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annotate points2label.xml @ 4:64c155acb864 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
author imgteam
date Mon, 12 May 2025 14:01:09 +0000
parents 2ae122d5d85a
children dc91192a7150
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64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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1 <tool id="ip_points_to_label" name="Convert coordinates to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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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>
3
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6 <token name="@TOOL_VERSION@">0.4.1</token>
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64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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7 <token name="@VERSION_SUFFIX@">1</token>
2
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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>
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10 <expand macro="creators/bmcv" />
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11 </creator>
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12 <edam_operations>
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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>
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15 <xrefs>
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16 <xref type="bio.tools">galaxy_image_analysis</xref>
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17 </xrefs>
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18 <requirements>
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19 <requirement type="package" version="0.21">scikit-image</requirement>
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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20 <requirement type="package" version="1.26.4">numpy</requirement>
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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>
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64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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23 <requirement type="package" version="0.3.1">giatools</requirement>
2
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24 </requirements>
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25 <command detect_errors="aggressive"><![CDATA[
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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'
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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>
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64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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37 <inputs>
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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38 <param name="input" type="data" format="tabular,geojson" label="List of points in tabular or geojson format"/>
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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
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40 <param name="shapey" type="integer" value="500" min="1" label="Height of output image" />
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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. Ignored, if GeoJSON is used for input." />
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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." />
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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)." />
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44 </inputs>
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45 <outputs>
2
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46 <data name="output" format="tiff" />
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47 </outputs>
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48 <tests>
3
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49 <!-- Binary / TSV without header / Points -->
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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 -->
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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" />
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68 </test>
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69 <!-- Labeled / TSV with header / Circles -->
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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" />
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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" />
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87 <expand macro="tests/binary_image_diff" name="output" value="output3_binary.tiff" ftype="tiff" />
2
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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 -->
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100 <test>
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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" />
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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>
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109 <!-- Labeled / ROI / Rectangles -->
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110 <test>
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111 <param name="input" value="rois.geojson" />
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112 <param name="shapex" value="300" />
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113 <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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114 <param name="has_header" value="false" />
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115 <param name="swap_xy" value="false" />
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116 <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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117 <expand macro="tests/label_image_diff" name="output" value="output5.tiff" ftype="tiff" />
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118 </test>
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119 <test>
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120 <param name="input" value="rois-noname.geojson" />
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121 <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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122 <param name="shapey" value="300" />
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123 <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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124 <param name="swap_xy" value="false" />
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125 <param name="binary" value="false" />
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126 <expand macro="tests/label_image_diff" name="output" value="output5.tiff" ftype="tiff" />
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127 </test>
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128 <test>
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129 <param name="input" value="rois.geojson" />
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130 <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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131 <param name="shapey" value="300" />
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132 <param name="has_header" value="false" />
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133 <param name="swap_xy" value="true" />
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134 <param name="binary" value="false" />
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135 <expand macro="tests/label_image_diff" name="output" value="output6.tiff" ftype="tiff" />
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136 </test>
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137 <test expect_failure="true">
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138 <!-- The test should fail because the GeoJSON is not rectangular -->
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139 <param name="input" value="rois-illegal1.geojson" />
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140 <param name="shapex" value="300" />
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141 <param name="shapey" value="300" />
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142 <param name="has_header" value="false" />
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143 <param name="swap_xy" value="false" />
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144 <param name="binary" value="false" />
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145 </test>
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146 <test expect_failure="true">
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147 <!-- The test should fail because the GeoJSON is not of `Polygon` type -->
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148 <param name="input" value="rois-illegal2.geojson" />
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149 <param name="shapex" value="300" />
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150 <param name="shapey" value="300" />
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151 <param name="has_header" value="false" />
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152 <param name="swap_xy" value="false" />
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153 <param name="binary" value="false" />
3
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154 </test>
0
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155 </tests>
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156 <help>
2
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157
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158 **Converts a list of points to a label map by rasterizing the coordinates.**
2
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159
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160 The created image is a single-channel image with 16 bits per pixel (unsigned integer). The points are
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161 rasterized with unique labels, or the value 65535 (white) for binary image output. Pixels not corresponding to
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162 any points in the tabular file are assigned the value 0 (black).
0
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163
4
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164 **Using a tabular input file:** The tabular list of points can either be header-less. In this case, the first
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165 and second columns are expected to be the X and Y coordinates, respectively. Otherwise, if a header is present,
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166 it is searched for the following column names:
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167
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168 - ``pos_x`` or ``POS_X``: This column corresponds to the X coordinates.
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169 - ``pos_y`` or ``POS_Y``: This column corresponds to the Y coordinates.
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170 - If a ``radius`` or ``RADIUS`` column is present, then the points will be rasterized as circles of the
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171 corresponding radii.
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172 - If ``width`` or ``WIDTH`` and ``height`` or ``HEIGHT`` columns are present, then the points will be rasterized
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173 as rectangles of the corresponding size.
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174 - If a ``label`` or ``LABEL`` column is present, then the corresponding labels will be used for rasterization
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175 (unless "Produce binary image" is activated). Different points are allowed to use the same label. If used, the
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176 label must be numeric and integer.
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177
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178 **Using a GeoJSON input file:** Only rectangular specifications of `Polygon` type geometry is supported.
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179
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180 </help>
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181 <citations>
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182 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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183 </citations>
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184 </tool>