Mercurial > repos > bgruening > cp_display_data_on_image

annotate display_data_on_image.xml @ 5:6a7da2e5f696 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 14:06:13 +0000
parents 4e12ef887a2a
children 5d28ac336861
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6a7da2e5f696 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
bgruening
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1 <tool id="cp_display_data_on_image" name="DisplayDataOnImage" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
2
7c70e5268acd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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2 <description>produce an image with data on top of identified objects</description>
0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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3 <macros>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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4 <import>macros.xml</import>
5
6a7da2e5f696 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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5 <token name="@VERSION_SUFFIX@">0</token>
0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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6 <xml name="display_object">
3
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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7 <param name="select_input_obj" label="Enter the name of the input objects" type="text" help="Enter the name of the objects identified by some other tool used upstream in the workflow (such as IdentifyPrimaryObjects or IdentifySecondaryObjects)." />
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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8
0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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9 <conditional name="con_obj_measurement_category">
3
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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10 <param name="measurement_category" label="Measurement category" type="select" help="The measurement will be made by some other tool used upstream in the workflow on either the whole image or on the objects you selected.">
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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11
0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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12 <option value="Location">Location</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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13 <option value="Number">Number</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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14 </param>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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15 <when value="Number">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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16 <param name="measurement" label="Measurement" type="select">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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17 <option value="Object_Number">Object_Number</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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18 </param>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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19 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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20 <when value="Location">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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21 <param name="obj_measurement" label="Measurement" type="select">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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22 <option value="Center_X">Center_X</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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23 <option value="Center_Y">Center_Y</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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24 <option value="Center_Z">Center_Z</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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25 </param>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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26 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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27 </conditional>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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28 </xml>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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29 <xml name="display_image">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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30 <conditional name="con_obj_measurement_category">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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31 <param name="measurement_category" label="Measurement category" type="select">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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32 <option value="Count">Count</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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33 <option value="FileName">FileName</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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34 <option value="Frame">Frame</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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35 <option value="Height">Height</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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36 <option value="MD5Digest">MD5Digest</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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37 <option value="Metadata">Metadata</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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38 <option value="PathName">PathName</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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39 <option value="Scaling">Scaling</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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40 <option value="Series">Series</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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41 <option value="PathName">PathName</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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42 <option value="Threshold">Threshold</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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43 <option value="URL">URL</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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44 <option value="Width">Width</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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45 </param>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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46 <when value="Count">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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47 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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48 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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49 <when value="FileName">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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50 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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51 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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52 <when value="Frame">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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53 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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54 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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55 <when value="Height">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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56 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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57 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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58 <when value="MD5Digest">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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59 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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60 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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61 <when value="Metadata">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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62 <param name="measurement" label="Measurement" type="select">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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63 <option value="FileLocation">FileLocation</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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64 <option value="Frame">Frame</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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65 <option value="ImageId">ImageId</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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66 <option value="Screen">Screen</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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67 <option value="Series">Series</option>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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68 </param>
3
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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69 </when>
0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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70 <when value="PathName">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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71 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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72 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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73 <when value="Scaling">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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74 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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75 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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76 <when value="Series">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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77 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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78 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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79 <when value="PathName">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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80 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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81 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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82 <when value="Threshold">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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83 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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84 <param name="image_thresh_objects" label="Objects" type="text"/>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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85 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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86 <when value="URL">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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87 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
88 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
89 <when value="Width">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
90 <param name="measurement" label="Measurement" type="text" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
91 </when>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
92 </conditional>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
93 </xml>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
94 </macros>
3
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
95
0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
96 <expand macro="py_requirements"/>
3
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
97 <expand macro="cmd_modules" />
0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
98
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
99 <configfiles>
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
100 <inputs name="inputs" />
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
101 <configfile name="script_file">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
102 import json
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
103 import sys
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
104 import os
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
105
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
106 FOURSPACES=@SPACES@
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
107
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
108 input_json_path = sys.argv[1]
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
109 input_pipeline= sys.argv[2]
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
110
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
111 params = json.load(open(input_json_path, "r"))
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
112
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
113 def writemi():
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
114 _str = "\nDisplayDataOnImage:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:6|show_window:False|notes:\\x5B\\'Add nuclei id as label\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
115
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
116 obj_img_params = params['con_display_obj_image']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
117 display_mode_params = params['con_display_mode']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
118
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
119 _str += FOURSPACES + "Display object or image measurements?:%s\n" % obj_img_params['display_obj_image']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
120
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
121 input_obj = obj_img_params['select_input_obj'] if obj_img_params['display_obj_image'] == "Object" else "None"
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
122
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
123 _str += FOURSPACES + "Select the input objects:%s\n" % input_obj
3
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
124 _str += FOURSPACES + "Measurement to display:%s_%s\n" % (obj_img_params['con_obj_measurement_category']['measurement_category'],obj_img_params['con_obj_measurement_category']['measurement'])
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
125 _str += FOURSPACES + "Select the image on which to display the measurements:%s\n" % params['image_to_display_measurements']
0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
126
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
127 display_mode = display_mode_params['display_mode']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
128
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
129 if display_mode == "Text":
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
130 text_color = display_mode_params['text_color']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
131 font_size = display_mode_params['font_size']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
132 no_of_decimals = display_mode_params['number_of_decimals']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
133 annotation_offset = display_mode_params['annotation_offset']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
134 color_map = "Default"
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
135 color_map_scale = "Use this image's measurement range"
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
136 color_map_range = "0.0,1.0"
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
137 else:
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
138 text_color = "#ff0000"
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
139 font_size = 11
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
140 no_of_decimals = 0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
141 annotation_offset = 0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
142 color_map = display_mode_params['color_map']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
143 color_map_scale = display_mode_params['con_color_map_scale']['color_map_scale']
3
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
144
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
145 if color_map_scale == "Manual":
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
146 color_map_range ="%.1f,%.1f" % (display_mode_params['con_color_map_scale']['min_color_map_range'],display_mode_params['con_color_map_scale']['max_color_map_range'])
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
147 else:
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
148 color_map_range = "0.0,1.0"
0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
149
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
150 _str += FOURSPACES + "Text color:%s\n" % text_color
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
151 _str += FOURSPACES + "Name the output image that has the measurements displayed:%s\n" % params['name_output_image']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
152 _str += FOURSPACES + "Font size (points):%d\n" % font_size
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
153 _str += FOURSPACES + "Number of decimals:%d\n" % no_of_decimals
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
154 _str += FOURSPACES + "Image elements to save:%s\n" % params['element_to_save']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
155 _str += FOURSPACES + "Annotation offset (in pixels):%d\n" % annotation_offset
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
156 _str += FOURSPACES + "Display mode:%s\n" % display_mode
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
157 _str += FOURSPACES + "Color map:%s\n" % color_map
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
158 _str += FOURSPACES + "Display background image?:%s\n" % params['display_background_image']
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
159 _str += FOURSPACES + "Color map scale:%s\n" % color_map_scale
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
160 _str += FOURSPACES + "Color map range:%s\n" % color_map_range
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
161
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
162 return _str
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
163
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
164
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
165 with open(input_pipeline) as fin:
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
166 lines = fin.readlines()
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
167
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
168 k, v = lines[4].strip().split(':')
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
169
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
170 module_count = int(v)
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
171 new_count = module_count + 1
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
172 lines[4] = k + ":%d\n" % new_count
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
173
3
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
174 with open("output.cppipe", "w") as f:
0
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
175 f.writelines(lines)
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
176 f.write(writemi())
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177
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178 f.close()
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179 </configfile>
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180 </configfiles>
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181
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182 <inputs>
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183 <expand macro="input_pipeline_param" />
0
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184 <conditional name="con_display_obj_image">
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185 <param name="display_obj_image" type="select" label="Display object or image measurements?">
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186 <option value="Object">Object</option>
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187 <option value="Image">Image</option>
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188 </param>
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189 <when value="Object">
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190 <expand macro="display_object" />
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191 </when>
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192 <when value="Image">
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193 <expand macro="display_image" />
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194 </when>
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195 </conditional>
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196
3
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197 <param name="display_background_image" label="Display background image?" type="select" display="radio" help="Usually, you will want to see the image context for the measurements, but it may be useful to save just the overlay of the text measurements and composite the overlay image and the original image later.">
0
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198 <option value="Yes">Yes</option>
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199 <option value="No">No</option>
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200 </param>
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201
3
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202 <param name="image_to_display_measurements" label="Enter the name of the image on which to display the measurements" type="text">
0
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203 <expand macro="text_validator" />
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204 </param>
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205
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206 <conditional name="con_display_mode">
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207 <param name="display_mode" type="select" label="Display mode" help="If you choose Text, DisplayDataOnImage will display the numeric value on top of each object. If you choose Color, DisplayDataOnImage will convert the image to grayscale, if necessary, and display the portion of the image within each object using a hue that indicates the measurement value relative to the other objects in the set using the default color map.">
0
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208 <option value="Text">Text</option>
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209 <option value="Color">Color</option>
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210 </param>
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211 <when value="Text">
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212 <param name="text_color" type="color" label="Text color" />
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213 <param name="font_size" type="integer" label="Font size (points)" value="11" min="5">
0
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214 </param>
3
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215 <param name="number_of_decimals" type="integer" label="Number of decimals" value="2" min="0" max="10"/>
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216 <param name="annotation_offset" type="integer" label="Annotation offset (in pixels)" value="0" min="0" help="Normally, the text is placed at the object (or image) center, which can obscure relevant features of the object. This setting adds a specified offset to the text, in a random direction." />
0
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217 </when>
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218 <when value="Color">
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219 <param name="color_map" label="Color map" type="select" help="DisplayDataOnImage assigns a color to each object’s measurement value from a colormap when in colormap-mode, mapping the value to a color along the colormap’s continuum. This mapping has implicit upper and lower bounds to its range which are the extremes of the colormap. This setting determines whether the extremes are the minimum and maximum ">
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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220 <option value="Default">Default</option>
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221 </param>
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222 <conditional name="con_color_map_scale">
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223 <param name="color_map_scale" label="Color map scale" type="select">
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224
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225 <help>
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226 <![CDATA[
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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227 This tool assigns a color to each object’s measurement value from a colormap when in colormap-mode, mapping the value to a color along the colormap’s continuum. This mapping has implicit upper and lower bounds to its range which are the extremes of the colormap. This setting determines whether the extremes are the minimum and maximum values of the measurement from among the objects in the current image or manually-entered extremes.
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228 <br>- Use this image's measurement range: Use the full range of colors to get the maximum contrast within the image.
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229 <br>- Manual: Manually set the upper and lower bounds so that images with different maxima and minima can be compared by a uniform color mapping.
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230 ]]>
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231 </help>
0
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232 <option value="Use this image's measurement range">Use this image's measurement range</option>
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233 <option value="Manual">Manual</option>
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234 <sanitizer sanitize="false"/>
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235 </param>
0
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236 <when value="Manual">
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237 <param name="min_color_map_range" label="Min. color map range" type="float" help="This setting determines the lower bounds of the values for the color map" value="0.0" min="0.0" />
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238 <param name="max_color_map_range" label="Max. color map range" type="float" help="This setting determines the upper bounds of the values for the color map" value="1.0" max="1.0" />
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239 </when>
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240 <when value="Use this image's measurement range" />
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241 </conditional>
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242 </when>
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243 </conditional>
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244
c49a557b4e3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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245 <param name="name_output_image" label="Name the output image that has the measurements displayed" type="text">
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246 <expand macro="text_validator" />
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247 </param>
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248 <param name="element_to_save" type="select" label="Image elements to save">
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249 <help>
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250 <![CDATA[
4e12ef887a2a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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251 This setting controls the level of annotation on the image:
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252 <br>- Image: Saves the image with the overlaid measurement annotations.
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253 <br>- Figure: Adds a title and other decorations.
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254 <br>- Axes: Adds axes with tick marks and image coordinates.
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255 ]]>
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256 </help>
0
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257 <option value="Image">Image</option>
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258 <option value="Figure">Figure</option>
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259 <option value="Axes">Axes</option>
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260 </param>
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261 </inputs>
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262
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263 <outputs>
3
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264 <expand macro="output_pipeline_param" />
0
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265 </outputs>
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266
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267 <tests>
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268 <test>
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269 <expand macro="test_input_pipeline_param" />
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270 <conditional name="con_display_obj_image">
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271 <param name="display_obj_image" value="Object" />
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272 <param name="select_input_obj" value="Nuclei" />
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273 <conditional name="con_obj_measurement_category">
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274 <param name="measurement_category" value="Number" />
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275 <param name="measurement" value="Object_Number" />
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276 </conditional>
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277 </conditional>
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278 <param name="display_background_image" value="Yes" />
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279 <param name="image_to_display_measurements" value="DNA" />
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280 <conditional name="con_display_mode">
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281 <param name="display_mode" value="Text" />
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282 <param name="text_color" value="#ff0000"/>
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283 <param name="font_size" value="11" />
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284 <param name="number_of_decimals" value="0" />
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285 <param name="annotation_offset" value="0" />
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286 </conditional>
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287 <param name="name_output_image" value="ImageDisplay" />
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288 <param name="element_to_save" value="Image" />
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289
3
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290 <expand macro="test_out_file" file="display_data_on_image.cppipe" />
0
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291 </test>
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292 </tests>
3
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293 <help>
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294 <![CDATA[
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295 .. class:: infomark
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296
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297 **What it does**
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298
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299 This module displays either a single image measurement on an image of your choosing, or one object measurement per object on top of every object in an image. The display itself is an image which you can save to a file using *SaveImages*.
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300
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301 @COMMON_HELP@
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302 ]]>
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303 </help>
0
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304 <expand macro="citations" />
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305 </tool>