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comparison silac_analyzer.xml @ 4:1183846e70a1 draft

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author galaxyp
date Wed, 19 Jun 2013 13:15:44 -0400
parents cf0d72c7b482
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3:8fa16707e162 4:1183846e70a1
25 algorithm!model_deviation=$model_deviation 25 algorithm!model_deviation=$model_deviation
26 </configfile> 26 </configfile>
27 </configfiles> 27 </configfiles>
28 <inputs> 28 <inputs>
29 <param name="input1" type="data" format="mzml" label="Input peak list" /> 29 <param name="input1" type="data" format="mzml" label="Input peak list" />
30 <!-- TODO -->
31 <param name="labels" type="select" multiple="true" label="Labels"> 30 <param name="labels" type="select" multiple="true" label="Labels">
32 <option value="Arg6" >Arg6</option> 31 <option value="Arg6" >Arg6</option>
33 <option value="Arg10">Arg10</option> 32 <option value="Arg10">Arg10</option>
34 <option value="Lys4" >Lys4</option> 33 <option value="Lys4" >Lys4</option>
35 <option value="Lys6" >Lys6</option> 34 <option value="Lys6" >Lys6</option>
44 <option value="Methyl24" >Methyl24</option> 43 <option value="Methyl24" >Methyl24</option>
45 <option value="Methyl32" >Methyl32</option> 44 <option value="Methyl32" >Methyl32</option>
46 </param> 45 </param>
47 <param name="missed_cleavages" type="integer" value="2" label="Allowed Missed Cleavages" /> 46 <param name="missed_cleavages" type="integer" value="2" label="Allowed Missed Cleavages" />
48 <expand macro="raw_feature_finder_params" /> 47 <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> 48 </inputs>
61 <outputs> 49 <outputs>
62 <data format="consensusxml" name="out" /> 50 <data format="consensusxml" name="out" />
63 </outputs> 51 </outputs>
64 <help> 52 <help>