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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="TMTAnalyzer" name="TMTAnalyzer" version="1.12.0">
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3 <description>Calculates TMT quantitative values for peptides</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">TMTAnalyzer</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>TMTAnalyzer
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -out_stats ${param_out_stats}
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15 -threads \${GALAXY_SLOTS:-24}
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16 -id_pool ${param_id_pool}
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17 -algorithm:Extraction:select_activation ${param_select_activation}
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18 -algorithm:Extraction:reporter_mass_shift ${param_reporter_mass_shift}
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19 -algorithm:Extraction:channel_active ${param_channel_active}
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20 -algorithm:Quantification:channel_reference ${param_channel_reference}
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21 #if $adv_opts.adv_opts_selector=='advanced':
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22 -out_mzq ${adv_opts.param_out_mzq}
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23 -algorithm:Quantification:isotope_correction:tmt-6plex ${adv_opts.param_tmt-6plex}
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24 ${adv_opts.param_do_normalization}
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25 -algorithm:MetaInformation:Program ${adv_opts.param_Program}
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26 #end if
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27 </command>
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28 <inputs>
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29 <param name="param_in" type="data" format="mzML" optional="False" label="input raw/picked data file " help="(-in)"/>
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30 <param name="param_id_pool" type="text" size="20" label="ID pool file to DocumentID's for all generated output files. Disabled by default. (Set to 'main' to use /home/thouwaar/Projects/OpenMS/share/OpenMS/IDPool/IDPool.txt)" help="(-id_pool)"/>
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31 <param name="param_select_activation" type="select" optional="True" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ). Set to empty string if you want to disable filtering." help="(-select_activation)">
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32 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
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33 <option value="Post-source decay">Post-source decay</option>
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34 <option value="Plasma desorption">Plasma desorption</option>
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35 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
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36 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
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37 <option value="Electron capture dissociation">Electron capture dissociation</option>
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38 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
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39 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
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40 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
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41 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
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42 <option value="Photodissociation">Photodissociation</option>
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43 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
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44 <option value=""></option>
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45 </param>
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46 <param name="param_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position." help="(-reporter_mass_shift)"/>
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47 <param name="param_channel_active" type="text" size="20" value="126:liver 131:lung" label="Each channel that was used in the experiment and its description (126-131 for TMT-6-plex) in format <channel>:<name>, e.g. "114:myref","115:liver"." help="(-channel_active)"/>
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48 <param name="param_channel_reference" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)." help="(-channel_reference)"/>
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49 <expand macro="advanced_options">
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50 <param name="param_tmt-6plex" type="text" size="20" value="126:0/0/0/0 127:0/0/0/0 128:0/0/0/0 129:0/0/0/0 130:0/0/0/0 131:0/0/0/0" label="Override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'." help="(-tmt-6plex)"/>
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51 <param name="param_do_normalization" type="boolean" truevalue="-algorithm:Quantification:do_normalization true" falsevalue="-algorithm:Quantification:do_normalization false" checked="false" optional="True" label="Normalize channels? Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!" help="(-do_normalization)"/>
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52 <param name="param_Program" type="text" size="20" value="OpenMS::TMTAnalyzer" label="" help="(-Program)"/>
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53 </expand>
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54 </inputs>
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55 <outputs>
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56 <data name="param_out" label="output consensusXML file with quantitative information" format="consensusXML"/>
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57 <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/>
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58 <data name="param_out_stats" label="output statistics as tab-separated file (readable by R or Excel or ...)" format="data"/>
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59 </outputs>
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60 <help>**What it does**
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61
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62 Calculates TMT quantitative values for peptides
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63
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64
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65 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html
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66
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67 @REFERENCES@
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68 </help>
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69 </tool>
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