annotate mahotas_features.xml @ 1:0c76d029dbe3 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d

<tool id="ip_mahotas_features" name="Compute image features" version="0.7-2">
    <description>with Mahotas</description>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="biii">mahotas-feature-computation</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="1.4.3">mahotas</requirement>
        <requirement type="package" version="4.0.0">pillow</requirement>
        <requirement type="package" version="1.12">numpy</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements> 
    <command detect_errors="aggressive"><![CDATA[mahotas-features.py
#set files = '" "'.join( [ str( $file ) for $file in $inputs ] )
"${files}"

--output $output
--convert-to-bw $convertbw
$haralick 
$lbp 
--clobber
#if $lbpradius and $lbpradius is not None:
--lbp-radius $lbpradius
#end if

#if $lbppoints and $lbppoints is not None:
--lbp-points $lbppoints
#end if]]></command>
    <inputs>
        <param name="inputs" type="data" format="tiff,png,jpg,bmp" multiple="True" label="Image files"/>
        <param name="convertbw" type="select" label="Convert color images to greyscale">
            <option value="no" selected="True">no</option>
            <option value="max">max projection</option>
            <option value="yes">yes</option>
        </param>
        <param checked="true" help="(--haralick)" label="Compute Haralick features" name="haralick" type="boolean" truevalue="--haralick" falsevalue=""/>
        <param checked="true" help="(--lbp)" label="Compute LBP (linear binary patterns) features" name="lbp" type="boolean" truevalue="--lbp" falsevalue=""/>
        <param help="(--lbp-radius)" label="Radius to use for LBP features" name="lbpradius" optional="true" type="integer" value="8"/>
        <param help="(--lbp-points)" label="Nr of points to use for LBP features" name="lbppoints" optional="true" type="integer" value="6"/>
    </inputs>
    <outputs>
        <data format="tsv" hidden="false" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="inputs" value="galaxyIcon_noText.png"/>
            <param name="haralick" value="--haralick" />
            <param name="lbp" value="--lbp" />
            <param name="convertbw" value="max" />
            <output name="output" file="features.tsv" ftype="tsv" lines_diff="2"/>
        </test>
    </tests>
    <help>
    **What it does**

    Mahotas is a computer vision and image processing library for Python. This tools computes features using mahotas.
    </help>
    <citations>
        <citation type="doi">10.5334/jors.ac</citation>
    </citations>
</tool>