Mercurial > repos > thomaswollmann > mahotas_features

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit 6dd3802614ab7940792e184944fc90d78c71cf51
author thomaswollmann
date Tue, 03 Jan 2017 04:36:37 -0500
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43bf7c3775f3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit 6dd3802614ab7940792e184944fc90d78c71cf51
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1 <tool id="mahotas_features" name="mahotas-features" version="0.6">
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2 <requirements>
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3 <requirement type="package">mahotas</requirement>
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4 <requirement type="package">pillow</requirement>
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5 <requirement type="package">numpy</requirement>
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6 </requirements>
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7 <description>Compute features using mahotas</description>
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8 <stdio>
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9 <exit_code level="fatal" range="1:"/>
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10 </stdio>
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11 <command><![CDATA[mahotas-features.py
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12 #set files = '" "'.join( [ str( $file ) for $file in $inputs ] )
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13 "${files}"
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14
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15 --output $output
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16 --convert-to-bw $convertbw
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17 $haralick
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18 $lbp
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19 --clobber
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20 #if $lbpradius and $lbpradius is not None:
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21 --lbp-radius $lbpradius
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22 #end if
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23
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24 #if $lbppoints and $lbppoints is not None:
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25 --lbp-points $lbppoints
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26 #end if]]></command>
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27 <inputs>
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28 <param name="inputs" type="data" format="tiff,png,jpg,bmp" multiple="True" label="Image files"/>
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29 <param name="convertbw" type="select" label="Convert color images to greyscale">
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30 <option value="no" selected="True">no</option>
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31 <option value="max">max projection</option>
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32 <option value="yes">yes</option>
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33 </param>
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34 <param checked="true" help="(--haralick)" label="Compute Haralick features" name="haralick" type="boolean" truevalue="--haralick" falsevalue=""/>
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35 <param checked="true" help="(--lbp)" label="Compute LBP (linear binary patterns) features" name="lbp" type="boolean" truevalue="--lbp" falsevalue=""/>
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36 <param help="(--lbp-radius)" label="Radius to use for LBP features" name="lbpradius" optional="true" type="integer" value="8"/>
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37 <param help="(--lbp-points)" label="Nr of points to use for LBP features" name="lbppoints" optional="true" type="integer" value="6"/>
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38 </inputs>
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39 <outputs>
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40 <data format="tsv" hidden="false" name="output"/>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="inputs" value="galaxyIcon_noText.png"/>
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45 <param name="haralick" value="--haralick" />
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46 <param name="lbp" value="--lbp" />
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47 <param name="convertbw" value="max" />
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48 <output name="output" file="features.tsv" ftype="tsv" lines_diff="2"/>
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49 </test>
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50 </tests>
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51 <help>Mahotas is a computer vision and image processing library for Python. This tools computes features using mahotas.</help>
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52 <citations>
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53 <citation type="doi">10.5334/jors.ac</citation>
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54 </citations>
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55 </tool>