Mercurial > repos > imgteam > bfconvert
changeset 4:10eed33aa9b2 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit e27798cf1f9eb7fd34bf9b6fce21f6825f3872a1
| author | imgteam |
|---|---|
| date | Wed, 30 Aug 2023 13:14:08 +0000 |
| parents | f3360fbeda64 |
| children | 85edbb7a436b |
| files | bfconvert.xml test-data/input.tiff test-data/input.tiff.png |
| diffstat | 3 files changed, 15 insertions(+), 7 deletions(-) [+] |
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--- a/bfconvert.xml Thu Sep 15 17:19:04 2022 +0000 +++ b/bfconvert.xml Wed Aug 30 13:14:08 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="ip_convertimage" name="Convert image" version="6.7.0+galaxy0"> +<tool id="ip_convertimage" name="Convert image" version="6.7.0+galaxy1"> <description>Convert image</description> <requirements> <requirement type="package" version="6.7.0">bftools</requirement> @@ -27,7 +27,7 @@ #if $tile_options['extract'] == 'True' -tilex $tile_options.tile_x -tiley $tile_options.tile_y #end if - #if $pyramid_options.generate == 'True' + #if $pyramid_options.generate == 'True' and $out_format not in ['png', 'jpg', 'eps', 'avi'] -pyramid-resolutions $pyramid_options.pyramid_resolutions -pyramid-scale $pyramid_options.pyramid_scale #end if @@ -36,7 +36,7 @@ #if $compression != 'False' -compression $compression #end if - '$input_file' './res.$out_format' && + '$input_file' './res.$out_format' && mv './res.$out_format' ./result_image ]]> </command> @@ -128,7 +128,7 @@ </when> </conditional> <conditional name="pyramid_options"> - <param label="Pyramid image" name="generate" type="select"> + <param label="Pyramid image" name="generate" type="select" help="Pyramids will be generated only if the selected output format supports pyramids (OME TIFF, JPEG 2000)."><!-- see: https://docs.openmicroscopy.org/bio-formats/6.7.0/supported-formats.html --> <option selected="True" value="True">Generate Pyramid</option> <option value="False">No Pyramid</option> </param> @@ -136,6 +136,7 @@ <param name="pyramid_resolutions" type="integer" value="4" label="Pyramid Resolutions"/> <param name="pyramid_scale" type="integer" value="2" label="Pyramid Scale" /> </when> + <when value="False" /> </conditional> <param name="bigtiff" label="Big TIFF" type="boolean" checked="false" truevalue="-bigtiff" falsevalue=""/> <param name="noflat" label="No Flatten" type="boolean" checked="true" truevalue="-noflat" falsevalue=""/> @@ -170,11 +171,18 @@ <test> <param name="input_file" value="input.png" /> <param name="out_format" value="ome.tiff" /> - <param name="pyramid_options.generate" value="True"/> - <param name="pyramid_options.pyramid_resolutions" value="4"/> - <param name="pyramid_options.pyramid_scale" value="2"/> + <conditional name="pyramid_options"> + <param name="generate" value="True"/> + <param name="pyramid_resolutions" value="4"/> + <param name="pyramid_scale" value="2"/> + </conditional> <output name="output" value="res.ome.tiff" ftype="ome.tiff" compare="sim_size"/> </test> + <test> + <param name="input_file" value="input.tiff" /> + <param name="out_format" value="png" /> + <output name="output" value="input.tiff.png" ftype="png" compare="sim_size"/> + </test> </tests> <help> **What it does**