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comparison feature_finder_raw.xml @ 2:cf0d72c7b482 draft

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author galaxyp
date Fri, 10 May 2013 17:31:05 -0400
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1 <tool id="openms_feature_finder_raw" version="0.1.0" name="Feature Finder (Raw)">
2 <description>
3 Identifies peptide features in raw (i.e. profile) LC-MS data.
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio" />
9 <expand macro="requires" />
10 <command interpreter="python">
11 openms_wrapper.py --executable 'FeatureFinderRaw' --config $config
12 </command>
13 <configfiles>
14 <configfile name="config">[simple_options]
15 in=$input1
16 out=$output
17 sample!charge=${min_charge}:${max_charge}
18 sample!peaks_per_peptide=${min_peaks_per_peptide}:${max_peaks_per_peptide}
19 algorithm!rt_threshold=$rt_threshold
20 algorithm!rt_min=$rt_min
21 algorithm!intensity_cutoff=$intensity_cutoff
22 algorithm!intensity_correlation=$intensity_correlation
23 algorithm!model_deviation=$model_deviation
24 </configfile>
25 </configfiles>
26 <inputs>
27 <param name="input1" label="mzML Input" type="data" format="mzml" />
28 <expand macro="raw_feature_finder_params" />
29 </inputs>
30 <outputs>
31 <data format="featurexml" name="output" />
32 </outputs>
33 <help>
34 **What it does**
35
36 FeatureFinderRaw is a tool for the identification of peptide features in profile LC-MS data.
37
38 **Citation**
39
40 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.``
41
42 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
43 </help>
44 </tool>