diff feature_finder_isotope_wavelet.xml @ 2:cf0d72c7b482 draft

Update.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/feature_finder_isotope_wavelet.xml	Fri May 10 17:31:05 2013 -0400
@@ -0,0 +1,41 @@
+<tool id="openms_feature_finder_isotope_wavelet" version="0.1.0" name="Feature Finder (Isotope Wavelet)">
+  <description>
+    The feature detection application for quantitation.
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio" />
+  <expand macro="requires" />
+  <command interpreter="python">
+    openms_wrapper.py --executable 'FeatureFinderIsotopeWavelet' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=$input1
+out=$output
+</configfile>
+  </configfiles>
+  <inputs>
+    <param name="input1" label="mzML Input" type="data" format="mzml" />
+  </inputs>
+  <outputs>
+    <data format="featurexml" name="output" />
+  </outputs>
+  <help>
+**What it does**
+
+This module identifies "features" in a LC/MS map. By feature, we understand a peptide in a MS sample that reveals a characteristic isotope distribution. The algorithm computes positions in rt and m/z dimension and a charge estimate of each peptide.
+
+The algorithm identifies pronounced regions of the data around so-called seeds. In the next step, we iteratively fit a model of the isotope profile and the retention time to these data points. Data points with a low probability under this model are removed from the feature region. The intensity of the feature is then given by the sum of the data points included in its regions.
+
+Note:
+that the wavelet transform is very slow on high-resolution spectra (i.e. FT, Orbitrap). We recommend to use a noise or intensity filter to remove spurious points first and to speed-up the feature detection process.
+
+**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>