Mercurial > repos > bgruening > cp_measure_image_quality
annotate measure_image_quality.xml @ 5:6f4715b8540a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author | bgruening |
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date | Fri, 26 Feb 2021 14:14:18 +0000 |
parents | 08a2cf887a44 |
children | d3890df07463 |
rev | line source |
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5
6f4715b8540a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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1 <tool id="cp_measure_image_quality" name="MeasureImageQuality" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@"> |
2
4dcd464c22ff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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2 <description>measure features that indicate image quality</description> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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3 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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4 <macros> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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5 <import>macros.xml</import> |
5
6f4715b8540a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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6 <token name="@VERSION_SUFFIX@">0</token> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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7 <xml name="macro_calc_threshold"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
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8 <conditional name="con_use_all_methods"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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9 <param name="use_all_methods" type="select" display="radio" label="Use all thresholding methods?"> |
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08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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10 <help> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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11 <![CDATA[ |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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12 Select 'Yes' to calculate thresholds using all the available methods. Only the global methods are used. While most methods are straightfoward, some methods have additional parameters that require special handling: |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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13 <br> - Otsu: Thresholds for all combinations of class number, minimization parameter and middle class assignment are computed. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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14 <br> - Mixture of Gaussians (MoG): Thresholds for image coverage fractions of 0.05, 0.25, 0.75 and 0.95 are computed. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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15 See the IdentifyPrimaryObjects module for more information on thresholding methods. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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16 ]]> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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17 </help> |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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18 <option value="Yes">Yes</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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19 <option value="No">No</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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20 </param> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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21 <when value="Yes" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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22 <when value="No"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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23 <repeat name="rpt_threshold_method" title="new threshold method" min="1"> |
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26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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24 <conditional name="con_threshold_methods"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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25 <param name="select_threshold_method" type="select" label="Select a thresholding method"> |
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08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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26 <help> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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27 This setting allows you to apply automatic thresholding methods used in the Identify modules. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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28 Only the global methods are applied. For more help on thresholding, see the Identify modules. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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29 </help> |
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26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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30 <option value="Otsu">Otsu</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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31 <option value="MoG">MoG</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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32 <option value="Background">Background</option> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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33 <option value="RobustBackground">Robust background</option> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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34 <option value="RidlerCalvard">Ridler Calvard</option> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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35 <option value="Kapur">Kapur</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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36 <option value="MCT">MCT</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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37 </param> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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38 <when value="Otsu"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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39 <expand macro="otsu_method" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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40 </when> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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41 <when value="MoG"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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42 <expand macro="mog_method" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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43 </when> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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44 <when value="Background" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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45 <when value="RobustBackground" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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46 <when value="RidlerCalvard" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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47 <when value="Kapur" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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48 <when value="MCT" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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49 </conditional> |
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50 </repeat> |
26945c55ddff
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51 </when> |
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52 </conditional> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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53 </xml> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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54 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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55 <xml name="otsu_method"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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56 <param name="otsu_weighted_entropy" label="Minimize the weighted variance or the entropy?" type="select"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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57 <option value="Weighted variance">Weighted variance</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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58 <option value="Entropy">Entropy</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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59 </param> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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60 <conditional name="con_threshold_classes"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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61 <param name="threshold_classes" label="Two-class or three-class thresholding?" type="select"> |
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62 <help> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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63 Select Two classes if the grayscale levels are readily distinguishable into foreground (i.e., objects) and background. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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64 Select Three classes if there is a middle set of grayscale levels that belongs to neither the foreground nor background. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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65 For example, three-class thresholding may be useful for images in which you have nuclear staining along with a low-intensity non-specific cell staining. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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66 Where two-class thresholding might incorrectly assign this intermediate staining to the nuclei objects, three-class thresholding allows you to assign it to the foreground or background as desired. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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67 However, in extreme cases where either there are almost no objects or the entire field of view is covered with objects, three-class thresholding may perform worse than two-class. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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68 </help> |
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69 <option value="Two classes">Two classes</option> |
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70 <option value="Three classes">Three classes</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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71 </param> |
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72 <when value="Three classes"> |
26945c55ddff
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73 <param name="pixel_foreground_or_background" label="Assign pixels in the middle intensity class to the foreground or the background?" type="select"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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74 <option value="Foreground">Foreground</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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75 <option value="Background">Background</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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76 </param> |
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77 </when> |
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78 <when value="Two classes" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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79 </conditional> |
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80 </xml> |
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81 |
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82 <xml name="mog_method"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
83 <param name="mog_fraction_cover" label="Typical fraction of the image covered by objects" type="float" value="0.1" min="0.0" max="1.0"/> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
84 </xml> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
85 </macros> |
3
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
2
diff
changeset
|
86 |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
87 <expand macro="py_requirements"/> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
88 <expand macro="cmd_modules" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
89 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
90 <configfiles> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
91 <inputs name="inputs" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
92 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
93 <configfile name="script_file"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
94 import json |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
95 import sys |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
96 import os |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
97 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
98 FOURSPACES=@SPACES@ |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
99 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
100 input_json_path = sys.argv[1] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
101 input_pipeline= sys.argv[2] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
102 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
103 params = json.load(open(input_json_path, "r")) |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
104 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
105 def writemiq(): |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
106 _str = "\nMeasureImageQuality:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:5|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
107 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
108 for_images = params['calc_for_images'] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
109 selected_images = "" |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
110 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
111 if for_images == "All loaded images": |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
112 _str += FOURSPACES + "Calculate metrics for which images?:%s\n" % for_images |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
113 else: |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
114 _str += FOURSPACES + "Calculate metrics for which images?:Select...\n" |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
115 selected_images = params['calc_for_images'] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
116 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
117 image_count = 1 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
118 _str += FOURSPACES + "Image count:%d\n" % image_count |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
119 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
120 if 'rpt_blur_measurements' in params['con_calc_blur_metrics']: |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
121 scale_count = len(params['con_calc_blur_metrics']['rpt_blur_measurements']) |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
122 else: |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
123 scale_count = 1 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
124 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
125 _str += FOURSPACES + "Scale count:%d\n" % scale_count |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
126 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
127 calc_threshold = params['con_calc_threshold']['calc_threshold'] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
128 if calc_threshold == "No": |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
129 threshold_count = 1 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
130 all_method = "No" |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
131 else: |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
132 all_method = params['con_calc_threshold']['con_use_all_methods']['use_all_methods'] |
3
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
2
diff
changeset
|
133 if all_method == "No": |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
2
diff
changeset
|
134 threshold_count = 1 |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
2
diff
changeset
|
135 else: |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
2
diff
changeset
|
136 threshold_count = len(params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method']) |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
137 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
138 _str += FOURSPACES + "Threshold count:%d\n" % threshold_count |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
139 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
140 _str += FOURSPACES + "Select the images to measure:%s\n" % selected_images |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
141 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
142 include_rescaling = params['include_rescaling_value'] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
143 _str += FOURSPACES + "Include the image rescaling value?:%s\n" % include_rescaling |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
144 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
145 calc_blur_metrics = params['con_calc_blur_metrics']['calc_blur_metrics'] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
146 _str += FOURSPACES + "Calculate blur metrics?:%s\n" % calc_blur_metrics |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
147 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
148 if calc_blur_metrics == "Yes" and 'rpt_blur_measurements' in params['con_calc_blur_metrics']: |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
149 for bm in params['con_calc_blur_metrics']['rpt_blur_measurements']: |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
150 _str += FOURSPACES + "Spatial scale for blur measurements:%d\n" % bm['blur_measurements'] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
151 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
152 calc_saturation = params['calc_saturation_metrics'] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
153 _str += FOURSPACES + "Calculate saturation metrics?:%s\n" % calc_saturation |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
154 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
155 calc_intensity = params['calc_intensity_metrics'] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
156 _str += FOURSPACES + "Calculate intensity metrics?:%s\n" % calc_intensity |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
157 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
158 calc_threshold = params['con_calc_threshold']['calc_threshold'] |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
159 _str += FOURSPACES + "Calculate thresholds?:%s\n" % calc_threshold |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
160 _str += FOURSPACES + "Use all thresholding methods?:%s\n" % all_method |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
161 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
162 if all_method == "No": |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
163 for method in params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method']: |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff
changeset
|
164 _str += FOURSPACES + "Select a thresholding method:%s\n" % method['con_threshold_methods']['select_threshold_method'] |
3
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
2
diff
changeset
|
165 |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents:
2
diff
changeset
|
166 fraction_cover = method['con_threshold_methods']['mog_fraction_cover'] if 'mog_fraction_cover' in method['con_threshold_methods'] else 0.1 |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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167 |
3
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168 tt_classes = method['con_threshold_methods']['con_threshold_classes']['threshold_classes'] if 'con_threshold_classes' in method['con_threshold_methods'] else 'Two classes' |
0
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169 |
3
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170 minimize = method['con_threshold_methods']['otsu_weighted_entropy'] if 'otsu_weighted_entropy' in method['con_threshold_methods'] else 'Entropy' |
0
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171 |
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172 if tt_classes == "Three classes": |
3
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173 pixel_intensity = method['con_threshold_methods']['con_threshold_classes']['pixel_foreground_or_background'] |
0
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174 else: |
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175 pixel_intensity = "Foreground" |
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176 |
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177 _str += FOURSPACES + "Typical fraction of the image covered by objects:%.1f\n" % fraction_cover |
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178 |
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179 _str += FOURSPACES + "Two-class or three-class thresholding?:%s\n" % tt_classes |
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180 |
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181 _str += FOURSPACES + "Minimize the weighted variance or the entropy:%s\n" % minimize |
26945c55ddff
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182 |
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183 _str += FOURSPACES + "Assign pixels in the middle intensity class to the foreground or the background?:%s\n" % pixel_intensity |
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184 |
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185 return _str |
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186 |
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187 with open(input_pipeline) as fin: |
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188 lines = fin.readlines() |
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189 |
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190 k, v = lines[4].strip().split(':') |
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191 |
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192 module_count = int(v) |
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193 new_count = module_count + 1 |
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194 lines[4] = k + ":%d\n" % new_count |
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195 |
3
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196 with open("output.cppipe", "w") as f: |
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197 f.writelines(lines) |
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198 f.write(writemiq()) |
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199 |
3
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200 f.close() |
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201 </configfile> |
0
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202 </configfiles> |
3
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203 |
0
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204 <inputs> |
3
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205 <expand macro="input_pipeline_param" /> |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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206 <param name="calc_for_images" type="text" label="Calculate metrics for which images?" value="All loaded images"> |
3
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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207 <help> |
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208 Image names are separated by comma and correspond to the values in the section NameAndType of the 'Starting module' tool. |
08a2cf887a44
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209 |
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210 </help> |
0
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211 <expand macro="text_validator" /> |
26945c55ddff
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212 </param> |
3
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213 |
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214 <param name="include_rescaling_value" type="select" display="radio" label="Include the image rescaling value?" help="Select 'Yes' to add the image’s rescaling value as a quality control metric. This value is recorded only for images loaded using the Input modules. This is useful in confirming that all images are rescaled by the same value, given that some acquisition device vendors may output this value differently. "> |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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215 <option value="Yes">Yes</option> |
26945c55ddff
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216 <option value="No">No</option> |
26945c55ddff
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217 </param> |
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218 |
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219 <conditional name="con_calc_blur_metrics"> |
26945c55ddff
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220 <param name="calc_blur_metrics" type="select" display="radio" label="Calculate blur metrics?"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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221 <option value="Yes">Yes</option> |
3
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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222 <option value="No" selected="True">No</option> |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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223 </param> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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224 <when value="Yes"> |
3
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225 <repeat name="rpt_blur_measurements" title="new scale" min="1"> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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226 <param name="blur_measurements" label="Spatial scale for blur measurements" type="integer" value="20"> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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227 <help> |
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228 Enter an integer for the window size N, in units of pixels. The LocalFocusScore is measured within an N × N pixel window applied to the image, and the Correlation of a pixel is measured with respect to its neighbors N pixels away. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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229 A higher number for the window size N measures larger patterns of image blur whereas smaller numbers measure more localized patterns of blur. We suggest selecting a window size that is on the order of the feature of interest (e.g., the object diameter). You can measure these metrics for multiple window sizes by selecting additional scales for each image. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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230 </help> |
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231 </param> |
0
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232 </repeat> |
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233 </when> |
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234 <when value="No" /> |
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235 </conditional> |
3
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236 |
0
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237 <param name="calc_intensity_metrics" type="select" display="radio" label="Calculate intensity metrics?"> |
3
08a2cf887a44
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238 <help> |
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239 Select 'Yes' to calculate image-based intensity measures, namely the mean, maximum, minimum, standard deviation and median absolute deviation of pixel intensities. These measures are identical to those calculated by MeasureImageIntensity. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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240 </help> |
0
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241 <option value="Yes">Yes</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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242 <option value="No">No</option> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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243 </param> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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244 <param name="calc_saturation_metrics" type="select" display="radio" label="Calculate saturation metrics"> |
3
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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245 <help> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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246 Select 'Yes' to calculate the saturation metrics PercentMaximal and PercentMinimal, i.e., the percentage of pixels at the upper or lower limit of each individual image. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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247 For this calculation, the hard limits of 0 and 1 are not used because images often have undergone some kind of transformation such that no pixels ever reach the absolute maximum or minimum of the image format. Given the noise typical in images, both these measures should be a low percentage but if the images were saturated during imaging, a higher than usual PercentMaximal will be observed, and if there are no objects, the PercentMinimal value will increase. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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248 </help> |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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249 <option value="Yes">Yes</option> |
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250 <option value="No">No</option> |
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251 </param> |
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252 |
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253 <conditional name="con_calc_threshold"> |
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254 <param name="calc_threshold" type="select" display="radio" label="Calculate thresholds?"> |
3
08a2cf887a44
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255 <help> |
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256 Automatically calculate a suggested threshold for each image. One indicator of image quality is that these threshold values lie within a typical range. Outlier images with high or low thresholds often contain artifacts. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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257 </help> |
0
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258 <option value="Yes">Yes</option> |
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259 <option value="No">No</option> |
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260 </param> |
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261 <when value="Yes"> |
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262 <expand macro="macro_calc_threshold" /> |
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263 </when> |
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264 <when value="No" /> |
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265 </conditional> |
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266 |
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267 </inputs> |
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268 |
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269 <outputs> |
3
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270 <expand macro="output_pipeline_param" /> |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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271 </outputs> |
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272 |
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273 <tests> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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274 <test> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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275 <expand macro="test_input_pipeline_param" /> |
3
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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276 |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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277 <param name="calc_for_images" value="All loaded images" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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278 <param name="include_rescaling_value" value="Yes" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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279 |
26945c55ddff
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280 <conditional name="con_calc_blur_metrics"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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281 <param name="calc_blur_metrics" value="Yes" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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282 <repeat name="rpt_blur_measurements"> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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283 <param name="blur_measurements" value="20" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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284 </repeat> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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285 </conditional> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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286 |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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287 <param name="calc_intensity_metrics" value="Yes" /> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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288 <param name="calc_saturation_metrics" value="Yes" /> |
3
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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289 <conditional name="con_calc_threshold"> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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290 <param name="calc_threshold" value="Yes" /> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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291 </conditional> |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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292 |
3
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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293 <conditional name="con_use_all_methods"> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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294 <param name="use_all_methods" value="No" /> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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295 <repeat name="rpt_threshold_method"> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
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296 <conditional name="con_threshold_methods"> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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297 <param name="select_threshold_method" value="Otsu" /> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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298 <param name="otsu_weighted_entropy" value="Weighted variance" /> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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299 <conditional name="con_threshold_classes"> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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300 <param name="threshold_classes" value="Two classes" /> |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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301 </conditional> |
3
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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302 </conditional> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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303 </repeat> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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304 </conditional> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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305 |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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306 <expand macro="test_out_file" file="measure_image_quality.cppipe" /> |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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307 </test> |
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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308 </tests> |
3
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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309 |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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310 <help> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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311 <![CDATA[ |
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312 |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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313 .. class:: infomark |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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314 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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315 **What it does** |
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316 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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317 This tool collects measurements indicating possible image aberrations, e.g., blur (poor focus), intensity, saturation (i.e., the percentage of pixels in the image that are at/near the maximum possible value, and at/near the minimum possible value). |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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318 Details and guidance for each of these measures is provided in the settings help. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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319 Please note that for best results, this module should be applied to the original raw images, rather than images that have already been corrected for illumination. |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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320 |
08a2cf887a44
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321 @COMMON_HELP@ |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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322 ]]> |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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323 </help> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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324 |
08a2cf887a44
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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325 <expand macro="citations" /> |
0
26945c55ddff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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326 </tool> |