comparison colorize_labels.xml @ 2:3aa2d054848a draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels commit c045f067a57e8308308cf6329060c7ccd3fc372f

1:43c80f3c3b60

<tool id="colorize_labels" name="Colorize label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>with NetworkX</description>
    <macros>
        <token name="@TOOL_VERSION@">3.2.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="3.2.1">networkx</requirement>
        <requirement type="package" version="1.22">numpy</requirement>
        <requirement type="package" version="0.18.1">scikit-image</requirement>
    </requirements>
    <command><![CDATA[
    

        <test>
            <param name="input" value="input1.tif" />
            <param name="radius" value="1" />
            <param name="bg_label" value="0" />
            <param name="bg_color" value="#5a5a5a" />
            <output name="output" value="output1.png" ftype="png" compare="sim_size" delta_frac="0.1" />
        </test>
        <test>
            <param name="input" value="input2.tif" />
            <param name="radius" value="10" />
            <param name="bg_label" value="0" />
            <param name="bg_color" value="#ffffff" />
            <output name="output" value="output2.png" ftype="png" compare="sim_size" delta_frac="0.1" />
        </test>
    </tests>
    <help>
        Colorize a 2-D label map for visualization using greedy coloring.

        Label maps are produced by segmentation and other image analysis steps.
        Direct inspection of label maps can be difficult,
        because labels usually correspond to gray values which are difficult to
        distinguish visually from each other and from the image background.
        To facilitate the visual inspection of label maps, this tools converts
        label maps to color images, by assigning each label a unique color.
    </help>
    <citations>
        <citation type="bibtex">
        @inproceedings{networkx,
          author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.},

2:3aa2d054848a

<tool id="colorize_labels" name="Colorize label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>with NetworkX</description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
        <token name="@TOOL_VERSION@">3.2.1</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <creator>
        <expand macro="creators/bmcv" />
    </creator>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">networkx</requirement>
        <requirement type="package" version="1.22">numpy</requirement>
        <requirement type="package" version="0.18.1">scikit-image</requirement>
    </requirements>
    <command><![CDATA[
    

        <test>
            <param name="input" value="input1.tif" />
            <param name="radius" value="1" />
            <param name="bg_label" value="0" />
            <param name="bg_color" value="#5a5a5a" />
            <expand macro="tests/intensity_image_diff" name="output" value="output1.png" ftype="png">
                <has_image_channels channels="3"/>
            </expand>
        </test>
        <test>
            <param name="input" value="input2.tif" />
            <param name="radius" value="10" />
            <param name="bg_label" value="0" />
            <param name="bg_color" value="#ffffff" />
            <expand macro="tests/intensity_image_diff" name="output" value="output2.png" ftype="png">
                <has_image_channels channels="3"/>
            </expand>
        </test>
    </tests>
    <help>

        **Colorizes a 2-D label map for visualization using greedy coloring.**

        Label maps are produced by segmentation and other image analysis steps.
        Direct inspection of label maps can be difficult,
        because labels usually correspond to gray values which are difficult to
        distinguish visually from each other and from the image background.
        To facilitate the visual inspection of label maps, this tools converts
        label maps to color images, by assigning each label a unique color.

    </help>
    <citations>
        <citation type="bibtex">
        @inproceedings{networkx,
          author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.},