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comparison silac_analyzer.xml @ 2:cf0d72c7b482 draft

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author galaxyp
date Fri, 10 May 2013 17:31:05 -0400
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1:5c65f8116244 2:cf0d72c7b482
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 ) &lt; observed_ratio &lt; ( 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>