Mercurial > repos > thomaswollmann > mahotas_features
comparison mahotas_features.xml @ 0:43bf7c3775f3 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit 6dd3802614ab7940792e184944fc90d78c71cf51
| author | thomaswollmann |
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| date | Tue, 03 Jan 2017 04:36:37 -0500 |
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| -1:000000000000 | 0:43bf7c3775f3 |
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| 1 <tool id="mahotas_features" name="mahotas-features" version="0.6"> | |
| 2 <requirements> | |
| 3 <requirement type="package">mahotas</requirement> | |
| 4 <requirement type="package">pillow</requirement> | |
| 5 <requirement type="package">numpy</requirement> | |
| 6 </requirements> | |
| 7 <description>Compute features using mahotas</description> | |
| 8 <stdio> | |
| 9 <exit_code level="fatal" range="1:"/> | |
| 10 </stdio> | |
| 11 <command><![CDATA[mahotas-features.py | |
| 12 #set files = '" "'.join( [ str( $file ) for $file in $inputs ] ) | |
| 13 "${files}" | |
| 14 | |
| 15 --output $output | |
| 16 --convert-to-bw $convertbw | |
| 17 $haralick | |
| 18 $lbp | |
| 19 --clobber | |
| 20 #if $lbpradius and $lbpradius is not None: | |
| 21 --lbp-radius $lbpradius | |
| 22 #end if | |
| 23 | |
| 24 #if $lbppoints and $lbppoints is not None: | |
| 25 --lbp-points $lbppoints | |
| 26 #end if]]></command> | |
| 27 <inputs> | |
| 28 <param name="inputs" type="data" format="tiff,png,jpg,bmp" multiple="True" label="Image files"/> | |
| 29 <param name="convertbw" type="select" label="Convert color images to greyscale"> | |
| 30 <option value="no" selected="True">no</option> | |
| 31 <option value="max">max projection</option> | |
| 32 <option value="yes">yes</option> | |
| 33 </param> | |
| 34 <param checked="true" help="(--haralick)" label="Compute Haralick features" name="haralick" type="boolean" truevalue="--haralick" falsevalue=""/> | |
| 35 <param checked="true" help="(--lbp)" label="Compute LBP (linear binary patterns) features" name="lbp" type="boolean" truevalue="--lbp" falsevalue=""/> | |
| 36 <param help="(--lbp-radius)" label="Radius to use for LBP features" name="lbpradius" optional="true" type="integer" value="8"/> | |
| 37 <param help="(--lbp-points)" label="Nr of points to use for LBP features" name="lbppoints" optional="true" type="integer" value="6"/> | |
| 38 </inputs> | |
| 39 <outputs> | |
| 40 <data format="tsv" hidden="false" name="output"/> | |
| 41 </outputs> | |
| 42 <tests> | |
| 43 <test> | |
| 44 <param name="inputs" value="galaxyIcon_noText.png"/> | |
| 45 <param name="haralick" value="--haralick" /> | |
| 46 <param name="lbp" value="--lbp" /> | |
| 47 <param name="convertbw" value="max" /> | |
| 48 <output name="output" file="features.tsv" ftype="tsv" lines_diff="2"/> | |
| 49 </test> | |
| 50 </tests> | |
| 51 <help>Mahotas is a computer vision and image processing library for Python. This tools computes features using mahotas.</help> | |
| 52 <citations> | |
| 53 <citation type="doi">10.5334/jors.ac</citation> | |
| 54 </citations> | |
| 55 </tool> |