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1 <tool id="silac_analyzer" version="0.1.0" name="SILACAnalyzer">
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2 <description>
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3 </description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="stdio" />
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8 <expand macro="requires" />
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9 <command interpreter="python">
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10 openms_wrapper.py
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11 --executable 'SILACAnalyzer' --config $config
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12 </command>
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13 <configfiles>
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14 <configfile name="config">[simple_options]
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15 in=$input1
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16 out=$out
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17 sample!labels=[${labels}]
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18 sample!missed_cleavages=${missed_cleavages}
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19 sample!charge=${min_charge}:${max_charge}
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20 sample!peaks_per_peptide=${min_peaks_per_peptide}:${max_peaks_per_peptide}
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21 algorithm!rt_threshold=$rt_threshold
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22 algorithm!rt_min=$rt_min
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23 algorithm!intensity_cutoff=$intensity_cutoff
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24 algorithm!intensity_correlation=$intensity_correlation
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25 algorithm!model_deviation=$model_deviation
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26 </configfile>
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27 </configfiles>
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28 <inputs>
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29 <param name="input1" type="data" format="mzml" label="Input peak list" />
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30 <param name="labels" type="select" multiple="true" label="Labels">
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31 <option value="Arg6" >Arg6</option>
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32 <option value="Arg10">Arg10</option>
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33 <option value="Lys4" >Lys4</option>
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34 <option value="Lys6" >Lys6</option>
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35 <option value="Lys8" >Lys8</option>
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36 <option value="dICPL4" >dICPL4</option>
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37 <option value="dICPL6" >dICPL6</option>
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38 <option value="dICPL10" >dICPL10</option>
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39 <option value="Methyl4" >Methyl4</option>
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40 <option value="Methyl8" >Methyl8</option>
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41 <option value="Methyl12" >Methyl12</option>
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42 <option value="Methyl16" >Methyl16</option>
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43 <option value="Methyl24" >Methyl24</option>
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44 <option value="Methyl32" >Methyl32</option>
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45 </param>
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46 <param name="missed_cleavages" type="integer" value="2" label="Allowed Missed Cleavages" />
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47 <expand macro="raw_feature_finder_params" />
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48 </inputs>
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49 <outputs>
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50 <data format="consensusxml" name="out" />
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51 </outputs>
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52 <help>
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53 **What it does**
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54
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55
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56 **Citation**
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57
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58 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.``.
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59
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60 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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61 </help>
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62 </tool>
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