annotate filter.xml @ 2:f70b215d155c draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab

<tool id="ip_filter_standard" name="Filter 2D image" version="0.0.3-3">
    <description>with scikit-image</description>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">scikit-image</xref>
        <xref type="biii">scikit-image</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="1.15.4">numpy</requirement>
        <requirement type="package" version="5.3.0">pillow</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
      <![CDATA[
        python '$__tool_directory__/filter_image.py' '$input' '$output' $filter_type $radius
      ]]>
    </command>
    <inputs>
        <param name="filter_type" type="select" label="Filter type">
          <option value="median" selected="True">Median</option>
          <option value="gaussian">Gaussian Blur</option>
          <option value="prewitt">Prewitt</option>
          <option value="sobel">Sobel</option>
          <option value="scharr">Scharr</option>
        </param>
        <param name="radius" type="integer" value="3" label="Radius/Sigma" />
        <param name="input" type="data" format="tiff" label="Source file" />
    </inputs>
    <outputs>
       <data format="tiff" name="output" />
    </outputs> 
    <tests>
      <test>
        <param name="input" value="sample.tif" />
        <output name="output" value="res.tif" ftype="tiff" compare="sim_size"/>
        <param name="filter_type" value="prewitt" />
        <param name="radius" value="4" />
      </test>
    </tests>
    <help>
    **What it does**

    Applies a standard filter to an image.
    </help>
    <citations>
       <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>