Mercurial > repos > imgteam > points2labelimage

annotate points2label.xml @ 3:de611b3b5ae8 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
author imgteam
date Fri, 27 Sep 2024 17:41:21 +0000
parents 30ca5d5d03ec
children
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3
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
parents: 2
diff changeset
1 <tool id="ip_points_to_label" name="Convert point coordinates to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2
30ca5d5d03ec planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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2 <description></description>
3
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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3 <macros>
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imgteam
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4 <import>creators.xml</import>
de611b3b5ae8 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>
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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6 <token name="@TOOL_VERSION@">0.4</token>
de611b3b5ae8 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>
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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8 </macros>
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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9 <creator>
de611b3b5ae8 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" />
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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11 </creator>
2
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12 <edam_operations>
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13 <edam_operation>operation_3443</edam_operation>
30ca5d5d03ec planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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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>
30ca5d5d03ec planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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17 </xrefs>
3
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imgteam
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18 <requirements>
de611b3b5ae8 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>
de611b3b5ae8 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>
de611b3b5ae8 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>
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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22 <requirement type="package" version="2024.6.18">tifffile</requirement>
de611b3b5ae8 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>
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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24 </requirements>
de611b3b5ae8 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[
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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26
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27 python '$__tool_directory__/points2label.py'
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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28 '$input'
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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29 '$output'
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30 $shapex
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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31 $shapey
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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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>
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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37 <inputs>
de611b3b5ae8 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"/>
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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39 <param name="shapex" type="integer" value="500" min="1" label="Width of output image" />
de611b3b5ae8 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" />
de611b3b5ae8 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." />
de611b3b5ae8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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, regardless of whether the tabular list has a header or not." />
de611b3b5ae8 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
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44 </inputs>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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45 <outputs>
3
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46 <data name="output" format="tiff" />
0
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47 </outputs>
dcc8c1d6af48 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 -->
0
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50 <test>
3
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51 <param name="input" value="input1.tsv" />
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52 <param name="shapex" value="30" />
de611b3b5ae8 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" />
de611b3b5ae8 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" />
de611b3b5ae8 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" />
de611b3b5ae8 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" />
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57 <expand macro="tests/binary_image_diff" name="output" value="output1_binary.tif" ftype="tiff" />
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58 </test>
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59 <!-- Binary / TSV with header -->
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60 <test>
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61 <param name="input" value="input2.tsv" />
de611b3b5ae8 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" />
de611b3b5ae8 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" />
de611b3b5ae8 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" />
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65 <param name="swap_xy" value="false" />
de611b3b5ae8 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" />
de611b3b5ae8 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" />
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68 </test>
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69 <!-- Labeled / TSV with header -->
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70 <test>
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71 <param name="input" value="input2.tsv" />
de611b3b5ae8 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" />
de611b3b5ae8 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" />
de611b3b5ae8 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" />
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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.tif" ftype="tiff" />
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78 </test>
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79 <!-- Binary / TSV with header / TSV with labels -->
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80 <test>
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81 <param name="input" value="input3.tsv" />
de611b3b5ae8 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" />
de611b3b5ae8 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" />
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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 -->
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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 </tests>
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100 <help>
3
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101
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102 **Converts a tabular list of points to a label map by rasterizing the point coordinates.**
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103
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104 The created image is a single-channel image with 16 bits per pixel (unsigned integer). The points are
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105 rasterized with unique labels, or the value 65535 (white) for binary image output. Pixels not corresponding to
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106 any points in the tabular file are assigned the value 0 (black).
0
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107
3
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108 The tabular list of points can either be header-less. In this case, the first and second columns are expected
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109 to be the X and Y coordinates, respectively. Otherwise, if a header is present, it is searched for the
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110 following column names:
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111
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112 - ``pos_x`` or ``POS_X``: This column corresponds to the X coordinates.
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113 - ``pos_y`` or ``POS_Y``: This column corresponds to the Y coordinates.
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114 - If a ``radius`` or ``RADIUS`` column is present, then the points will be rasterized as circles of the
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115 corresponding radii.
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116 - If a ``label`` or ``LABEL`` column is present, then the corresponding labels will be used for rasterization
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117 (unless "Produce binary image" is activated). Different points are allowed to use the same label.
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118
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119 </help>
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120 <citations>
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121 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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122 </citations>
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123 </tool>