Mercurial > repos > recetox > recetox_msfinder

annotate macros.xml @ 0:cb4a8b1e744e draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
author recetox
date Tue, 13 Dec 2022 13:26:17 +0000
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cb4a8b1e744e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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1 <macros>
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2 <token name="@TOOL_VERSION@">3.5.2</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <container type="docker">recetox/recetox-msfinder:3.5.2-0</container>
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6 </requirements>
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7 </xml>
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8 <xml name="creator">
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9 <creator>
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10 <person
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11 givenName="Zargham"
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12 familyName="Ahmad"
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13 url="https://github.com/zargham-ahmad"
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14 identifier="0000-0002-6096-224X" />
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15 <organization
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16 url="https://www.recetox.muni.cz/"
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17 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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18 name="RECETOX MUNI" />
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19 </creator>
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20 </xml>
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21 <xml name="input">
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22 <param name="input_data" type="data" format="msp" label="Input mass spectral library file to which to add peak annotations."
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23 help="Formula and InChI (or SMILES) codes are required to be present in the library file" />
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24 </xml>
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25 <xml name="parameter">
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26 <param type="float" value="0.01" name="Ms2Tolerance" label="Ms2Tolerance" help="The mass tolerance used for fragment peak matching and annotation." />
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27 <param name="IsTmsMeoxDerivative" type="boolean" checked="False" truevalue="True" falsevalue="False" label="IsTmsMeoxDerivative"
cb4a8b1e744e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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28 help="Check TMS-MeOX derivative to use EIMS database; otherwise, MSMS database is used." />
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29 <param type="integer" value="1" name="RelativeAbundanceCutOff" label="RelativeAbundanceCutOff"
cb4a8b1e744e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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30 help="Remove peaks with less than specified % relative intensity from the spectra." />
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31 <param type="float" value="0.001" name="Ms1Tolerance" label="Ms1Tolerance" help="The precursor m/z tolerance to generate formula candidates." />
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32 <param type="select" name="MassToleranceType" label="MassToleranceType" help="Da stands for Daltons (amu), and Ppm stands for parts per million">
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33 <option value="Da" selected="True">Da</option>
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34 <option value="Ppm">Ppm</option>
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35 </param>
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36 <param type="integer" value="-1" name="StructurePredictionTimeOut" label="StructurePredictionTimeOut" help="Time out parameter, value of -1 means no timeout" />
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37 <param name="LewisAndSeniorCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="LewisAndSeniorCheck"
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38 help="Generate formula candidates that match the valence rules of formula elements." />
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39 </xml>
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40 <xml name="element_check_parameter">
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41 <!-- Element Checks -->
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42 <param name="Ocheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Ocheck" />
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43 <param name="Ncheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Ncheck" />
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44 <param name="Pcheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Pcheck" />
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45 <param name="Scheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Scheck" />
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46 <param name="Fcheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Fcheck" />
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47 <param name="ClCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="ClCheck" />
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48 <param name="BrCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="BrCheck" />
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49 <param name="Icheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Icheck" />
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50 <param name="SiCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="SiCheck" />
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51 </xml>
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52 <xml name="output">
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53 <data name="annotated_data" format="msp" />
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54 </xml>
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55
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56 <token name="@HELP@"><![CDATA[
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57 **Description**
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58
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59 MS-FINDER was launched as a universal program for compound annotation that supports EI-MS (GC/MS) and
cb4a8b1e744e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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60 MS/MS spectral mining. MS-FINDER provide solution for fragment annotations. The program can annotate
cb4a8b1e744e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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61 your unknowns by the public spectral databases such as MassBank, LipidBlast, and GNPS. MS-FINDER has
cb4a8b1e744e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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62 been developed as the collaborative work between Prof. Masanori Arita team (RIKEN, Reifycs Inc.) and
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63 Prof. Oliver Fiehn team (UC Davis) supported by the JST/NSF SICORP Metabolomics for the low carbon society
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64 project.
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65
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66 This galaxy wrapper only peforms MS2 peak annotation given a correctly formatted mass spectral library file.
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67 FORMULA, PRECURSORMZ and SMILES (or INCHI) metadata entries are required to be present in the input mass spectral library file.
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68 Each spectrum has to be separated by a single blank line.
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69
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70 For detailed documentation of the tool please visit https://mtbinfo-team.github.io/mtbinfo.github.io/MS-FINDER/tutorial
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71 ]]>
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72 </token>
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73
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74 <xml name="citations">
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75 <citation type="doi">10.1021/acs.analchem.6b00770</citation>
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76 </xml>
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77 </macros>