Mercurial > repos > imgteam > clip_image
changeset 1:eb5a84e77beb draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
| author | imgteam |
|---|---|
| date | Sun, 04 Jan 2026 22:20:07 +0000 |
| parents | 969840610383 |
| children | |
| files | clip_image.xml |
| diffstat | 1 files changed, 31 insertions(+), 49 deletions(-) [+] |
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--- a/clip_image.xml Sun Jan 04 20:30:27 2026 +0000 +++ b/clip_image.xml Sun Jan 04 22:20:07 2026 +0000 @@ -1,4 +1,4 @@ -<tool id="clip_image" name="Clip image intensities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> +<tool id="clip_image" name="Clip image intensities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1"> <description>with giatools</description> <macros> <import>creators.xml</import> @@ -6,15 +6,7 @@ <token name="@TOOL_VERSION@">0.7.3</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="bound" tokens="name,label,help"> - <param name="@NAME@" type="float" label="@LABEL@" help="@HELP@"/> - </xml> - <xml name="lower_bound"> - <expand macro="bound" name="lower_bound" label="Lower bound" - help="Image intensities below this value will be set to this value."/> - </xml> - <xml name="upper_bound"> - <expand macro="bound" name="upper_bound" label="Upper bound" - help="Image intensities above this value will be set to this value."/> + <param name="@NAME@" type="float" optional="true" label="@LABEL@" help="@HELP@"/> </xml> </macros> <creator> @@ -55,12 +47,12 @@ <configfile name="params"><![CDATA[ { - #if "lower" in str($setup.mode) - "lower_bound": $setup.lower_bound, + #if str($lower_bound) != "" + "lower_bound": $lower_bound, #end if - #if "upper" in str($setup.mode) - "upper_bound": $setup.upper_bound, + #if str($upper_bound) != "" + "upper_bound": $upper_bound, #end if "": null @@ -69,23 +61,10 @@ </configfiles> <inputs> <param name="input" type="data" format="tiff,zarr,png,jpg" label="Input image"/> - <conditional name="setup"> - <param name="mode" type="select" label="Clipping"> - <option value="lower-upper" selected="true">Clip to lower and upper bounds</option> - <option value="lower">Clip to lower bound</option> - <option value="upper">Clip to upper bound</option> - </param> - <when value="lower-upper"> - <expand macro="lower_bound"/> - <expand macro="upper_bound"/> - </when> - <when value="lower"> - <expand macro="lower_bound"/> - </when> - <when value="upper"> - <expand macro="upper_bound"/> - </when> - </conditional> + <expand macro="bound" name="lower_bound" label="Lower bound" + help="Image intensities below this value will be set to this value."/> + <expand macro="bound" name="upper_bound" label="Upper bound" + help="Image intensities above this value will be set to this value."/> </inputs> <outputs> <data format="tiff" name="output" from_work_dir="output.tiff"/> @@ -93,10 +72,7 @@ <tests> <test> <param name="input" value="input/input4_float16.tiff"/> - <conditional name="setup"> - <param name="mode" value="lower"/> - <param name="lower_bound" value="0.5"/> - </conditional> + <param name="lower_bound" value="0.5"/> <expand macro="tests/intensity_image_diff" name="output" value="output/input4.tiff" ftype="tiff"/> <assert_stdout> <has_line line="[input] Input image axes: ZYX"/> @@ -112,10 +88,7 @@ </test> <test> <param name="input" value="input/input5.jpg"/> - <conditional name="setup"> - <param name="mode" value="upper"/> - <param name="upper_bound" value="100.5"/> - </conditional> + <param name="upper_bound" value="100.5"/> <expand macro="tests/intensity_image_diff" name="output" value="output/input5.tiff" ftype="tiff"/> <assert_stdout> <has_line line="[input] Input image axes: YXC"/> @@ -129,22 +102,16 @@ </test> <test expect_failure="true"> <param name="input" value="input/input5.jpg"/> - <conditional name="setup"> - <param name="mode" value="lower-upper"/> - <param name="lower_bound" value="60"/> - <param name="upper_bound" value="50"/> - </conditional> + <param name="lower_bound" value="60"/> + <param name="upper_bound" value="50"/> <assert_stderr> <has_line line="Lower bound (60) must be less or equal compared to the upper bound (50)."/> </assert_stderr> </test> <test> <param name="input" value="input/input6_yx.zarr"/> - <conditional name="setup"> - <param name="mode" value="lower-upper"/> - <param name="lower_bound" value="-21.5"/> - <param name="upper_bound" value="101.5"/> - </conditional> + <param name="lower_bound" value="-21.5"/> + <param name="upper_bound" value="101.5"/> <expand macro="tests/intensity_image_diff" name="output" value="output/input6.tiff" ftype="tiff"/> <assert_stdout> <has_line line="[input] Input image axes: YX"/> @@ -158,6 +125,21 @@ <has_line line="[output] Output image resolution=(1.0, 1.0), unit='um'"/> </assert_stdout> </test> + <test> + <param name="input" value="input/input4_float16.tiff"/> + <expand macro="tests/intensity_image_diff" name="output" value="input/input4_float16.tiff" ftype="tiff"/> + <assert_stdout> + <has_line line="[input] Input image axes: ZYX"/> + <has_line line="[input] Input image shape: (10, 15, 18)"/> + <has_line line="[input] Input image dtype: float16"/> + <has_line line="[input] Input image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/> + <has_line line="Applying clipping: [-inf, inf]"/> + <has_line line="[output] Output image axes: ZYX"/> + <has_line line="[output] Output image shape: (10, 15, 18)"/> + <has_line line="[output] Output image dtype: float16"/> + <has_line line="[output] Output image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/> + </assert_stdout> + </test> </tests> <help>