annotate feature_finder_metabo.xml @ 6:42b843627623 draft default tip

Uploaded
author galaxyp
date Fri, 21 Jun 2013 17:01:53 -0400
parents cf0d72c7b482
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
1 <tool id="openms_feature_finder_metabo" version="0.1.0" name="Feature Finder (Metabolites)">
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
2 <description>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
3 Assembles metabolite features from singleton mass traces.
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
4 </description>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
5 <macros>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
6 <import>macros.xml</import>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
7 </macros>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
8 <expand macro="stdio" />
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
9 <expand macro="requires" />
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
10 <command interpreter="python">
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
11 openms_wrapper.py --executable 'FeatureFinderMetabo' --config $config
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
12 </command>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
13 <configfiles>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
14 <configfile name="config">[simple_options]
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
15 in=$input1
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
16 out=$output
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
17 </configfile>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
18 </configfiles>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
19 <inputs>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
20 <param name="input1" label="mzML Input" type="data" format="mzml" />
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
21 </inputs>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
22 <outputs>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
23 <data format="featurexml" name="output" />
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
24 </outputs>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
25 <help>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
26 **What it does**
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
27
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
28 Mass traces alone would allow for further analyzes such as metabolite ID or statistical evaluation. However, in general, monoisotopic mass traces are accompanied with satellite C13 peaks and thus may render the analysis more difficult. FeatureFinderMetabo fulfills a further data reduction step by assembling compatible mass traces to metabolite features (that is, mass traces all stemming from one metabolite). To this end, multiple metabolite hypotheses are formulated and scored according to how well differences in RT and m/z or intensity ratios match to those of theoretical isotope patterns.
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
29
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
30 **Citation**
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
31
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
32 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.``
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
33
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
34 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
35 </help>
cf0d72c7b482 Update.
galaxyp
parents:
diff changeset
36 </tool>