Mercurial > repos > recetox > recetox_msfinder
annotate macros.xml @ 3:d1f44632f206 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit 14d90155d2579b399ad04010dcade97aa8543d30
author | recetox |
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date | Sat, 21 Oct 2023 12:31:00 +0000 |
parents | 42ec41fe2329 |
children | ae66b58846cd |
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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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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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2 <token name="@TOOL_VERSION@">v3.5.2</token> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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3 <xml name="requirements"> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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4 <requirements> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit 7fc8ad942c34ccd1f80cfc67bfb0254631bac16c
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5 <container type="docker">recetox/recetox-msfinder:v3.5.2-rcx0</container> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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6 </requirements> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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7 </xml> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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8 <xml name="creator"> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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9 <creator> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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10 <person |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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11 givenName="Zargham" |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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12 familyName="Ahmad" |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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13 url="https://github.com/zargham-ahmad" |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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14 identifier="0000-0002-6096-224X" /> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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15 <organization |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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16 url="https://www.recetox.muni.cz/" |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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17 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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18 name="RECETOX MUNI" /> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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19 </creator> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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20 </xml> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit 14d90155d2579b399ad04010dcade97aa8543d30
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21 <xml name="refs"> |
d1f44632f206
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit 14d90155d2579b399ad04010dcade97aa8543d30
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22 <xrefs> |
d1f44632f206
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit 14d90155d2579b399ad04010dcade97aa8543d30
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23 <xref type="bio.tools">recetox-msfinder</xref> |
d1f44632f206
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit 14d90155d2579b399ad04010dcade97aa8543d30
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24 </xrefs> |
d1f44632f206
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit 14d90155d2579b399ad04010dcade97aa8543d30
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25 </xml> |
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7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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26 <xml name="input"> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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27 <param name="input_data" type="data" format="msp" label="Input mass spectral library file to which to add peak annotations." |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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28 help="Formula and InChI (or SMILES) codes are required to be present in the library file" /> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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29 </xml> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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30 <xml name="parameter"> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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31 <param type="float" value="0.01" name="Ms2Tolerance" label="Ms2Tolerance" help="The mass tolerance used for fragment peak matching and annotation." /> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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32 <param name="IsTmsMeoxDerivative" type="boolean" checked="False" truevalue="True" falsevalue="False" label="IsTmsMeoxDerivative" |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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33 help="Check TMS-MeOX derivative to use EIMS database; otherwise, MSMS database is used." /> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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34 <param type="integer" value="1" name="RelativeAbundanceCutOff" label="RelativeAbundanceCutOff" |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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35 help="Remove peaks with less than specified % relative intensity from the spectra." /> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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36 <param type="float" value="0.001" name="Ms1Tolerance" label="Ms1Tolerance" help="The precursor m/z tolerance to generate formula candidates." /> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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37 <param type="select" name="MassToleranceType" label="MassToleranceType" help="Da stands for Daltons (amu), and Ppm stands for parts per million"> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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38 <option value="Da" selected="True">Da</option> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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39 <option value="Ppm">Ppm</option> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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40 </param> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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41 <param type="integer" value="-1" name="StructurePredictionTimeOut" label="StructurePredictionTimeOut" help="Time out parameter, value of -1 means no timeout" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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42 <param name="LewisAndSeniorCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="LewisAndSeniorCheck" |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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43 help="Generate formula candidates that match the valence rules of formula elements." /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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44 </xml> |
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45 <!-- Element Checks <xml name="element_check_parameter"> |
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46 <param name="Ocheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Ocheck" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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47 <param name="Ncheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Ncheck" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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48 <param name="Pcheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Pcheck" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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49 <param name="Scheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Scheck" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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50 <param name="Fcheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Fcheck" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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51 <param name="ClCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="ClCheck" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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52 <param name="BrCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="BrCheck" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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53 <param name="Icheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Icheck" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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54 <param name="SiCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="SiCheck" /> |
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55 </xml> --> |
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56 <xml name="output"> |
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57 <data name="annotated_data" format="msp" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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58 </xml> |
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59 |
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60 <token name="@HELP@"><![CDATA[ |
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61 **Description** |
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62 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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63 MS-FINDER was launched as a universal program for compound annotation that supports EI-MS (GC/MS) and |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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64 MS/MS spectral mining. MS-FINDER provide solution for fragment annotations. The program can annotate |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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65 your unknowns by the public spectral databases such as MassBank, LipidBlast, and GNPS. MS-FINDER has |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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66 been developed as the collaborative work between Prof. Masanori Arita team (RIKEN, Reifycs Inc.) and |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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67 Prof. Oliver Fiehn team (UC Davis) supported by the JST/NSF SICORP Metabolomics for the low carbon society |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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68 project. |
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69 |
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70 This galaxy wrapper only peforms MS2 peak annotation given a correctly formatted mass spectral library file. |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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71 FORMULA, PRECURSORMZ and SMILES (or INCHI) metadata entries are required to be present in the input mass spectral library file. |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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72 Each spectrum has to be separated by a single blank line. |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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73 |
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74 For detailed documentation of the tool please visit https://mtbinfo-team.github.io/mtbinfo.github.io/MS-FINDER/tutorial |
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75 ]]> |
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76 </token> |
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77 |
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78 <xml name="citations"> |
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79 <citation type="doi">10.1021/acs.analchem.6b00770</citation> |
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80 </xml> |
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81 </macros> |