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 |
|---|---|
| date | Fri, 17 Nov 2023 23:34:57 +0000 |
| parents | 22ff7c705a83 |
| children | 002f7bad3e82 |
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| 3:22ff7c705a83 | 4:37662cbf44b8 |
|---|---|
| 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> |