Mercurial > repos > galaxyp > openms
comparison feature_linker_unlabeled.xml @ 2:cf0d72c7b482 draft
Update.
| author | galaxyp |
|---|---|
| date | Fri, 10 May 2013 17:31:05 -0400 |
| parents | |
| 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> |