Mercurial > repos > imgteam > overlay_images
comparison overlay_images.xml @ 4:37662cbf44b8 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
author | imgteam |
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date | Fri, 17 Nov 2023 23:34:57 +0000 |
parents | 22ff7c705a83 |
children | 002f7bad3e82 |
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3:22ff7c705a83 | 4:37662cbf44b8 |
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1 <tool id="ip_overlay_images" name="Overlay images" version="0.0.3-3" profile="20.05"> | 1 <tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
2 <description></description> | 2 <description></description> |
3 <macros> | |
4 <token name="@TOOL_VERSION@">0.0.4</token> | |
5 <token name="@VERSION_SUFFIX@">0</token> | |
6 </macros> | |
3 <edam_operations> | 7 <edam_operations> |
4 <edam_operation>operation_3443</edam_operation> | 8 <edam_operation>operation_3443</edam_operation> |
5 </edam_operations> | 9 </edam_operations> |
6 <xrefs> | 10 <xrefs> |
7 <xref type="bio.tools">galaxy_image_analysis</xref> | 11 <xref type="bio.tools">galaxy_image_analysis</xref> |
79 <param name="method" value="blending"/> | 83 <param name="method" value="blending"/> |
80 <param name="alpha" value="0.3"/> | 84 <param name="alpha" value="0.3"/> |
81 <output name="out_tiff" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> | 85 <output name="out_tiff" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> |
82 </test> | 86 </test> |
83 <test expect_num_outputs="1"> | 87 <test expect_num_outputs="1"> |
84 <param name="im1" value="sample1.tif"/> | 88 <param name="im1" value="sample1_uint8.tif"/> |
85 <param name="im2" value="mask1.tif"/> | 89 <param name="im2" value="mask1.tif"/> |
86 <param name="method" value="seg_contour"/> | 90 <param name="method" value="seg_contour"/> |
87 <param name="thickness" value="2"/> | 91 <param name="thickness" value="2"/> |
88 <param name="color" value="#ff0000"/> | 92 <param name="color" value="#ff0000"/> |
89 <param name="show_label" value="--show_label"/> | 93 <param name="show_label" value="--show_label"/> |
90 <output name="out_png" value="test3.png" ftype="png" compare="sim_size" delta_frac="0.1"/> | 94 <output name="out_png" value="test3.png" ftype="png" compare="sim_size" delta_frac="0.1"/> |
91 </test> | 95 </test> |
92 <test expect_num_outputs="1"> | 96 <test expect_num_outputs="1"><!-- segemtation overlay, 8bit test --> |
93 <param name="im1" value="sample1.tif"/> | 97 <param name="im1" value="sample1_uint8.tif"/> |
98 <param name="im2" value="mask2.tif"/> | |
99 <param name="method" value="seg_contour"/> | |
100 <param name="thickness" value="2"/> | |
101 <param name="color" value="#ff0000"/> | |
102 <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/> | |
103 </test> | |
104 <test expect_num_outputs="1"><!-- segmentation overlay, 16bit test --> | |
105 <param name="im1" value="sample1_uint16.tif"/> | |
94 <param name="im2" value="mask2.tif"/> | 106 <param name="im2" value="mask2.tif"/> |
95 <param name="method" value="seg_contour"/> | 107 <param name="method" value="seg_contour"/> |
96 <param name="thickness" value="2"/> | 108 <param name="thickness" value="2"/> |
97 <param name="color" value="#ff0000"/> | 109 <param name="color" value="#ff0000"/> |
98 <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/> | 110 <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/> |
99 </test> | 111 </test> |
100 </tests> | 112 </tests> |
101 <help> | 113 <help> |
102 **What it does** | 114 <![CDATA[ |
103 | 115 This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. |
104 This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. | 116 ]]> |
105 </help> | 117 </help> |
106 <citations> | 118 <citations> |
107 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> | 119 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
108 </citations> | 120 </citations> |
109 </tool> | 121 </tool> |