Mercurial > repos > thomaswollmann > mahotas_features
changeset 0:f2ed647d792c draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit b48e9075026da7cca0b91ccf621e8a899681aeff
| author | thomaswollmann |
|---|---|
| date | Sat, 31 Dec 2016 09:12:04 -0500 |
| parents | |
| children | a95f9d6ea1ca |
| files | mahotas_features.xml |
| diffstat | 1 files changed, 59 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mahotas_features.xml Sat Dec 31 09:12:04 2016 -0500 @@ -0,0 +1,59 @@ +<tool id="mahotas_features" name="mahotas-features" version="0.1"> + <requirements> + <requirement type="package" version="1.4.3">mahotas</requirement> + <requirement type="package">mahotas</requirement> + <requirement type="package">numpy</requirement> + </requirements> + <description>Compute features using mahotas</description> + <stdio> + <exit_code level="fatal" range="1:"/> + </stdio> + <version_command>python mahotas-features.py --version</version_command> + <command interpreter="python"><![CDATA[mahotas-features.py +#set repeat_var_1 = '" "'.join([ str($var.positional_1) for $var in $repeat_1 ]) +"$repeat_var_1" + + +#if $output and $output is not None: +--output $output +#end if +$clobber + +#if $convert-to-bw and $convert-to-bw is not None: +--convert-to-bw $convert-to-bw +#end if +$no-color +$haralick +$lbp + +#if $lbp-radius and $lbp-radius is not None: +--lbp-radius $lbp-radius +#end if + +#if $lbp-points and $lbp-points is not None: +--lbp-points $lbp-points +#end if +> $default]]></command> + <inputs> + <repeat min="1" name="repeat_1" title="repeat_title"> + <param area="false" label="Image files names" name="positional_1" type="text"/> + </repeat> + <param area="false" help="(--output)" label="Output file for feature files" name="output" optional="true" type="text" value="features.tsv"/> + <param checked="false" help="(--clobber)" label="Overwrite output file (if it exists)" name="clobber" type="boolean" truevalue="--clobber" falsevalue=""/> + <param area="false" help="(--convert-to-bw)" label="Convert color images to greyscale. Acceptable values: 	no: raises an error (default) 	max: use max projection 	yes: use rgb2gray" name="convert-to-bw" optional="true" type="text" value="no"/> + <param checked="false" help="(--no-color)" label="Do not print in color (for error and warning messages)" name="no-color" type="boolean" truevalue="--no-color" falsevalue=""/> + <param checked="false" help="(--haralick)" label="Compute Haralick features" name="haralick" type="boolean" truevalue="--haralick" falsevalue=""/> + <param checked="false" 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="lbp-radius" optional="true" type="integer" value="8"/> + <param help="(--lbp-points)" label="Nr of points to use for LBP features" name="lbp-points" optional="true" type="integer" value="6"/> + </inputs> + <outputs> + <data format="txt" hidden="false" name="default"/> + </outputs> + <help>Compute features using mahotas</help> + <tests> + </tests> + <citations> + <citation type="doi">10.5334/jors.ac</citation> + </citations> +</tool>