Mercurial > repos > imgteam > overlay_images
changeset 3:22ff7c705a83 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 8cd85b185acbfaa9ee6f4e9a389abc1f7b7c44bb
| author | imgteam |
|---|---|
| date | Wed, 08 Nov 2023 19:57:15 +0000 |
| parents | b74693340624 |
| children | 37662cbf44b8 |
| files | overlay_images.xml test-data/test3.png test-data/test3.tif test-data/test4.png test-data/test4.tif |
| diffstat | 5 files changed, 28 insertions(+), 12 deletions(-) [+] |
line wrap: on
line diff
--- a/overlay_images.xml Thu Aug 10 07:29:34 2023 +0000 +++ b/overlay_images.xml Wed Nov 08 19:57:15 2023 +0000 @@ -1,5 +1,11 @@ -<tool id="ip_overlay_images" name="Overlay Images" version="0.0.3" profile="20.05"> - <description>for visualization</description> +<tool id="ip_overlay_images" name="Overlay images" version="0.0.3-3" profile="20.05"> + <description></description> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">galaxy_image_analysis</xref> + </xrefs> <requirements> <requirement type="package" version="0.18.1">scikit-image</requirement> <requirement type="package" version="3.3.4">matplotlib</requirement> @@ -9,7 +15,12 @@ <command detect_errors="aggressive"> <![CDATA[ python '$__tool_directory__/overlay_images.py' - '$method_option.im1' '$method_option.im2' ./output.tif + '$method_option.im1' '$method_option.im2' + #if $method_option.method == "seg_contour" + ./output.png + #else + ./output.tif + #end if --method $method_option.method #if $method_option.method == "blending" --alpha $method_option.alpha @@ -48,38 +59,43 @@ </conditional> </inputs> <outputs> - <data format="tiff" name="out" from_work_dir="output.tif" /> + <data format="tiff" name="out_tiff" from_work_dir="output.tif" label="${tool.name} on ${on_string} output:tiff"> + <filter>method_option['method'] != 'seg_contour'</filter> + </data> + <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string} output:png"> + <filter>method_option['method'] == 'seg_contour'</filter> + </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="im1" value="mask1.tif"/> <param name="im2" value="mask1r.tif"/> <param name="method" value="coloc_vis"/> - <output name="out" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + <output name="out_tiff" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> </test> - <test> + <test expect_num_outputs="1"> <param name="im1" value="mask1.tif"/> <param name="im2" value="mask1r.tif"/> <param name="method" value="blending"/> <param name="alpha" value="0.3"/> - <output name="out" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + <output name="out_tiff" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> </test> - <test> + <test expect_num_outputs="1"> <param name="im1" value="sample1.tif"/> <param name="im2" value="mask1.tif"/> <param name="method" value="seg_contour"/> <param name="thickness" value="2"/> <param name="color" value="#ff0000"/> <param name="show_label" value="--show_label"/> - <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + <output name="out_png" value="test3.png" ftype="png" compare="sim_size" delta_frac="0.1"/> </test> - <test> + <test expect_num_outputs="1"> <param name="im1" value="sample1.tif"/> <param name="im2" value="mask2.tif"/> <param name="method" value="seg_contour"/> <param name="thickness" value="2"/> <param name="color" value="#ff0000"/> - <output name="out" value="test4.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/> </test> </tests> <help>