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annotate create_msp.xml @ 17:e1990c07bb5a draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
author tomnl
date Thu, 14 Jun 2018 09:25:22 -0400
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children 49e063070647
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1 <tool id="create_msp" name="Create MSP Files from msPurity" version="0.1.1">
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2 <description> </description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 </expand>
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10 <command interpreter="Rscript" ><![CDATA[
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11 create_msp.R
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12 --purity "$purity"
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13 --mode "$mode"
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14 --ppm "$ppm"
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15 ]]></command>
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16 <inputs>
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17 <param name="purity" type="data" format="rdata" label="msPurity frag4feature dataset" argument="--purity"/>
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18 <param name="mode" type="select" label="Spectra use mode (if precursor was fragmented in >1 scans)" help='WARNING: The averaging and max options are still being developed and will likely fail' argument="--mode">
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19 <option value="max" >Max Intensity</option>
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20 <option value="average">Weighted Average</option>
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21 <option value="all" selected="true">All</option>
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22 </param>
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23 <param name="ppm" optional="true" type="float" label="Allowed mass deviation between fragment MZs for spectra averaging (in ppm)" argument="--ppm"/>
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24 </inputs>
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25 <outputs>
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26 <data name="output" format="txt" label="log" />
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27 <data name="msp_out" format="msp" from_work_dir="outfile.msp" label="${purity.name} MSP file"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="mode" value="all"/>
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32 <param name="purity" value="lightpurity.RData"/>
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33 <output name="msp_out" file="input.msp"/>
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34 </test>
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36 </tests>
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37 <help><![CDATA[
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38 ------------------------------
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39 Create MSP Files from msPurity
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40 ------------------------------
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42 * TO-DO: Averaging functionality
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43 * TO-DO: Add citation for MSP
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44 * TO-DO: Add PRECURSORTYPE if adducts available
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45 * TO-DO: Create MSP from xcms/mzml files
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47 Description
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48 -----------
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49
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50 | This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format.
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51 | Linking each precursor with its corresponding fragmentation spectra and associating the index within the msPurity object as the name UID.
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52 | Currently, there are three different methods for extracting the data in case that more than one MSMS scan was acquired for the same precursor m/z. See Parameters.
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53
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54 Parameters
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55 ----------
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56
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57 **\1. msPurity frag4feature dataset**
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58
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59 Result object from msPurity purityA-frag4feature functions.
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61 **\2. Spectra use mode (if precursor was fragmented in >1 scans)**
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62
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63 * "Max Intensity" will only use the scan where the precursor m/z signal was maximal.
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64
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65 * "Weighted Average" will merge all the scans, group fragment m/z using a PPM deviation (see 3.) and weight the intensities based on the precursor intensity of that scan.
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66
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67 * "All" will generate a single entry in the MSP file for each MSMS scan independently.
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68
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69 **\3. PPM deviation for fragmentation spectra averaging**
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70
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71 Set the value only if you selected "Weighted Average" above, the PPM value is used to define the limits for m/z grouping into a single fragment.
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72 The weighting is based on the precursor intensity, meaning that the more intense the precursor signal was, the more intensity will its fragments contribute to the averaged spectra.
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73
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75 Developers and contributors
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76 ---------------------------
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78 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
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79 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
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80
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81 ]]></help>
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83 <expand macro="citations" >
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84 <citation type="doi">10.1186/s13321-016-0115-9</citation>
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85 </expand>
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86
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87 </tool>