comparison projective_transformation.xml @ 6:2f504e075496 draft

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

5:f5744f0e5a81

<tool id="ip_projective_transformation" name="Performs projective transformation with/without labels" version="0.1.2-2" profile="20.05"> 
    <description></description>
    <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="0.18.1">scikit-image</requirement>
        <requirement type="package" version="1.2.4">pandas</requirement>
        <requirement type="package" version="1.20.2">numpy</requirement>
        <requirement type="package" version="1.6.2">scipy</requirement>
        <requirement type="package" version="2020.10.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
        ln -s '$moving' ./in.${moving.ext} && 
        python '$__tool_directory__/projective_transformation.py'

        ./out.${moving.ext}
        && mv ./out.${moving.ext} ./result_image
    ]]>
    </command>
    <inputs>
        <param name="moving" type="data" format="tiff,png" label="Moving image (to be transformed)" />
        <param name="fixed" type="data" format="tiff,png" label="Fixed image (the reference)" />
        <param name="tmat" type="data" format="tabular" label="Transformation matrix" />
    </inputs>
    <outputs>
        <data name="warped" format_source="moving" metadata_source="moving" from_work_dir="result_image" />
    </outputs>
    <tests>
        <test>
            <param name="fixed" value="fixed.png"/>
            <param name="moving" value="moving.png"/>
            <param name="tmat" value="tmat.tsv"/>
            <output name="warped" value="moving_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" />
        </test>
        <test>
            <param name="fixed" value="fixed_rgb.png"/>
            <param name="moving" value="moving_rgb.png"/>
            <param name="tmat" value="tmat.tsv"/>
            <output name="warped" value="moving_rgb_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" />
        </test>
        <test>
            <param name="fixed" value="multi_f.tif"/>
            <param name="moving" value="multi_m.tif"/>
            <param name="tmat" value="tmat.tsv"/>
            <output name="warped" value="multi_m_warped.tif" ftype="tiff" compare="sim_size" delta_frac="0.1" />
      </test>
    </tests>
    <help>

**What it does**

    This tool performs a projective transformation of the moving 2D image so that it fits the fixed 2D image. 
    Multi-channel and RGB images are supported.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>

6:2f504e075496

<tool id="ip_projective_transformation" name="Perform projective transformation of an image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 
    <description></description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
        <token name="@TOOL_VERSION@">0.1.2</token>
        <token name="@VERSION_SUFFIX@">3</token>
    </macros>
    <creator>
        <expand macro="creators/bmcv"/>
    </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="0.18.3">scikit-image</requirement>
        <requirement type="package" version="1.2.4">pandas</requirement>
        <requirement type="package" version="1.24.4">numpy</requirement>
        <requirement type="package" version="1.10.1">scipy</requirement>
        <requirement type="package" version="2021.7.2">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
        ln -s '$moving' ./in.${moving.ext} && 
        python '$__tool_directory__/projective_transformation.py'

        ./out.${moving.ext}
        && mv ./out.${moving.ext} ./result_image
    ]]>
    </command>
    <inputs>
        <param name="moving" type="data" format="tiff,png" label="Moving image" help="The image to be transformed." />
        <param name="fixed" type="data" format="tiff,png" label="Fixed image" help="The reference image." />
        <param name="tmat" type="data" format="tabular" label="Transformation matrix" help="Homogeneous transformation matrix (3⨉3)." />
    </inputs>
    <outputs>
        <data name="warped" format_source="moving" metadata_source="moving" from_work_dir="result_image" />
    </outputs>
    <tests>
        <test>
            <param name="fixed" value="fixed.png"/>
            <param name="moving" value="moving.png"/>
            <param name="tmat" value="tmat.tsv"/>
            <expand macro="tests/intensity_image_diff" name="warped" value="moving_warped.png" ftype="png"/>
        </test>
        <test>
            <param name="fixed" value="fixed_rgb.png"/>
            <param name="moving" value="moving_rgb.png"/>
            <param name="tmat" value="tmat.tsv"/>
            <expand macro="tests/intensity_image_diff" name="warped" value="moving_rgb_warped.png" ftype="png"/>
        </test>
        <test>
            <param name="fixed" value="multi_f.tif"/>
            <param name="moving" value="multi_m.tif"/>
            <param name="tmat" value="tmat.tsv"/>
            <expand macro="tests/intensity_image_diff" name="warped" value="multi_m_warped.tif" ftype="tiff"/>
      </test>
    </tests>
    <help>

        **Performs projective transformation.**

        This tool performs a projective transformation of 2-D image into the coordinate system of another 2-D image. 
        Multi-channel images are supported (e.g., RGB).

    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>