Mercurial > repos > galaxyp > openms
comparison feature_linker_unlabeled_qt.xml @ 4:1183846e70a1 draft
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author | galaxyp |
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date | Wed, 19 Jun 2013 13:15:44 -0400 |
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3:8fa16707e162 | 4:1183846e70a1 |
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1 <tool id="openms_feature_linker_unlabeled_qt" version="0.1.0" name="Feature Linker (Unlabeled QT)"> | |
2 <description> | |
3 Groups corresponding features from multiple maps using a QT clustering approach. | |
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 'FeatureLinkerUnlabeledQT' --config $config | |
12 </command> | |
13 <configfiles> | |
14 <configfile name="config">[simple_options] | |
15 in=${",".join(map(str, $inputs))} | |
16 out=$output | |
17 #if $type.input_type == "consensusxml" | |
18 $keep_subelements | |
19 #end if | |
20 $ignore_charge | |
21 $use_identifications | |
22 algorithm!distance_RT!max_difference=$rt_max_difference | |
23 algorithm!distance_MZ!max_difference=$mz_max_difference | |
24 algorithm!distance_MZ!unit=$mz_max_difference_unit | |
25 #if $advanced.specify | |
26 algorithm!distance_RT!weight=$advanced.rt_weight | |
27 algorithm!distance_MZ!weight=$advanced.mz_weight | |
28 algorithm!distance_intensity!weight=$advanced.intensity_weight | |
29 algorithm!distance_RT!exponent=$advanced.rt_exponent | |
30 algorithm!distance_MZ!exponent=$advanced.mz_exponent | |
31 algorithm!distance_intensity!exponent=$advanced.intensity_exponent | |
32 #end if | |
33 </configfile> | |
34 </configfiles> | |
35 <inputs> | |
36 <expand macro="feature_linker_input" /> | |
37 | |
38 <expand macro="feature_linker_algorithm_options" /> | |
39 </inputs> | |
40 <outputs> | |
41 <data format="consensusxml" name="output" /> | |
42 </outputs> | |
43 <help> | |
44 **What it does** | |
45 | |
46 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. | |
47 | |
48 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. | |
49 | |
50 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. | |
51 | |
52 **Citation** | |
53 | |
54 For the underlying tool, please cite ``Weisser et al.: An automated pipeline for high-throughput label-free quantitative proteomics (J. Proteome Res., 2013, PMID: 23391308).`` | |
55 | |
56 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms | |
57 </help> | |
58 </tool> |