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Add tool: parse_image_metadata (#226)
* Add parse_image_metadata.xml * Fix * Add more outputs * Add .shed.yml * Update help and description * Clean up test-data * Clean up `expression` * Revert "Clean up test-data" This reverts commit fcfda53. * Fix test-data * Bump `GALAXY_BRANCH` to `release_25.1` * Bump `GALAXY_BRANCH` to `release_26.0` * Bump `profile` to `25.1` * Add `label` for each `output` * Add `jpg` support * Add test comments * Update `label`
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‎.github/workflows/ci.yaml‎

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workflow_dispatch:
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env:
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GALAXY_FORK: galaxyproject
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GALAXY_BRANCH: release_25.0
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GALAXY_BRANCH: release_26.0
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MAX_CHUNKS: 40
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jobs:
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setup:

‎.github/workflows/pr.yaml‎

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- '*'
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env:
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GALAXY_FORK: galaxyproject
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GALAXY_BRANCH: release_25.0
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GALAXY_BRANCH: release_26.0
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MAX_CHUNKS: 4
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MAX_FILE_SIZE: 1M
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concurrency:

‎tools/parse_image_metadata/.shed.yml‎

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categories:
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- Imaging
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description: Parse image metadata as parameter values (width, height, number of channels, etc.)
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long_description: |
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This tool can be used in workflows to parse parameter values from image metadata.
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name: parse_image_metadata
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owner: imgteam
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homepage_url: https://github.com/bmcv
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remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/parse_image_metadata/
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type: unrestricted

‎tools/parse_image_metadata/creators.xml‎

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../../macros/creators.xml

‎tools/parse_image_metadata/parse_image_metadata.xml‎

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<tool name="Parse value from image metadata" id="param_image_metadata" version="0.1.0" tool_type="expression" profile="25.1">
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<description/>
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<macros>
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<import>creators.xml</import>
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</macros>
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<creator>
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<expand macro="creators/bmcv"/>
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<expand macro="creators/kostrykin"/>
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</creator>
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<macros/>
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<edam_operations>
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<edam_operation>operation_3443</edam_operation>
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</edam_operations>
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<expression type="ecma5.1">
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{
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return {
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'width': parseInt($job.input1.metadata.width),
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'height': parseInt($job.input1.metadata.height),
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'channels': parseInt($job.input1.metadata.channels),
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'depth': parseInt($job.input1.metadata.depth),
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'frames': parseInt($job.input1.metadata.frames)
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};
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}
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</expression>
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<inputs>
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<param type="data" format="tiff,png,jpg" label="Input file to parse the metadata of" load_contents="0" name="input1"/>
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</inputs>
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<outputs>
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<output type="integer" name="width" from="width" label="Parse image width"/>
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<output type="integer" name="height" from="height" label="Parse image height"/>
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<output type="integer" name="channels" from="channels" label="Parse image channels"/>
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<output type="integer" name="depth" from="depth" label="Parse image depth"/>
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<output type="integer" name="frames" from="frames" label="Parse image frames"/>
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</outputs>
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<tests>
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<test expect_num_outputs="5">
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<!-- Test for PNG metadata -->
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<param name="input1" value="input_yxc.png"/>
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<output name="width">
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<assert_contents>
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<has_line line="265"/>
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</assert_contents>
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</output>
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<output name="height">
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<assert_contents>
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<has_line line="530"/>
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</assert_contents>
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</output>
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<output name="channels">
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<assert_contents>
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<has_line line="4"/>
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</assert_contents>
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</output>
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<output name="depth">
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<assert_contents>
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<has_line line="0"/>
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</assert_contents>
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</output>
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<output name="frames">
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<assert_contents>
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<has_line line="1"/>
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</assert_contents>
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</output>
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</test>
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<test expect_num_outputs="5">
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<!-- Test for TIFF metadata (with Z axis, without T axis) -->
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<param name="input1" value="input_yxz.tiff"/>
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<output name="width">
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<assert_contents>
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<has_line line="265"/>
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</assert_contents>
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</output>
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<output name="height">
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<assert_contents>
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<has_line line="530"/>
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</assert_contents>
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</output>
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<output name="channels">
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<assert_contents>
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<has_line line="0"/>
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</assert_contents>
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</output>
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<output name="depth">
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<assert_contents>
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<has_line line="4"/>
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</assert_contents>
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</output>
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<output name="frames">
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<assert_contents>
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<has_line line="0"/>
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</assert_contents>
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</output>
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</test>
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<test expect_num_outputs="5">
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<!-- Test for TIFF metadata (with T axis, without Z axis) -->
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<param name="input1" value="input_yxt.tiff"/>
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<output name="width">
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<assert_contents>
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<has_line line="265"/>
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</assert_contents>
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</output>
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<output name="height">
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<assert_contents>
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<has_line line="530"/>
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</assert_contents>
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</output>
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<output name="channels">
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<assert_contents>
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<has_line line="0"/>
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</assert_contents>
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</output>
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<output name="depth">
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<assert_contents>
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<has_line line="0"/>
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</assert_contents>
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</output>
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<output name="frames">
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<assert_contents>
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<has_line line="4"/>
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</assert_contents>
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</output>
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</test>
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<test expect_num_outputs="5">
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<!-- Test for JPG metadata -->
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<param name="input1" value="input_yxc.jpg"/>
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<output name="width">
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<assert_contents>
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<has_line line="10"/>
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</assert_contents>
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</output>
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<output name="height">
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<assert_contents>
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<has_line line="10"/>
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</assert_contents>
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</output>
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<output name="channels">
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<assert_contents>
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<has_line line="3"/>
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</assert_contents>
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</output>
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<output name="depth">
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<assert_contents>
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<has_line line="0"/>
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</assert_contents>
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</output>
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<output name="frames">
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<assert_contents>
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<has_line line="0"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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<help><![CDATA[
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**Parse image metadata as parameter values.**
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This tool can be used in workflows to parse parameter values from image metadata (e.g., width, height, etc.).
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]]></help>
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</tool>

‎tools/parse_image_metadata/test-data/input_yxc.jpg‎

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‎tools/parse_image_metadata/test-data/input_yxc.png‎

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‎tools/parse_image_metadata/test-data/input_yxt.tiff‎

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‎tools/parse_image_metadata/test-data/input_yxz.tiff‎

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