Mercurial > repos > imgteam > points2labelimage

annotate points2label.xml @ 5:dc91192a7150 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
author imgteam
date Thu, 06 Nov 2025 09:59:19 +0000
parents 64c155acb864
children
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5
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
imgteam
parents: 4
diff changeset
1 <tool id="ip_points_to_label" name="Convert coordinates to label map" version="@TOOL_VERSION@" profile="20.05">
2
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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2 <description></description>
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3 <macros>
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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
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5 <import>tests.xml</import>
5
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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6 <token name="@TOOL_VERSION@">0.5.0</token>
2
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7 </macros>
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8 <creator>
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9 <expand macro="creators/bmcv" />
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10 </creator>
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11 <edam_operations>
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12 <edam_operation>operation_3443</edam_operation>
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13 </edam_operations>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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14 <xrefs>
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15 <xref type="bio.tools">galaxy_image_analysis</xref>
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16 </xrefs>
4
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17 <requirements>
5
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18 <requirement type="package" version="0.25.2">scikit-image</requirement>
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19 <requirement type="package" version="2.3.4">numpy</requirement>
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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20 <requirement type="package" version="2.3.3">pandas</requirement>
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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21 <requirement type="package" version="2025.10.16">tifffile</requirement>
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22 <requirement type="package" version="0.3.1">giatools</requirement>
2
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23 </requirements>
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24 <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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25
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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26 python '$__tool_directory__/points2label.py'
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27 '$input.file_ext'
2
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28 '$input'
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29 '$output'
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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
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32 $has_header
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33 $swap_xy
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34 $binary
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35
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36 ]]></command>
4
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37 <inputs>
5
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38 <param name="input" type="data" format="tabular,geojson" label="Shapes to be rasterized"/>
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
imgteam
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39 <param name="shapex" type="integer" value="500" min="1" label="Width of the output image" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
imgteam
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40 <param name="shapey" type="integer" value="500" min="1" label="Height of the output image" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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41 <param name="has_header" type="boolean" checked="true" truevalue="--has_header True" falsevalue="" optional="true" label="Tabular list of shapes has header" help="Only used if the input is a tabular file (ignored for GeoJSON). Turning this off will interpret the tabular file as a list of points, where the X and Y coordinates correspond to the first and second column, respectively." />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
imgteam
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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 before rasterization. The width and height of the output image is not affected." />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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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 shapes (65535)." />
0
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44 </inputs>
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45 <outputs>
2
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46 <data name="output" format="tiff" />
0
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47 </outputs>
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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" />
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52 <param name="shapex" value="30" />
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53 <param name="shapey" value="20" />
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54 <param name="has_header" value="false" />
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55 <param name="swap_xy" value="true" />
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56 <param name="binary" value="true" />
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57 <expand macro="tests/binary_image_diff" name="output" value="output1_binary.tiff" ftype="tiff" />
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58 </test>
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59 <!-- Binary / TSV with header / Circles -->
2
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60 <test>
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61 <param name="input" value="input2.tsv" />
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62 <param name="shapex" value="205" />
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63 <param name="shapey" value="84" />
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64 <param name="has_header" value="true" />
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65 <param name="swap_xy" value="false" />
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66 <param name="binary" value="true" />
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67 <expand macro="tests/binary_image_diff" name="output" value="output2_binary.tiff" ftype="tiff" />
2
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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" />
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72 <param name="shapex" value="205" />
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73 <param name="shapey" value="84" />
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74 <param name="has_header" value="true" />
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75 <param name="swap_xy" value="false" />
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76 <param name="binary" value="false" />
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77 <expand macro="tests/label_image_diff" name="output" value="output2.tiff" ftype="tiff" />
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78 </test>
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79 <!-- Binary / TSV with header / TSV with labels / Circles -->
2
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80 <test>
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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" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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83 <param name="shapey" value="100" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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84 <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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85 <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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86 <param name="binary" value="true" />
4
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87 <expand macro="tests/binary_image_diff" name="output" value="output3_binary.tiff" ftype="tiff" />
2
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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88 </test>
3
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89 <!-- Labeled / TSV with header / TSV with labels / Circles -->
2
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90 <test>
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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91 <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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92 <param name="shapex" value="200" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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93 <param name="shapey" value="100" />
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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94 <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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95 <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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96 <param name="binary" value="false" />
4
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97 <expand macro="tests/label_image_diff" name="output" value="output3.tiff" ftype="tiff" />
0
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98 </test>
3
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99 <!-- Labeled / TSV with header / TSV with labels / Rectangles -->
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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100 <test>
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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101 <param name="input" value="input4.tsv" />
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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102 <param name="shapex" value="200" />
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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103 <param name="shapey" value="100" />
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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104 <param name="has_header" value="true" />
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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105 <param name="swap_xy" value="false" />
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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106 <param name="binary" value="false" />
4
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107 <expand macro="tests/label_image_diff" name="output" value="output4.tiff" ftype="tiff" />
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108 </test>
5
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109 <!-- Labeled / TSV with header / TSV with labels / Circles + Rectangles -->
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110 <test>
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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111 <param name="input" value="input5.tsv" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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112 <param name="shapex" value="200" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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113 <param name="shapey" value="100" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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114 <param name="has_header" value="true" />
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115 <param name="swap_xy" value="false" />
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116 <param name="binary" value="false" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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117 <expand macro="tests/label_image_diff" name="output" value="output8.tiff" ftype="tiff" />
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118 </test>
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119 <test expect_failure="true">
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120 <!-- The test should fail because simultaneous usage of radius and width/height on a row is forbidden -->
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121 <param name="input" value="input6.tsv" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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122 <param name="shapex" value="200" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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123 <param name="shapey" value="100" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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124 <param name="has_header" value="true" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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125 <param name="swap_xy" value="false" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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126 <param name="binary" value="false" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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127 <assert_stderr>
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128 <has_text text="Ambiguous shape type (circle or rectangle)" />
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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129 </assert_stderr>
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130 </test>
dc91192a7150 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit edac062b00490276ef00d094e0594abdb3a3f23c
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131 <!-- Labeled / GeoJSON / mixed name and no-name -->
4
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132 <test>
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133 <param name="input" value="rois.geojson" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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134 <param name="shapex" value="300" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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135 <param name="shapey" value="300" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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136 <param name="has_header" value="false" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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137 <param name="swap_xy" value="false" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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138 <param name="binary" value="false" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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139 <expand macro="tests/label_image_diff" name="output" value="output5.tiff" ftype="tiff" />
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140 </test>
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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141 <test>
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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142 <param name="input" value="rois.geojson" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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143 <param name="shapex" value="300" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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144 <param name="shapey" value="300" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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145 <param name="has_header" value="false" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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146 <param name="swap_xy" value="true" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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147 <param name="binary" value="false" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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148 <expand macro="tests/label_image_diff" name="output" value="output6.tiff" ftype="tiff" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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149 </test>
5
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150 <!-- Labeled / GeoJSON / no-name -->
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151 <test>
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152 <param name="input" value="rois-noname.geojson" />
4
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153 <param name="shapex" value="300" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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154 <param name="shapey" value="300" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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155 <param name="has_header" value="false" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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156 <param name="swap_xy" value="false" />
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157 <param name="binary" value="false" />
5
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158 <expand macro="tests/label_image_diff" name="output" value="output7.tiff" ftype="tiff" />
4
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159 </test>
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160 <test expect_failure="true">
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161 <!-- The test should fail because the GeoJSON uses the `LineString` primitive type that is not supported yet -->
4
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162 <param name="input" value="rois-illegal2.geojson" />
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163 <param name="shapex" value="300" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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164 <param name="shapey" value="300" />
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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165 <param name="has_header" value="false" />
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166 <param name="swap_xy" value="false" />
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167 <param name="binary" value="false" />
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168 <assert_stderr>
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169 <has_text text='Unsupported geometry type: "LineString"' />
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170 </assert_stderr>
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171 </test>
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172 </tests>
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173 <help>
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174
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175 **Converts a list of shapes to a label map via rasterization.**
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176
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177 The created image is a single-channel image with 16 bits per pixel (unsigned integers). The shapes are
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178 rasterized with unique labels, explicitly given labels (custom), or the value 65535 (white) for binary image
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179 output. Pixels not corresponding to any shapes are assigned the value 0 (black).
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180
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181 **Using a GeoJSON input file (recommended).** Only features (shape specifications) of `Polygon` and `Point`
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182 type are supported. In conjunction with the `radius` property, a `Point` type feature can also be used to
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183 represent circles. Custom labels can be encoded in the `name` property (must be numeric and integer), and
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184 different features are allowed to use the same labels.
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185
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186 **Using a tabular input file (deprecated).** The tabular list of points can either be header-less. In this
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187 case, the first and second columns are expected to be the X and Y coordinates, respectively, and each row
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188 corresponds to a single point. Otherwise, if a header is present, it is searched for the following column
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189 names:
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190
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191 - Column ``pos_x`` or ``POS_X`` is mandatory and corresponds to the X coordinates.
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192 - Column ``pos_y`` or ``POS_Y`` is mandatory and corresponds to the Y coordinates.
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193 - If a ``radius`` or ``RADIUS`` column is present and the value in a row is positive, then the row will be
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194 rasterized as a circle of the corresponding size, centered at the given X and Y coordinates.
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195 - If ``width`` or ``WIDTH`` and ``height`` or ``HEIGHT`` columns are present and the values in a row are
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196 positive, then the rows will be rasterized as rectangles of the corresponding size, with the upper-left
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197 corner given by the X and Y coordinates.
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198 - If a ``label`` or ``LABEL`` column is present, then the corresponding labels will be used for rasterization
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199 (unless "Produce binary image" is activated). Different rows are allowed to use the same label. If used,
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200 the label must be numeric and integer.
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201
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202 </help>
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203 <citations>
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204 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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205 </citations>
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206 </tool>