view mahotas_features.xml @ 0:43bf7c3775f3 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit 6dd3802614ab7940792e184944fc90d78c71cf51

<tool id="mahotas_features" name="mahotas-features" version="0.6">
  <requirements>
    <requirement type="package">mahotas</requirement>
    <requirement type="package">pillow</requirement>
    <requirement type="package">numpy</requirement>
  </requirements>
  <description>Compute features using mahotas</description>
  <stdio>
    <exit_code level="fatal" range="1:"/>
  </stdio>
  <command><![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>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>