Mercurial > repos > imgteam > points2binaryimage
comparison points2binaryimage.xml @ 4:4c0f16fb9f8d draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
author | imgteam |
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date | Wed, 25 Sep 2024 08:29:59 +0000 |
parents | a80f92ec6f89 |
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3:a80f92ec6f89 | 4:4c0f16fb9f8d |
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1 <tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> | 1 <tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
2 <description></description> | 2 <description></description> |
3 <macros> | 3 <macros> |
4 <import>creators.xml</import> | 4 <import>creators.xml</import> |
5 <token name="@TOOL_VERSION@">0.2</token> | 5 <import>tests.xml</import> |
6 <token name="@VERSION_SUFFIX@">3</token> | 6 <token name="@TOOL_VERSION@">0.3</token> |
7 <token name="@VERSION_SUFFIX@">0</token> | |
7 </macros> | 8 </macros> |
8 <creator> | 9 <creator> |
9 <expand macro="creators/bmcv" /> | 10 <expand macro="creators/bmcv" /> |
10 </creator> | 11 </creator> |
11 <edam_operations> | 12 <edam_operations> |
13 </edam_operations> | 14 </edam_operations> |
14 <xrefs> | 15 <xrefs> |
15 <xref type="bio.tools">galaxy_image_analysis</xref> | 16 <xref type="bio.tools">galaxy_image_analysis</xref> |
16 </xrefs> | 17 </xrefs> |
17 <requirements> | 18 <requirements> |
18 <requirement type="package" version="0.14.2">scikit-image</requirement> | 19 <requirement type="package" version="0.21">scikit-image</requirement> |
19 <requirement type="package" version="1.15.4">numpy</requirement> | 20 <requirement type="package" version="1.26.4">numpy</requirement> |
20 <requirement type="package" version="0.23.4">pandas</requirement> | 21 <requirement type="package" version="1.2.4">pandas</requirement> |
21 <requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed--> | 22 <requirement type="package" version="2024.6.18">tifffile</requirement> |
22 <requirement type="package" version="2.5.2">python-dateutil</requirement> | |
23 <requirement type="package" version="0.15.1">tifffile</requirement> | |
24 </requirements> | 23 </requirements> |
25 <command detect_errors="aggressive"> | 24 <command detect_errors="aggressive"><![CDATA[ |
26 <![CDATA[ | 25 |
27 python '$__tool_directory__/points2binaryimage.py' '$input' '$output' $shapex $shapey $has_header $invert_xy | 26 python '$__tool_directory__/points2binaryimage.py' |
28 ]]> | 27 '$input' |
29 </command> | 28 '$output' |
29 $shapex | |
30 $shapey | |
31 $has_header | |
32 $swap_xy | |
33 | |
34 ]]></command> | |
30 <inputs> | 35 <inputs> |
31 <param name="input" type="data" format="tabular" label="CSV point file"/> | 36 <param name="input" type="data" format="tabular" label="Tabular list of points"/> |
32 <param name="shapex" type="integer" value="500" optional="true" min="1" max="2000" label="Width of output image" /> | 37 <param name="shapex" type="integer" value="500" min="1" label="Width of output image" /> |
33 <param name="shapey" type="integer" value="500" optional="true" min="1" max="2000" label="Height of output image" /> | 38 <param name="shapey" type="integer" value="500" min="1" label="Height of output image" /> |
34 <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" /> | 39 <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Tabular list of points has header" /> |
35 <param name="invert_xy" type="boolean" checked="false" falsevalue="" truevalue="--invert_xy True" optional="true" label="Inverts x and y in CSV point file" /> | 40 <param name="swap_xy" type="boolean" checked="false" falsevalue="" truevalue="--swap_xy True" optional="true" label="Swap X and Y coordinates" /> |
36 </inputs> | 41 </inputs> |
37 <outputs> | 42 <outputs> |
38 <data name="output" format="tiff" /> | 43 <data name="output" format="tiff" /> |
39 </outputs> | 44 </outputs> |
40 <tests> | 45 <tests> |
46 <!-- TSV without header --> | |
41 <test> | 47 <test> |
42 <param name="input" value="points.tsv" /> | 48 <param name="input" value="input1.tsv" /> |
43 <param name="shapex" value="20" /> | 49 <param name="shapex" value="30" /> |
44 <param name="shapey" value="30" /> | 50 <param name="shapey" value="20" /> |
45 <param name="has_header" value="false" /> | 51 <param name="has_header" value="false" /> |
46 <param name="invert_xy" value="true" /> | 52 <param name="swap_xy" value="true" /> |
47 <output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/> | 53 <expand macro="tests/binary_image_diff" name="output" value="output1.tif" ftype="tiff" /> |
54 </test> | |
55 <!-- TSV with header --> | |
56 <test> | |
57 <param name="input" value="input2.tsv" /> | |
58 <param name="shapex" value="205" /> | |
59 <param name="shapey" value="84" /> | |
60 <param name="has_header" value="true" /> | |
61 <param name="swap_xy" value="false" /> | |
62 <expand macro="tests/binary_image_diff" name="output" value="output2.tif" ftype="tiff" /> | |
48 </test> | 63 </test> |
49 </tests> | 64 </tests> |
50 <help> | 65 <help> |
51 | 66 |
52 This tool converts a CSV list of points to a binary image by rasterizing the point coordinates. | 67 **Converts a tabular list of points to a binary image by rasterizing the point coordinates.** |
53 | 68 |
54 The created image is a single-channel image with 16 bits per pixel (unsigned integer). | 69 The created image is a single-channel image with 16 bits per pixel (unsigned integer). |
55 The points are rasterized with value 32767 (white). | 70 The points are rasterized with value 65535 (white). |
56 Pixels not corresponding to any points in the CSV are assigned the value 0 (black). | 71 Pixels not corresponding to any points in the tabular file are assigned the value 0 (black). |
72 | |
73 The tabular list of points can either be header-less. | |
74 In this case, the first and second columns are expected to be the X and Y coordinates, respectively. | |
75 Otherwise, if a header is present, it is searched for the following column names: | |
76 | |
77 - ``pos_x`` or ``POS_X``: This column corresponds to the X coordinates. | |
78 - ``pos_y`` or ``POS_Y``: This column corresponds to the Y coordinates. | |
79 - If a ``radius`` or ``RADIUS`` column is present, | |
80 then the points will be rasterized as circles of the corresponding radii. | |
57 | 81 |
58 </help> | 82 </help> |
59 <citations> | 83 <citations> |
60 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> | 84 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
61 </citations> | 85 </citations> |