diff feature_finder_raw.xml @ 2:cf0d72c7b482 draft

Update.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/feature_finder_raw.xml	Fri May 10 17:31:05 2013 -0400
@@ -0,0 +1,44 @@
+<tool id="openms_feature_finder_raw" version="0.1.0" name="Feature Finder (Raw)">
+  <description>
+    Identifies peptide features in raw (i.e. profile) LC-MS data.
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio" />
+  <expand macro="requires" />
+  <command interpreter="python">
+    openms_wrapper.py --executable 'FeatureFinderRaw' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=$input1
+out=$output
+sample!charge=${min_charge}:${max_charge}
+sample!peaks_per_peptide=${min_peaks_per_peptide}:${max_peaks_per_peptide}
+algorithm!rt_threshold=$rt_threshold
+algorithm!rt_min=$rt_min
+algorithm!intensity_cutoff=$intensity_cutoff
+algorithm!intensity_correlation=$intensity_correlation
+algorithm!model_deviation=$model_deviation
+</configfile>
+  </configfiles>
+  <inputs>
+    <param name="input1" label="mzML Input" type="data" format="mzml" />
+    <expand macro="raw_feature_finder_params" />
+  </inputs>
+  <outputs>
+    <data format="featurexml" name="output" />
+  </outputs>
+  <help>
+**What it does**
+
+FeatureFinderRaw is a tool for the identification of peptide features in profile LC-MS data.
+
+**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>