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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
author imgteam
date Fri, 10 Nov 2023 14:23:28 +0000
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0c76d029dbe3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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1 <tool id="ip_mahotas_features" name="Compute image features" version="0.7-2">
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2 <description>with Mahotas</description>
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3 <edam_operations>
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4 <edam_operation>operation_3443</edam_operation>
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5 </edam_operations>
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6 <xrefs>
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7 <xref type="biii">mahotas-feature-computation</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="1.4.3">mahotas</requirement>
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11 <requirement type="package" version="4.0.0">pillow</requirement>
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12 <requirement type="package" version="1.12">numpy</requirement>
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0c76d029dbe3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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13 <requirement type="package" version="0.15.1">tifffile</requirement>
0c76d029dbe3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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14 </requirements>
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15 <command detect_errors="aggressive"><![CDATA[mahotas-features.py
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16 #set files = '" "'.join( [ str( $file ) for $file in $inputs ] )
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17 "${files}"
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18
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19 --output $output
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20 --convert-to-bw $convertbw
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21 $haralick
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22 $lbp
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23 --clobber
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24 #if $lbpradius and $lbpradius is not None:
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25 --lbp-radius $lbpradius
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26 #end if
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27
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28 #if $lbppoints and $lbppoints is not None:
7f3d9a1a0447 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 --lbp-points $lbppoints
7f3d9a1a0447 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 #end if]]></command>
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31 <inputs>
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32 <param name="inputs" type="data" format="tiff,png,jpg,bmp" multiple="True" label="Image files"/>
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33 <param name="convertbw" type="select" label="Convert color images to greyscale">
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34 <option value="no" selected="True">no</option>
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35 <option value="max">max projection</option>
7f3d9a1a0447 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 <option value="yes">yes</option>
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37 </param>
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38 <param checked="true" help="(--haralick)" label="Compute Haralick features" name="haralick" type="boolean" truevalue="--haralick" falsevalue=""/>
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39 <param checked="true" help="(--lbp)" label="Compute LBP (linear binary patterns) features" name="lbp" type="boolean" truevalue="--lbp" falsevalue=""/>
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40 <param help="(--lbp-radius)" label="Radius to use for LBP features" name="lbpradius" optional="true" type="integer" value="8"/>
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41 <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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42 </inputs>
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43 <outputs>
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44 <data format="tsv" hidden="false" name="output"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="inputs" value="galaxyIcon_noText.png"/>
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49 <param name="haralick" value="--haralick" />
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50 <param name="lbp" value="--lbp" />
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51 <param name="convertbw" value="max" />
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52 <output name="output" file="features.tsv" ftype="tsv" lines_diff="2"/>
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53 </test>
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54 </tests>
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55 <help>
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56 **What it does**
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57
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58 Mahotas is a computer vision and image processing library for Python. This tools computes features using mahotas.
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59 </help>
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60 <citations>
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61 <citation type="doi">10.5334/jors.ac</citation>
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62 </citations>
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63 </tool>