diff peak_picker_hi_res.xml @ 0:ba86fd127f5a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peak_picker_hi_res.xml	Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,39 @@
+<tool id="openms_peak_picker_hi_res" version="0.1" name="Peak Peaker (Hi Res)">
+  <description>
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command>
+    openms_wrapper.py --executable 'PeakPickerHiRes' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${input}
+out=${out}
+algorithm!signal_to_noise=${signal_to_noise}
+algorithm!ms1_only=${ms1_only}
+</configfile>
+  </configfiles>  
+  <inputs>
+    <param format="mzML" name="input" type="data" label="Input profile peak list"/>
+    <param type="float" name="signal_to_noise" value="1" label="Signal-to-noise ratio" help="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" />
+    <param type="boolean" name="ms1_only" label="MS1 Only" help="If checked, peak picking is only applied to MS1 scans. Other scans are copied to the output without changes." />
+  </inputs>
+  <outputs>
+    <data format="mzML" name="out" />
+  </outputs>
+  <help>
+**What it does**
+
+This peak-picking algorithm detects ion signals in raw data and reconstructs the corresponding peak shape by cubic spline interpolation. Signal detection depends on the signal-to-noise ratio which is adjustable by the user (see parameter signal_to_noise). A picked peak's m/z and intensity value is given by the maximum of the underlying peak spline. Please notice that this method is still experimental since it has not been tested thoroughly yet.
+
+The algorithm used by this tool is best suited for high-resolution MS data (FT-ICR-MS, Orbitrap). In high-resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. These properties faciliate a fast computation of picked peaks so that even large data sets can be processed very quickly.
+
+**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>