Mercurial > repos > galaxyp > openms
comparison feature_linker_unlabeled.xml @ 2:cf0d72c7b482 draft
Update.
author | galaxyp |
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date | Fri, 10 May 2013 17:31:05 -0400 |
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children | 1183846e70a1 |
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1:5c65f8116244 | 2:cf0d72c7b482 |
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1 <tool id="openms_feature_linker_unlabeled" version="0.1.0" name="Feature Linker (Labeled)"> | |
2 <description> | |
3 Groups corresponding features from multiple maps. | |
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 'FeatureLinkedUnlabeled' --config $config | |
12 </command> | |
13 <configfiles> | |
14 <configfile name="config">[simple_options] | |
15 in=$input1 | |
16 out=$output | |
17 </configfile> | |
18 </configfiles> | |
19 <inputs> | |
20 <conditional name="type"> | |
21 <param name="input_type" type="select" label="Input Type"> | |
22 <option value="featurexml">Features (FeatureXML)</option> | |
23 <option value="consensusxml">Consensus (ConsensusXML)</option> | |
24 </param> | |
25 <when value="featurexml"> | |
26 <param format="featurexml" name="input1" type="data" label="Input Features" /> | |
27 </when> | |
28 <when value="consensusxml"> | |
29 <param format="consensusxml" name="input1" type="data" label="Input Consensus" /> | |
30 </when> | |
31 </conditional> | |
32 </inputs> | |
33 <outputs> | |
34 <data format="consensusxml" name="output" /> | |
35 </outputs> | |
36 <help> | |
37 **What it does** | |
38 | |
39 This tool provides an algorithm for grouping corresponding features in multiple runs of label-free experiments. For more details and algorithm-specific parameters (set in the INI file) see "Detailed Description" in the algorithm documentation or the INI file table below. | |
40 | |
41 FeatureLinkerUnlabeled takes several feature maps (featureXML files) and stores the corresponding features in a consensus map (consensusXML file). Feature maps can be created from MS experiments (peak data) using one of the FeatureFinder TOPP tools. | |
42 | |
43 Advanced users can convert the consensusXML generated by this tool to EDTA using FileConverter and plot the distribution of distances in RT (or m/z) between different input files (can be done in Excel). The distribution should be Gaussian-like with very few points beyond the tails. Points far away from the Gaussian indicate a too wide tolerance. A Gaussian with its left/right tail trimmed indicates a too narrow tolerance. | |
44 | |
45 **Citation** | |
46 | |
47 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.`` | |
48 | |
49 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms | |
50 </help> | |
51 </tool> |