annotate starting_modules_nameandtypes.xml @ 5:d0178bdcd00e draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 14:12:26 +0000
parents 72a7f23f3a79
children
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1 <macros>
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2 <xml name="macro_image_type" token_thing="images">
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3 <param name="name_to_assign" type="text" value="DNA" label="Name to assign these @THING@" />
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4 </xml>
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6 <xml name="image_type_condition">
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7 <conditional name="con_set_intensity">
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8 <param name="set_intensity_range_from" type="select" label="Set intensity range from" help="This option determines how the image intensity should be rescaled from 0.0 - 1.0.">
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9 <option value="Image metadata">Image metadata</option>
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10 <option value="Image bit-depth">Image bit-depth</option>
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11 <option value="Manual">Manual</option>
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12 </param>
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13 <when value="Manual">
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14 <param name="maximum_intensity" type="float" value="255.0" label="Maximum intensity" help="The pixel value is divided, as read from the image file, by this value to get the loaded image’s per-pixel intensity." />
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15
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16 </when>
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17 <when value="Image metadata" />
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18 <when value="Image bit-depth" />
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19 </conditional>
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20 </xml>
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21 <xml name="name_type_rule_matching_file">
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22 <param name="operator" type="select">
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23 <option value="does">Does</option>
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24 <option value="doesnot">Does not</option>
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25 </param>
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26 <param name="contain" type="select">
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27 <option value="contain">Contain</option>
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28 <option value="containregexp">Contain regular expression</option>
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29 <option value="startwith">Start with</option>
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30 <option value="endwith">End with</option>
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31 <option value="Exactly match">Exactly match</option>
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32 </param>
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33 <param name="match_value" type="text"/>
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34 </xml>
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35 <xml name="name_type_rule_image">
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36 <param name="operator" type="select">
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37 <option value="does">Is</option>
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38 <option value="doesnot">Is not</option>
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39 </param>
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40 <param name="match_type" type="select">
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41 <option value="iscolor">Color</option>
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42 <option value="ismonochrome">Monochrome</option>
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43 <option value="isstack">Stack</option>
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44 <option value="isstackframe">Stack frame</option>
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45 </param>
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46 </xml>
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47 <xml name="name_type_rule_metadata">
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48 <param name="operator" type="select">
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49 <option value="does">Does</option>
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50 <option value="doesnot">Does not</option>
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51 </param>
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52 <param name="match_type" type="select">
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53 <option value="FileLocation">Have FileLocation matching</option>
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54 <option value="Frame">Have Frame matching</option>
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55 <option value="Screen">Have Screen matching</option>
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56 <option value="Series">Have Series matching</option>
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57 </param>
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58 <param name="match_value" type="text"/>
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59 </xml>
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60 <xml name="name_type_rule_ext">
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61 <param name="operator" type="select">
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62 <option value="does">Is</option>
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63 <option value="doesnot">Is not</option>
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64 </param>
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65 <param name="match_type" type="select">
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66 <option value="istif">tif, tiff, ome.tif or ome.tiff</option>
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67 <option value="isjpeg">jpg, jpeg</option>
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68 <option value="ispng">png</option>
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69 <option value="isimage">the extension of an image file</option>
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70 <option value="isflex">flex</option>
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71 <option value="ismovie">mov, avi</option>
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72
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73 </param>
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74 </xml>
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75 <xml name="image_matching_rules">
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76 <repeat name="r_match_rule" title="Another image">
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77 <param name="match_all_any" type="select" display="radio" label="Match the following rules">
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78 <option value="and">All</option>
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79 <option value="or">Any</option>
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80 </param>
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81 <repeat name="r_match" title="rule">
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82 <conditional name="con_match">
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83 <param name="rule_type" type="select" label="Select rule criteria">
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84 <option value="file">File</option>
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85 <option value="directory">Directory</option>
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86 <option value="extension">Extension</option>
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87 <option value="image">Image</option>
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88 <option value="metadata">Metadata</option>
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89 </param>
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90 <when value="file">
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91 <expand macro="name_type_rule_matching_file"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
92 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
93 <when value="directory">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
94 <expand macro="name_type_rule_matching_file"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
95 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
96 <when value="extension">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
97 <expand macro="name_type_rule_ext" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
98 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
99 <when value="image">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
100 <expand macro="name_type_rule_image" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
101 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
102 <when value="metadata">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
103 <expand macro="name_type_rule_metadata" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
104 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
105 </conditional>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
106 </repeat>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
107 <conditional name="con_select_image_type">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
108 <param name="select_image_type" type="select" label="Select the image type" help="You can specify how these images should be treated">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
109 <option value="Grayscale image">Grayscale image</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
110 <option value="Color image">Color image</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
111 <option value="Binary mask">Binary mask</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
112 <option value="Illumination function">Illumination function</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
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113 <option value="Objects">Objects</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
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114
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
diff changeset
115 </param>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
diff changeset
116 <when value ="Grayscale image">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
117 <expand macro="macro_image_type" thing="images"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
118 <expand macro="image_type_condition" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
119 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
120 <when value="Color image">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
121 <expand macro="macro_image_type" thing="images"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
122 <expand macro="image_type_condition" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
123 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
124 <when value="Binary mask">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
125 <expand macro="macro_image_type" thing="images"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
126 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
127 <when value="Illumination function">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
128 <expand macro="macro_image_type" thing="images"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
129 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
130 <when value="Objects">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
131 <expand macro="macro_image_type" thing="objects"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
diff changeset
132 </when>
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bgruening
parents:
diff changeset
133 </conditional>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
134 </repeat>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
135 </xml>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
136 <xml name="starting_modules_nameandtypes">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
137 <section name="nameandtypes" title="NamesAndTypes" expanded="false">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
138 <conditional name="pixel_space">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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139 <param name="process_3d" type="select" label="Process 3D" help="If you want to treat the data as three-dimensional, select 'Yes' to load files as volumes. Otherwise, select 'No' to load files as separate, two-dimensional images.">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
140 <option value="Yes">Yes, process 3D data</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
141 <option value="No">No, do not process 3D data</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
diff changeset
142 </param>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
143 <when value="Yes">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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144 <param name="x_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the X dimension, relative to Y and Z" help="Normally, you will set one of these values to 1 and the others relative to that." />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
145 <param name="y_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Y dimension, relative to X and Z"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
146 <param name="z_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Z dimension, relative to X and Y"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
147 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
148 <when value="No"/>
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bgruening
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diff changeset
149 </conditional>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
150 <conditional name="con_assign_a_name_to">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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diff changeset
151 <param name="assign_a_name_to" type="select" label="Assign a name to" help="This setting allows you to specify a name for types of images or subsets of images so they can be treated separately by downstream tools.">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
152 <option value="All images">Give every image the same name</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
153 <option value="Images matching rules">Give images one of several names depending on the metadata</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
154 </param>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
155 <when value="All images">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
156 <expand macro="macro_image_type" thing="images" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
157 <conditional name="con_select_image_type">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
158 <param name="select_image_type" type="select" label="Select the image type">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
159 <option value="Grayscale image">Grayscale image</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
diff changeset
160 <option value="Color image">Color image</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
161 <option value="Binary mask">Binary mask</option>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
diff changeset
162 </param>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
diff changeset
163 <when value ="Grayscale image">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
164 <expand macro="image_type_condition" />
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parents:
diff changeset
165 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
diff changeset
166 <when value="Color image">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
167 <expand macro="image_type_condition" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
168 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
diff changeset
169 <when value="Binary mask" />
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parents:
diff changeset
170 </conditional>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
171 </when>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
172 <when value="Images matching rules">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
diff changeset
173 <expand macro="image_matching_rules"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
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174 <param name="matching_method" type="select" label="Image set matching method">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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parents:
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175 <option value="Order">Order</option>
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176 <option value="Metadata">Metadata</option>
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parents:
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177 </param>
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parents:
diff changeset
178 </when>
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parents:
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179 </conditional>
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180 </section>
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181 </xml>
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182 </macros>