Mercurial > repos > recetox > recetox_msfinder
annotate recetox_msfinder.xml @ 1:29fc1af350f5 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit 7fc8ad942c34ccd1f80cfc67bfb0254631bac16c
author | recetox |
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date | Thu, 02 Feb 2023 09:19:40 +0000 |
parents | 7cda9aef13f3 |
children | 42ec41fe2329 |
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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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1 <tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy0"> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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2 <description>Annotation of fragment peaks in mass spectral libraries.</description> |
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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 <macros> |
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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 <import>macros.xml</import> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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5 </macros> |
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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 <expand macro="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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7 |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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8 <expand macro="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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9 <command> |
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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 <![CDATA[ |
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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 sh ${write_param} && |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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12 mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o "$annotated_data" |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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13 ]]> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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14 </command> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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15 |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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16 <configfiles> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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17 <configfile name="write_param"> |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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18 printf "%s\n" "Ms2Tolerance=$Ms2Tolerance" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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19 "IsTmsMeoxDerivative=$IsTmsMeoxDerivative" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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20 "RelativeAbundanceCutOff=$RelativeAbundanceCutOff" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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21 "Ms1Tolerance=$Ms1Tolerance" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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22 "MassToleranceType=$MassToleranceType" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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23 "StructurePredictionTimeOut=$StructurePredictionTimeOut" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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24 "LewisAndSeniorCheck=$LewisAndSeniorCheck" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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25 "IsUseRtForFilteringCandidates=False" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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26 "RtToleranceForStructureElucidation=2.5" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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27 "IsUsePredictedRtForStructureElucidation=False" \ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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28 "Coeff_RtPrediction=-1" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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29 "Intercept_RtPrediction=-1" \ |
7cda9aef13f3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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30 "IsUseRtInchikeyLibrary=True" \ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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31 "IsUsePredictedCcsForStructureElucidation=False" \ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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32 "IsUseCcsForFilteringCandidates=True" \ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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33 "CcsToleranceForStructureElucidation=10" \ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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34 "CanExcuteMS2AdductSearch=False" \ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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35 "IsUseXlogpPrediction=False" >MSFINDER.INI |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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36 </configfile> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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37 </configfiles> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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38 |
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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 <inputs> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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40 <expand macro="input" /> |
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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 <expand macro="parameter" /> |
1
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit 7fc8ad942c34ccd1f80cfc67bfb0254631bac16c
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42 <!-- <section name="element_selection" title="Element Selection" expanded="true" help="Generate formula candidates that just contain the elements selected by the users."> |
0
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43 <expand macro="element_check_parameter" /> |
1
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44 </section> --> |
0
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45 </inputs> |
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46 |
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47 <outputs> |
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48 <expand macro="output" /> |
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49 </outputs> |
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50 |
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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 <tests> |
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52 <test> |
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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="input_data" value="test.msp" ftype="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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54 <output name="annotated_data" file="out.msp" lines_diff="16 " /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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55 <!-- This is set to 16 since msfinder sometimes places double bonds between certain atoms and sometimes not - there are 16 such cases in this file. --> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
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56 |
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57 </test> |
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58 </tests> |
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59 |
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60 <help> |
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61 <![CDATA[ |
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62 @HELP@ |
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63 ]]> |
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64 </help> |
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65 |
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66 <citations> |
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67 <expand macro="citations" /> |
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68 </citations> |
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69 </tool> |