Mercurial > repos > imgteam > split_image
diff split_image.xml @ 2:227e8928af6e draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
| author | imgteam |
|---|---|
| date | Fri, 12 Dec 2025 21:02:25 +0000 |
| parents | 4b7940d0c051 |
| children |
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--- a/split_image.xml Sat Apr 12 15:05:17 2025 +0000 +++ b/split_image.xml Fri Dec 12 21:02:25 2025 +0000 @@ -3,19 +3,23 @@ <macros> <import>creators.xml</import> <import>tests.xml</import> - <token name="@TOOL_VERSION@">2.2.3</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.3.5</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> <creator> <expand macro="creators/bmcv"/> + <expand macro="creators/kostrykin"/> </creator> <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="@TOOL_VERSION@">numpy</requirement> - <requirement type="package" version="0.4.0">giatools</requirement> - <requirement type="package" version="2024.7.24">tifffile</requirement> + <requirement type="package" version="0.5.2">giatools</requirement> + <requirement type="package" version="2025.10.16">tifffile</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ @@ -37,8 +41,10 @@ <option value="C" selected="true">C-axis (split the channels of an image or image sequence)</option> <option value="S">S-axis (split the samples of an image or image sequence)</option> <option value="Q">Q-axis (other or unknown axis)</option> + <option value="">Split dataset that contains multiple images (e.g., multi-series TIFF)</option> </param> - <param name="squeeze" type="boolean" checked="false" truevalue="--squeeze" falsevalue="" label="Squeeze result imags" help="Only axes with more than one element will be retained in the result images. Does not apply for X and Y axes." /> + <param name="squeeze" type="boolean" checked="false" truevalue="--squeeze" falsevalue="" label="Squeeze result images" + help="Only non-singleton axes (axes with more than one element) will be retained in the result images. This does not apply for the X and Y axes which always are retained." /> </inputs> <outputs> <collection type="list" name="output" label="Split ${on_string} along ${axis} axis"> @@ -57,6 +63,27 @@ <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="rgb1_g.tiff" ftype="tiff"/> <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_b.tiff" ftype="tiff"/> </output_collection> + <assert_stdout> + <has_line line="Input image axes: YXC"/> + <has_line line="Input image shape: (32, 32, 3)"/> + <has_line line="Writing 3 image(s)"/> + <has_line line="Output axes: YXC"/> + <has_line line="Output shape: (32, 32, 1)"/> + </assert_stdout> + </test> + <test> + <param name="input" value="rgb1.png" /> + <param name="axis" value="" /> + <param name="squeeze" value="false" /> + <output_collection name="output" type="list" count="1"> + <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1.tiff" ftype="tiff"/> + </output_collection> + <assert_stdout> + <has_line line="Not a TIFF file"/> + <has_line line="Writing 1 image(s)"/> + <has_line line="Output axes: YXC"/> + <has_line line="Output shape: (32, 32, 3)"/> + </assert_stdout> </test> <!-- TIFF tests --> @@ -68,6 +95,13 @@ <expand macro="tests/intensity_image_diff/element" name="01.tiff" value="zcyx_slice01.tiff" ftype="tiff"/> <expand macro="tests/intensity_image_diff/element" name="25.tiff" value="zcyx_slice25.tiff" ftype="tiff"/> </output_collection> + <assert_stdout> + <has_line line="Input image axes: ZCYX"/> + <has_line line="Input image shape: (25, 2, 50, 50)"/> + <has_line line="Writing 25 image(s)"/> + <has_line line="Output axes: ZCYX"/> + <has_line line="Output shape: (1, 2, 50, 50)"/> + </assert_stdout> </test> <test> <param name="input" value="qyx.tiff" /> @@ -77,6 +111,51 @@ <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="qyx_q1.tiff" ftype="tiff"/> <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="qyx_q2.tiff" ftype="tiff"/> </output_collection> + <assert_stdout> + <has_line line="Input image axes: QYX"/> + <has_line line="Input image shape: (2, 256, 256)"/> + <has_line line="Writing 2 image(s)"/> + <has_line line="Output axes: QYX"/> + <has_line line="Output shape: (1, 256, 256)"/> + </assert_stdout> + </test> + <test> + <param name="input" value="qyx.tiff" /> + <param name="axis" value="" /> + <param name="squeeze" value="false" /> + <output_collection name="output" type="list" count="1"> + <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="qyx.tiff" ftype="tiff"/> + </output_collection> + <assert_stdout> + <has_line line="Found TIFF with 1 series"/> + </assert_stdout> + </test> + + <!-- Test splitting multi-series TIFF --> + <test> + <param name="input" value="multiseries.ome.tiff" /> + <param name="axis" value="" /> + <param name="squeeze" value="false" /> + <output_collection name="output" type="list" count="6"> + <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="multiseries_series1.tiff" ftype="tiff"/> + <expand macro="tests/intensity_image_diff/element" name="6.tiff" value="multiseries_series6.tiff" ftype="tiff"/> + </output_collection> + <assert_stdout> + <has_line line="Found TIFF with 6 series"/> + <has_line line="Writing 6 image(s)"/> + <has_line line="Output 1 axes: CYX"/> + <has_line line="Output 1 shape: (4, 5, 5)"/> + <has_line line="Output 2 axes: CYX"/> + <has_line line="Output 2 shape: (4, 5, 5)"/> + <has_line line="Output 3 axes: CYX"/> + <has_line line="Output 3 shape: (4, 5, 5)"/> + <has_line line="Output 4 axes: CYX"/> + <has_line line="Output 4 shape: (4, 5, 5)"/> + <has_line line="Output 5 axes: CYX"/> + <has_line line="Output 5 shape: (4, 5, 5)"/> + <has_line line="Output 6 axes: CYX"/> + <has_line line="Output 6 shape: (4, 5, 5)"/> + </assert_stdout> </test> <!-- Test squeezing --> @@ -89,6 +168,13 @@ <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="rgb1_squeezed_g.tiff" ftype="tiff"/> <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_squeezed_b.tiff" ftype="tiff"/> </output_collection> + <assert_stdout> + <has_line line="Input image axes: YXC"/> + <has_line line="Input image shape: (32, 32, 3)"/> + <has_line line="Writing 3 image(s)"/> + <has_line line="Output axes: YX"/> + <has_line line="Output shape: (32, 32)"/> + </assert_stdout> </test> <!-- Test with missing axes --> @@ -99,6 +185,13 @@ <output_collection name="output" type="list" count="1"> <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_split_z.tiff" ftype="tiff"/> </output_collection> + <assert_stdout> + <has_line line="Input image axes: YXC"/> + <has_line line="Input image shape: (32, 32, 3)"/> + <has_line line="Writing 1 image(s)"/> + <has_line line="Output axes: YXC"/> + <has_line line="Output shape: (32, 32, 3)"/> + </assert_stdout> </test> </tests>