Mercurial > repos > galaxyp > openms
diff noise_filter.xml @ 0:ba86fd127f5a draft
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author | galaxyp |
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date | Wed, 19 Dec 2012 00:32:25 -0500 |
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children | cf0d72c7b482 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/noise_filter.xml Wed Dec 19 00:32:25 2012 -0500 @@ -0,0 +1,48 @@ +<tool id="openms_noise_filter" version="0.1.0" name="Noise Filter"> + <description> + Utilize a filter to reduce the noise in an MS experiment. + </description> + <requirements> + <requirement type="package">openms</requirement> + </requirements> + <command interpreter="python"> + #if $filter.type == "gaussian" + #set $filter_exec = "NoiseFilterGaussian" + #elif $filter.type == "sgolay" + #set $filter_exec = "NoiseFilterSGolay" + #end if + openms_wrapper.py --executable '$filter_exec' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=${in} +out=${out} +</configfile> + </configfiles> + <inputs> + <param format="mzml" name="in" type="data" label="Input mzML"/> + <conditional name="filter"> + <param type="select" name="type" label="Filter Type"> + <option value="gaussian">Gaussian</option> + <option value="sgolay">Savitzky Golay</option> + </param> + </conditional> + </inputs> + <outputs> + <data format="mzml" name="out" /> + </outputs> + <help> +**What it does** + +TODO: Document + +http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterSGolay.html +http://ftp.mi.fu-berlin.de/OpenMS/doc-1.9-official/html/TOPP_NoiseFilterGaussian.html + +**Citation** + +For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>