" min="1">
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28 <param name="obj_to_display" type="text" label="Enter the name of the objects to display" help="Choose the objects whose outlines you would like to display. "/>
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29
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30 <param name="outline_color" type="color" label="Select outline color"/>
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31 </repeat>
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32 </when>
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33 <when value="Grayscale">
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34 <param name="method_brightness" type="select" label="Select method to determine brightness of outlines" help="If your image is quite dim, then putting bright white lines onto it may not be useful. It may be preferable to make the outlines equal to the maximal brightness already occurring in the image. ">
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35 <option value="Max of image">Max of image</option>
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36 <option value="Max possible">Max possible</option>
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37 </param>
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38 <repeat name="rpt_obj_to_display" title="Outline" min="1">
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39 <param name="obj_to_display" type="text" label="Enter the name of the objects to display" help="Choose the objects whose outlines you would like to display. "/>
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40 </repeat>
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41 </when>
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42 </conditional>
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43 </xml>
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44
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45 <xml name="common">
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46 <param name="name_output_image" type="text" label="Name the output image" />
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47 <param name="howto_outline" type="select" label="How to outline">
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48 <help>
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49 <![CDATA[
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50 Specify how to mark the boundaries around an object:
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51 <i>Inner:</i> outline the pixels just inside of objects, leaving background pixels untouched.
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52 <i>Outer:</i> outline pixels in the background around object boundaries. When two objects touch, their boundary is also marked.
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53 <i>Thick:</i> any pixel not completely surrounded by pixels of the same label is marked as a boundary. This results in boundaries that are 2 pixels thick.
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54 ]]>
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55 </help>
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56 <option value="Inner">Inner</option>
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57 <option value="Outer">Outer</option>
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58 <option value="Thick">Thick</option>
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59 </param>
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60 </xml>
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61
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62 </macros>
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63 <expand macro="py_requirements"/>
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64 <command detect_errors="exit_code">
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65 <![CDATA[
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66 python '$__tool_directory__/overlay_outlines.py' -p '$input_pipeline' -i '$input_json'
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67 ]]>
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68 </command>
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69 <configfiles>
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70 <inputs name="input_json"/>
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71 </configfiles>
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72 <inputs>
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73 <expand macro="input_pipeline_param"/>
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74 <conditional name="con_blank_img">
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75 <param name="blank_img" type="select" label="Display outlines on a blank image?">
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76 <option value="Yes">Yes</option>
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77 <option value="No">No</option>
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78 </param>
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79 <when value="Yes">
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80 <conditional name="con_display_mode">
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81 <param name="display_mode" type="select" label="Outline display mode">
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82 <help>
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83 <![CDATA[
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84 Specify how to display the outline contours around your objects.
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85 <i>Color:</i> outlines produce a clearer display for images where the cell borders have a high intensity, but take up more space in memory.
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86 <i>Grayscale:</i> outlines are displayed with either the highest possible intensity or the same intensity as the brightest pixel in the image.
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87 ]]>
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88 </help>
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89 <option value="Color">Color</option>
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90 <option value="Grayscale">Grayscale</option>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
91 </param>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
92 <when value="Color">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
93 <repeat name="rpt_obj_to_display" title="Outline" min="1">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
94 <param name="obj_to_display" type="text" label="Enter the name of the objects to display" help="Choose the objects whose outlines you would like to display. "/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
95 <param name="outline_color" type="color" label="Select outline color"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
96 </repeat>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
97 </when>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
98 <when value="Grayscale">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
99 <repeat name="rpt_obj_to_display" title="Outline" min="1">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
100 <param name="obj_to_display" type="text" label="Enter the name of the objects to display" help="Choose the objects whose outlines you would like to display. "/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
101 </repeat>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
102 </when>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
103 </conditional>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
104 </when>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
105 <when value="No">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
106 <expand macro= "non_blank" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
107 </when>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
108 </conditional>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
109 <expand macro ="common" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
110 </inputs>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
111 <outputs>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
112 <expand macro="output_pipeline_param" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
113 </outputs>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
114 <tests>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
115 <test>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
116 <param name="input_pipeline" value="common.cppipe"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
117 <conditional name="con_blank_img">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
118 <param name="blank_img" value="No"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
119 <param name="image_to_outline" value="OrigGray" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
120 <conditional name="con_display_mode">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
121 <param name="display_mode" value="Color"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
122 <repeat name="rpt_obj_to_display">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
123 <param name="obj_to_display" value = "Embryos" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
124 <param name="outline_color" value="#FF0000"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
125 </repeat>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
126 </conditional>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
127 </conditional>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
128 <param name="name_output_image" value="OutlineImage" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
129 <param name="howto_outline" value="Inner"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
130 <expand macro="test_out_file" file="overlay_outlines_non_blank_color.cppipe" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
131 </test>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
132 <test>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
133 <param name="input_pipeline" value="common.cppipe"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
134 <conditional name="con_blank_img">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
135 <param name="blank_img" value="Yes"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
136 <conditional name="con_display_mode">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
137 <param name="display_mode" value = "Grayscale"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
138 <repeat name="rpt_obj_to_display">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
139 <param name="obj_to_display" value = "DNA"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
140 </repeat>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
141 <repeat name="rpt_obj_to_display">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
142 <param name="obj_to_display" value = "DNA1"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
143 </repeat>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
144 </conditional>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
145 </conditional>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
146 <param name="name_output_image" value="OutputImage" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
147 <param name="howto_outline" value="Outer"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
148 <expand macro="test_out_file" file="overlay_outlines_blank_grayscale.cppipe" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
149 </test>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
150 <test>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
151 <param name="input_pipeline" value="common.cppipe"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
152 <conditional name="con_blank_img">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
153 <param name="blank_img" value="Yes"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
154 <conditional name="con_display_mode">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
155 <param name="display_mode" value = "Color"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
156 <repeat name="rpt_obj_to_display">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
157 <param name="obj_to_display" value = "DNA1"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
158 <param name="outline_color" value = "#548dd4"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
159 </repeat>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
160 <repeat name="rpt_obj_to_display">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
161 <param name="obj_to_display" value = "DNA3"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
162 <param name="outline_color" value = "#000000"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
163 </repeat>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
164 </conditional>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
165 </conditional>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
166 <param name="name_output_image" value="OutputImage" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
167 <param name="howto_outline" value="Inner"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
168 <expand macro="test_out_file" file="overlay_outlines_blank_color.cppipe" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
169 </test>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
170 <test>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
171 <param name="input_pipeline" value="common.cppipe"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
172 <conditional name="con_blank_img">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
173 <param name="blank_img" value="No"/>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
174 <param name="image_to_outline" value = "DNA1" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
175 <conditional name="con_display_mode">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
176 <param name="display_mode" value = "Grayscale" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
177
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
178 <param name="method_brightness" value = "Max possible" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
179 <repeat name="rpt_obj_to_display">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
180 <param name="obj_to_display" value = "Object1" />
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
181 </repeat>
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
182 <repeat name="rpt_obj_to_display">
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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183 <param name="obj_to_display" value = "Object2" />
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184 </repeat>
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185 </conditional>
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186 </conditional>
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187 <param name="name_output_image" value="OutputImage" />
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188 <param name="howto_outline" value="Thick"/>
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189 <expand macro="test_out_file" file="overlay_outlines_non_blank_grayscale.cppipe" />
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190 </test>
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191 </tests>
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192 <help>
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193 <![CDATA[
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194
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195 .. class:: infomark
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196
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197 **What it does**
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198
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199 This module places outlines of objects on any desired image (grayscale, color, or blank). The resulting image can be saved using the SaveImages module.
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200
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201 @COMMON_HELP@
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202 ]]>
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203 </help>
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204 <expand macro="citations"/>
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205 </tool>