comparison cellpose.xml @ 2:e5370bb71633 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 5846f23282167df28e6cc00e1bda31523b66b5b4

1:1857781df226

<tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.02">
    <description>with Cellpose</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <xml name="channel">
            <option value="0" selected="true">grayscale/None</option>
            <option value="1">red</option>
            <option value="2">green</option>
            <option value="3">blue</option>

        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
    </stdio>
    <version_command>echo "@VERSION@"</version_command>
    <command detect_errors="exit_code">
         <![CDATA[
        export CELLPOSE_LOCAL_MODELS_PATH='cellpose_models' &&
        mkdir -p segmentation &&
        ln -s '${img_in}' ./image.${img_in.ext} &&

        python '$__tool_directory__/cp_segmentation.py'

    </command>
    <configfiles>
        <inputs name="inputs" />
    </configfiles>
    <inputs>
        <param name="img_in" type="data" format="ome.tiff,tiff,jpeg,png" label="Choose the image file for segmention (usually after registration)"/>
        <param name="model_type" type="select" label="Choose the pre-trained model type">
            <option value="nuclei" selected="true">nuclei</option>
            <option value="cyto">cyto</option>
            <option value="cyto2">cyto2</option>
            <option value="cyto3">cyto3</option>

        <test expect_num_outputs="2">
            <param name="img_in" value="img02.png"/>
            <param name="model_type" value="cyto"/>
            <param name="chan" value="2"/>
            <param name="chan2" value="3"/>
            <param name="diameter" value="50"/>
            <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="image_diff"/>
            <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <param name="img_in" value="img02.png"/>

2:e5370bb71633

<tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.02">
    <description>with Cellpose</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <xml name="channel">
            <option value="0" selected="true">grayscale/None</option>
            <option value="1">red</option>
            <option value="2">green</option>
            <option value="3">blue</option>

        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
    </stdio>
    <version_command>echo "@VERSION@"</version_command>
    <command detect_errors="exit_code">
         <![CDATA[
        export MKL_NUM_THREADS=1 &&
        export CELLPOSE_LOCAL_MODELS_PATH='cellpose_models' &&
        mkdir -p segmentation &&
        ln -s '${img_in}' ./image.${img_in.ext} &&

        python '$__tool_directory__/cp_segmentation.py'

    </command>
    <configfiles>
        <inputs name="inputs" />
    </configfiles>
    <inputs>
        <param name="img_in" type="data" format="ome.tiff,tiff,jpg,png" label="Choose the image file for segmention (usually after registration)"/>
        <param name="model_type" type="select" label="Choose the pre-trained model type">
            <option value="nuclei" selected="true">nuclei</option>
            <option value="cyto">cyto</option>
            <option value="cyto2">cyto2</option>
            <option value="cyto3">cyto3</option>

        <test expect_num_outputs="2">
            <param name="img_in" value="img02.png"/>
            <param name="model_type" value="cyto"/>
            <param name="chan" value="2"/>
            <param name="chan2" value="3"/>
            <section name="options">
                <param name="diameter" value="50"/>
            </section>
            <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="image_diff"/>
            <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="2">
            <param name="img_in" value="img02.png"/>