Mercurial > repos > imgteam > points2labelimage

annotate points2label.xml @ 3:2ae122d5d85a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
author imgteam
date Wed, 23 Apr 2025 14:37:31 +0000
parents 714a57d6f3a1
children 64c155acb864
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
parents: 1
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1 <tool id="ip_points_to_label" name="Convert point coordinates to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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2 <description></description>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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3 <macros>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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4 <import>creators.xml</import>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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5 <import>tests.xml</import>
3
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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6 <token name="@TOOL_VERSION@">0.4.1</token>
2
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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7 <token name="@VERSION_SUFFIX@">0</token>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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8 </macros>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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9 <creator>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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10 <expand macro="creators/bmcv" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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11 </creator>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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12 <edam_operations>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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13 <edam_operation>operation_3443</edam_operation>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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14 </edam_operations>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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15 <xrefs>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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16 <xref type="bio.tools">galaxy_image_analysis</xref>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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17 </xrefs>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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18 <requirements>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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19 <requirement type="package" version="0.21">scikit-image</requirement>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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20 <requirement type="package" version="1.26.4">numpy</requirement>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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21 <requirement type="package" version="1.2.4">pandas</requirement>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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22 <requirement type="package" version="2024.6.18">tifffile</requirement>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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23 <requirement type="package" version="0.3.1">giatools</requirement>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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24 </requirements>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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25 <command detect_errors="aggressive"><![CDATA[
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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26
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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27 python '$__tool_directory__/points2label.py'
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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28 '$input'
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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29 '$output'
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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30 $shapex
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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31 $shapey
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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32 $has_header
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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33 $swap_xy
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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34 $binary
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35
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36 ]]></command>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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37 <inputs>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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38 <param name="input" type="data" format="tabular" label="Tabular list of points"/>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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39 <param name="shapex" type="integer" value="500" min="1" label="Width of output image" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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40 <param name="shapey" type="integer" value="500" min="1" label="Height of output image" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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41 <param name="has_header" type="boolean" checked="true" truevalue="--has_header True" falsevalue="" optional="true" label="Tabular list of points has header" help="Turning this off will ignore the first row and assume that the X and Y coordinates correspond to the first and second column, respectively." />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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42 <param name="swap_xy" type="boolean" checked="false" falsevalue="" truevalue="--swap_xy True" optional="true" label="Swap X and Y coordinates" help="Swap the X and Y coordinates, regardless of whether the tabular list has a header or not." />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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43 <param name="binary" type="boolean" checked="false" truevalue="--binary True" falsevalue="" optional="true" label="Produce binary image" help="Use the same label for all points (65535)." />
0
07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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44 </inputs>
07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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45 <outputs>
2
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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46 <data name="output" format="tiff" />
0
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47 </outputs>
07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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48 <tests>
3
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49 <!-- Binary / TSV without header / Points -->
0
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50 <test>
2
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51 <param name="input" value="input1.tsv" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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52 <param name="shapex" value="30" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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53 <param name="shapey" value="20" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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54 <param name="has_header" value="false" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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55 <param name="swap_xy" value="true" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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56 <param name="binary" value="true" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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57 <expand macro="tests/binary_image_diff" name="output" value="output1_binary.tif" ftype="tiff" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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58 </test>
3
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59 <!-- Binary / TSV with header / Circles -->
2
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60 <test>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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61 <param name="input" value="input2.tsv" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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62 <param name="shapex" value="205" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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63 <param name="shapey" value="84" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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64 <param name="has_header" value="true" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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65 <param name="swap_xy" value="false" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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66 <param name="binary" value="true" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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67 <expand macro="tests/binary_image_diff" name="output" value="output2_binary.tif" ftype="tiff" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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68 </test>
3
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69 <!-- Labeled / TSV with header / Circles -->
2
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70 <test>
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71 <param name="input" value="input2.tsv" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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72 <param name="shapex" value="205" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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73 <param name="shapey" value="84" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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74 <param name="has_header" value="true" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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75 <param name="swap_xy" value="false" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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76 <param name="binary" value="false" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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77 <expand macro="tests/label_image_diff" name="output" value="output2.tif" ftype="tiff" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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78 </test>
3
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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79 <!-- Binary / TSV with header / TSV with labels / Circles -->
2
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80 <test>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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81 <param name="input" value="input3.tsv" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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82 <param name="shapex" value="200" />
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83 <param name="shapey" value="100" />
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84 <param name="has_header" value="true" />
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85 <param name="swap_xy" value="false" />
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86 <param name="binary" value="true" />
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87 <expand macro="tests/binary_image_diff" name="output" value="output3_binary.tif" ftype="tiff" />
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88 </test>
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89 <!-- Labeled / TSV with header / TSV with labels / Circles -->
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90 <test>
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91 <param name="input" value="input3.tsv" />
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92 <param name="shapex" value="200" />
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93 <param name="shapey" value="100" />
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94 <param name="has_header" value="true" />
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95 <param name="swap_xy" value="false" />
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96 <param name="binary" value="false" />
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97 <expand macro="tests/label_image_diff" name="output" value="output3.tif" ftype="tiff" />
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98 </test>
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99 <!-- Labeled / TSV with header / TSV with labels / Rectangles -->
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100 <test>
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101 <param name="input" value="input4.tsv" />
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102 <param name="shapex" value="200" />
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103 <param name="shapey" value="100" />
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104 <param name="has_header" value="true" />
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105 <param name="swap_xy" value="false" />
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106 <param name="binary" value="false" />
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107 <expand macro="tests/label_image_diff" name="output" value="output4.tif" ftype="tiff" />
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108 </test>
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109 </tests>
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110 <help>
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111
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112 **Converts a tabular list of points to a label map by rasterizing the point coordinates.**
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113
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114 The created image is a single-channel image with 16 bits per pixel (unsigned integer). The points are
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115 rasterized with unique labels, or the value 65535 (white) for binary image output. Pixels not corresponding to
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116 any points in the tabular file are assigned the value 0 (black).
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117
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118 The tabular list of points can either be header-less. In this case, the first and second columns are expected
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119 to be the X and Y coordinates, respectively. Otherwise, if a header is present, it is searched for the
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120 following column names:
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121
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122 - ``pos_x`` or ``POS_X``: This column corresponds to the X coordinates.
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123 - ``pos_y`` or ``POS_Y``: This column corresponds to the Y coordinates.
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124 - If a ``radius`` or ``RADIUS`` column is present, then the points will be rasterized as circles of the
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125 corresponding radii.
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126 - If ``width`` or ``WIDTH`` and ``height`` or ``HEIGHT`` columns are present, then the points will be rasterized
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127 as rectangles of the corresponding size.
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128 - If a ``label`` or ``LABEL`` column is present, then the corresponding labels will be used for rasterization
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129 (unless "Produce binary image" is activated). Different points are allowed to use the same label.
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130
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131 </help>
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132 <citations>
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133 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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134 </citations>
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135 </tool>