|
2
|
1 <tool id="silac_analyzer" version="0.1.0" name="SILACAnalyzer">
|
|
|
2 <description>
|
|
|
3 </description>
|
|
|
4 <macros>
|
|
|
5 <import>macros.xml</import>
|
|
|
6 </macros>
|
|
|
7 <expand macro="stdio" />
|
|
|
8 <expand macro="requires" />
|
|
|
9 <command interpreter="python">
|
|
|
10 openms_wrapper.py
|
|
|
11 --executable 'SILACAnalyzer' --config $config
|
|
|
12 </command>
|
|
|
13 <configfiles>
|
|
|
14 <configfile name="config">[simple_options]
|
|
|
15 in=$input1
|
|
|
16 out=$out
|
|
|
17 sample!labels=[${labels}]
|
|
|
18 sample!missed_cleavages=${missed_cleavages}
|
|
|
19 sample!charge=${min_charge}:${max_charge}
|
|
|
20 sample!peaks_per_peptide=${min_peaks_per_peptide}:${max_peaks_per_peptide}
|
|
|
21 algorithm!rt_threshold=$rt_threshold
|
|
|
22 algorithm!rt_min=$rt_min
|
|
|
23 algorithm!intensity_cutoff=$intensity_cutoff
|
|
|
24 algorithm!intensity_correlation=$intensity_correlation
|
|
|
25 algorithm!model_deviation=$model_deviation
|
|
|
26 </configfile>
|
|
|
27 </configfiles>
|
|
|
28 <inputs>
|
|
|
29 <param name="input1" type="data" format="mzml" label="Input peak list" />
|
|
|
30 <!-- TODO -->
|
|
|
31 <param name="labels" type="select" multiple="true" label="Labels">
|
|
|
32 <option value="Arg6" >Arg6</option>
|
|
|
33 <option value="Arg10">Arg10</option>
|
|
|
34 <option value="Lys4" >Lys4</option>
|
|
|
35 <option value="Lys6" >Lys6</option>
|
|
|
36 <option value="Lys8" >Lys8</option>
|
|
|
37 <option value="dICPL4" >dICPL4</option>
|
|
|
38 <option value="dICPL6" >dICPL6</option>
|
|
|
39 <option value="dICPL10" >dICPL10</option>
|
|
|
40 <option value="Methyl4" >Methyl4</option>
|
|
|
41 <option value="Methyl8" >Methyl8</option>
|
|
|
42 <option value="Methyl12" >Methyl12</option>
|
|
|
43 <option value="Methyl16" >Methyl16</option>
|
|
|
44 <option value="Methyl24" >Methyl24</option>
|
|
|
45 <option value="Methyl32" >Methyl32</option>
|
|
|
46 </param>
|
|
|
47 <param name="missed_cleavages" type="integer" value="2" label="Allowed Missed Cleavages" />
|
|
|
48 <expand macro="raw_feature_finder_params" />
|
|
|
49 <!--
|
|
|
50 <param name="rt_threshold" type="float" value="50" label="RT Threshold" help="Upper bound for the retention time [s] over which a characteristic peptide elutes." />
|
|
|
51 <param name="rt_min" type="float" value="0" label="RT Minimum" help="Lower bound for the retention time [s]." />
|
|
|
52 <param name="intensity_cutoff" type="float" value="10000" label="Intensity Cutoff" help="Lower bound for the intensity of isotopic peaks in a SILAC pattern." />
|
|
|
53 <param name="intensity_correlation" type="float" value="0.9" label="Intensity Correlation" help="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." />
|
|
|
54 <param name="model_deviation" type="float" value="6" label="Model Deviation" help="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation )." />
|
|
|
55 <param name="min_charge" type="integer" value="1" label="Minimum Charge" />
|
|
|
56 <param name="max_charge" type="integer" value="5" label="Maximum Charge" />
|
|
|
57 <param name="min_peaks_per_peptide" type="integer" value="3" label="Minimum Number of Peaks Per Peptide" />
|
|
|
58 <param name="max_peaks_per_peptide" type="integer" value="5" label="Maximum Number of Peaks Per Peptide" />
|
|
|
59 -->
|
|
|
60 </inputs>
|
|
|
61 <outputs>
|
|
|
62 <data format="consensusxml" name="out" />
|
|
|
63 </outputs>
|
|
|
64 <help>
|
|
|
65 **What it does**
|
|
|
66
|
|
|
67
|
|
|
68 **Citation**
|
|
|
69
|
|
|
70 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.`` and ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``.
|
|
|
71
|
|
|
72 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
|
|
|
73 </help>
|
|
|
74 </tool>
|
