Mercurial > repos > computational-metabolomics > metfrag
annotate metfrag.xml @ 1:9ee2e2ceb2c9 draft
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 4378d616c184a24ef8cf8671bd7d68d9ce3876ac"
author | computational-metabolomics |
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date | Thu, 19 Mar 2020 06:04:18 -0400 |
parents | fd5c0b39569a |
children | f151ee133612 |
rev | line source |
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1
9ee2e2ceb2c9
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 4378d616c184a24ef8cf8671bd7d68d9ce3876ac"
computational-metabolomics
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1 <tool id="metfrag" name="MetFrag" version="2.4.5+galaxy2" profile="18.01"> |
0
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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2 <description> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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3 in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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4 </description> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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5 <macros> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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6 <import>macros.xml</import> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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7 </macros> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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8 <requirements> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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9 <requirement type="package" version="2.4.5">metfrag</requirement> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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10 </requirements> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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11 <stdio> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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12 <regex match="Cannot allocate memory" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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13 source="stderr" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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14 level="fatal_oom" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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15 description="Out of memory error occurred" /> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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16 </stdio> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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17 <command detect_errors="exit_code"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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18 <![CDATA[ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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19 python '$__tool_directory__/metfrag.py' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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20 --input_pth '$input' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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21 --result_pth '$results' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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22 --temp_dir './temp/' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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23 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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24 --cores_top_level \${GALAXY_SLOTS:-4} |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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25 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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26 --MetFragDatabaseType '$db_select.MetFragDatabaseType' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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27 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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28 #if $db_select.MetFragDatabaseType == 'LocalCSV': |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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29 --LocalDatabasePath '$db_select.LocalDatabasePath' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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30 #elif $db_select.MetFragDatabaseType == 'MetChem': |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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31 --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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32 #end if |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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33 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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34 --DatabaseSearchRelativeMassDeviation $DatabaseSearchRelativeMassDeviation |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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35 --FragmentPeakMatchRelativeMassDeviation $FragmentPeakMatchRelativeMassDeviation |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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36 --FragmentPeakMatchAbsoluteMassDeviation $FragmentPeakMatchAbsoluteMassDeviation |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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37 --polarity '$polarity' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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38 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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39 --MetFragScoreTypes '$suspectlist.MetFragScoreTypes' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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40 --MetFragScoreWeights '$suspectlist.MetFragScoreWeights' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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41 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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42 #if $suspectlist.suspectselector == 'includesuspects': |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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43 #if $suspectlist.includesuspects_default_cond: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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44 --ScoreSuspectLists '$__tool_directory__/UNPD_DB.inchikeys.txt' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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45 #else |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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46 --ScoreSuspectLists '$suspectlist.includesuspects_custom_cond.ScoreSuspectLists' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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47 #end if |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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48 #end if |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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49 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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50 --meta_select_col $meta_select_col |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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51 --minMSMSpeaks $minMSMSpeaks |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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52 --schema $schema |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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53 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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54 $PreProcessFilter.UnconnectedCompoundFilter |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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55 $PreProcessFilter.IsotopeFilter |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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56 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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57 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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58 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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59 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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60 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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61 --FilterIncludedElements '$PreProcessFilter.FilterIncludedElements' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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62 --FilterExcludedElements '$PreProcessFilter.FilterExcludedElements' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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63 --FilterIncludedExclusiveElements '$PreProcessFilter.FilterIncludedExclusiveElements' |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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64 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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65 $skip_invalid_adducts |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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66 --score_thrshld $PostProcessFilter.score_thrshld |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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67 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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68 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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69 ]]></command> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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70 <inputs> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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71 <param name="input" type="data" format="msp" label="MSP file (Output from Create MSP tool)"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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72 <conditional name="db_select"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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73 <param argument="--MetFragDatabaseType" type="select" label="Choose Compound Database"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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74 <option value="PubChem" selected="true">PubChem</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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75 <option value="KEGG">KEGG</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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76 <option value="LocalCSV">Local database (csv)</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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77 <option value="MetChem">MetChem</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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78 </param> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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79 <when value="MetChem"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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80 <param argument="--LocalMetChemDatabaseServerIp" type="text" label="MetChem URL"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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81 </when> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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82 <when value="LocalCSV"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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83 <param argument="--LocalDatabasePath" type="data" format="csv" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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84 label="Local database of compounds (CSV format)" /> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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85 </when> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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|
86 <when value="KEGG"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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87 <when value="PubChem"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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88 </conditional> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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89 <param argument="--DatabaseSearchRelativeMassDeviation" type="float" min="0" value="10" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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90 label="Relative Mass Deviation for database search (ppm)" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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91 help="A value in ppm that defines the deviation of theoretical masses in the database |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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92 vs. the measured masses"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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|
93 <param argument="--FragmentPeakMatchRelativeMassDeviation" type="float" min="0" value="5" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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|
94 label="Fragment Peak Match Relative Mass Deviation (ppm)" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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95 help="Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks" /> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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96 <param argument="--FragmentPeakMatchAbsoluteMassDeviation" type="float" min="0" value="0.001" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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97 label="Fragment Peak Match Absolute Mass Deviation (Da)" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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98 help="Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks" /> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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99 <param argument="--polarity" type="select" label="Polarity" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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100 help="The polarity used for the mode of acquisition"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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101 <option value="pos" selected="true">Positive</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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102 <option value="neg">Negative</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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103 </param> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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104 <param argument="--schema" type="select" label="Schema" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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105 help="The schema used for the MSP file (auto will try automatically determine the schema)"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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106 <option value="auto" selected="True">Auto</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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107 <option value="msp">Generic MSP</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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108 <option value="massbank">MassBank</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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109 </param> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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110 <param argument="--meta_select_col" type="select" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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111 label="Choose how additional metadata columns are extracted" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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112 help="The MetFrag output can have additional meta data columns added, these can be either extracted |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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113 from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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114 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and : |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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115 e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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116 <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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117 <option value="name_split">Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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118 <option value="all">Extra metadata columns from all MSP parameters</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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119 </param> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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120 <conditional name="suspectlist"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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121 <param name="suspectselector" type="select" label="Suspect list" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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122 help="Choose whether to include a suspect list"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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123 <option value="includesuspects" >Include suspect list</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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124 <option value="excludesuspects" selected="True">Do not include suspect list</option> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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125 </param> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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126 <when value="includesuspects"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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127 <conditional name="includesuspects_default_cond"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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128 <param name="includesuspects_default_bool" type="boolean" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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129 label="Use default list of suspect compounds?" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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130 help="Either provide a file containing a list of suspect compounds or a default file |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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131 of an aggregated list of in silico predicted MS/MS spectra of natural products |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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132 from the Universal Natural Products Database (http://pkuxxj.pku.edu.cn/UNPD/index.php). |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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133 The list is an aggregated version of the github repository https://github.com/oolonek/ISDB/tree/master/Data/dbs."/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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134 <when value="true"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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135 <when value="false"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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136 <param argument="--ScoreSuspectLists" type="data" format="txt" optional="True" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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137 label="Suspect list file" help="File containing a list of suspects inchikeys" /> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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138 </when> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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139 </conditional> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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140 <expand macro="metfrag_scoring"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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141 </when> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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142 <when value="excludesuspects"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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143 <expand macro="metfrag_scoring" suspectlistscore="False" weights="1.0,1.0"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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144 </when> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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145 </conditional> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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146 <param argument="--minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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147 <param argument="--skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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148 truevalue="--skip_invalid_adducts" falsevalue="" checked="true" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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149 help="If no adduct type is provided within the MSP file or if the adduct type is not usable |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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150 with MetFrag, set to 'yes' if these spectra should be skipped or 'no' if the default |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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151 of [M+H]+ for pos data or [M-H]- for neg data should be used"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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152 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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153 <param argument="--UnconnectedCompoundFilter" type="boolean" checked="false" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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154 truevalue="--UnconnectedCompoundFilter" falsevalue="" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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155 label="filter non-connected compounds (e.g. salts)" help=""/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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156 <param argument="--IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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157 falsevalue="" label="filter compounds containing non-standard isotopes" help=""/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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158 <param argument="--FilterMinimumElements" type="text" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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159 optional="true" label="Minimum Elements Filter" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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160 help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
161 2 nitrogens and 3 oxygens"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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162 <expand macro="text-alphanumeric-regex-validator"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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163 </param> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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164 <param argument="--FilterMaximumElements" type="text" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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165 optional="true" label="Maximum Elements Filter" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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166 help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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167 maximum 5 nitrogens and 7 oxygens"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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168 <expand macro="text-alphanumeric-regex-validator"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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169 </param> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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170 <param argument="--FilterSmartsInclusionList" type="text" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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171 optional="true" label="Include substructures" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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172 help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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173 containing benzene"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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174 <param argument="--FilterSmartsExclusionList" type="text" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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175 optional="true" label="Exclude substructures" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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176 help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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177 containing hydroxyl groups"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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178 <param argument="--FilterIncludedElements" type="text" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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179 optional="true" label="Include elements" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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180 help="Filter by presence of defined elements (other elements are allowed). |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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181 Ex: 'N,O' include compounds containing nitrogen and oxygen" > |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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182 <expand macro="text-alphanumeric-comma-regex-validator"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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183 </param> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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184 <param argument="--FilterIncludedExclusiveElements" type="text" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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185 optional="true" label="Include elements (exclusive)" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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186 help="Filter by presence of defined elements (no other elements are allowed). |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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187 Ex: 'N,O' include compounds only composed of nitrogen and oxygen" > |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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188 <expand macro="text-alphanumeric-comma-regex-validator"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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189 </param> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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190 <param argument="--FilterExcludedElements" type="text" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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191 optional="true" label="Exclude elements" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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192 help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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193 compounds including bromine or chlorine"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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194 <expand macro="text-alphanumeric-comma-regex-validator"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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195 </param> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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196 </section> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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197 <section name="PostProcessFilter" title="PostProcessing filters" expanded="False"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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198 <param argument="--score_thrshld" type="float" label="Threshold for score after MetFrag search" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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199 max="1" min="0" value="0"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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200 <param argument="--pctexplpeak_thrshld" type="float" label="Minimum percentage of explain peaks" |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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201 max="100" min="0" value="0"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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202 </section> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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203 </inputs> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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204 <outputs> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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205 <data name="results" format="tabular"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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206 </outputs> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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207 <tests> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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208 <test> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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209 <!-- Test "massbank" style data format --> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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210 <param name="input" value="massbank_format.txt"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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211 <param name="schema" value="massbank"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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212 <param name="skip_invalid_adducts" value="false"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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213 <param name="MetFragDatabaseType" value="PubChem"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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214 <param name="MetFragDatabaseType" value="LocalCSV"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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215 <param name="LocalDatabasePath" value="demo_db.csv"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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216 <output name="results" file="metfrag_massbank.tabular"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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217 </test> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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218 <test> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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219 <!-- Test "generic" style data format --> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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220 <param name="input" value="generic_format.msp"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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221 <param name="schema" value="msp"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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222 <param name="MetFragDatabaseType" value="PubChem"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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223 <param name="skip_invalid_adducts" value="false"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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224 <param name="MetFragDatabaseType" value="LocalCSV"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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225 <param name="LocalDatabasePath" value="demo_db.csv"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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226 <output name="results" file="metfrag_msp.tabular"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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227 </test> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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228 <test> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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229 <!-- Test PubChem API with "winter" dataset --> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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230 <param name="input" value="winter_pos.msp"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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231 <section name="PostProcessFilter"> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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232 <param name="score_thrshld" value="0.9"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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233 </section> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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234 <param name="MetFragDatabaseType" value="PubChem"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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235 <output name="results" file="winter_pos.tabular"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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236 </test> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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237 <test> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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238 <!-- Test actual MassBank data for Glucose --> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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239 <param name="input" value="RP022611.txt"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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240 <param name="MetFragDatabaseType" value="LocalCSV"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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241 <param name="LocalDatabasePath" value="demo_db.csv"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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242 <output name="results" file="RP022611.tabular"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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243 </test> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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244 <test> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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245 <!-- Test actual MassBank data for Glucose (all metadata columns in output--> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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246 <param name="input" value="RP022611.txt"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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247 <param name="schema" value="massbank"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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248 <param name="MetFragDatabaseType" value="LocalCSV"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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249 <param name="LocalDatabasePath" value="demo_db.csv"/> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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250 <param name="meta_select_col" value="all"/> |
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251 <output name="results" file="RP022611_all_col.tabular"/> |
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252 </test> |
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253 <test> |
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254 <!-- Test actual MassBank data for Glucose (include suspect list - default)--> |
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255 <param name="input" value="RP022611.txt"/> |
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256 <param name="schema" value="massbank"/> |
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257 <conditional name="suspectlist"> |
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258 <param name="suspectselector" value="includesuspects"/> |
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259 <conditional name="includesuspects_default_cond"> |
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260 <param name="includesuspects_default_bool" value="true"/> |
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261 </conditional> |
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262 </conditional> |
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263 <output name="results" file="RP022611_suspect_default.txt"/> |
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264 </test> |
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265 <test> |
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266 <!-- Test invalid adduct --> |
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267 <param name="input" value="invalid_adduct.msp"/> |
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268 <param name="skip_invalid_adducts" value="true"/> |
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269 <output name="results" file="invalid_adduct_result.txt" ftype="tabular"/> |
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270 </test> |
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271 </tests> |
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272 <help> |
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273 ------- |
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274 MetFrag |
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275 ------- |
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276 |
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277 Description |
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278 ----------- |
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279 |
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280 MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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281 a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases |
fd5c0b39569a
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282 are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak |
fd5c0b39569a
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283 matches gives hints to the quality of the candidate spectrum assignment. |
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284 |
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285 Website: http://ipb-halle.github.io/MetFrag/ |
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286 |
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287 Parameters |
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288 ---------- |
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289 |
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290 **\1. MSP file** |
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291 |
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292 MSP file created using *Create MSP* tool |
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293 |
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294 **\2a. MetFragDatabaseType (public databases)** |
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295 |
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296 * PubChem |
fd5c0b39569a
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297 |
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298 * KEGG |
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299 |
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300 |
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301 **\2b. MetFragDatabaseType (local CSV file database)** |
fd5c0b39569a
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302 |
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303 |
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304 Custom database file in CSV format with the following structure: |
fd5c0b39569a
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305 |
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306 +-------------+------------------+----------+---------------------------------------------+----------------------+---+ |
fd5c0b39569a
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307 | Identifier | MonoisotopicMass | SMILES | InChI | Name |...| |
fd5c0b39569a
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308 +-------------+------------------+----------+---------------------------------------------+----------------------+---+ |
fd5c0b39569a
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309 | HMDB0000123 | 75.03202841 | NCC(O)=O | InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) | Glycine |...| |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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310 +-------------+------------------+----------+---------------------------------------------+----------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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311 | HMDB0002151 | 78.0139355 | CS(C)=O | InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 | Dimethyl sulfoxide |...| |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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312 +-------------+------------------+----------+---------------------------------------------+----------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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313 | ... | ... | ... | ... | ... |...| |
fd5c0b39569a
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314 +-------------+------------------+----------+---------------------------------------------+----------------------+---+ |
fd5c0b39569a
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315 |
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316 |
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317 Table continued: |
fd5c0b39569a
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318 |
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319 +---+------------------+-----------------------------+------------------+------------+-------------+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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320 |...| MolecularFormula | InChIKey | InChIKey1 | InChIKey2 | InChIKey3 | |
fd5c0b39569a
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321 +---+------------------+-----------------------------+------------------+------------+-------------+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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322 |...| C2H5NO2 | DHMQDGOQFOQNFH-UHFFFAOYSA-N | DHMQDGOQFOQNFH | UHFFFAOYSA | N | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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323 +---+------------------+-----------------------------+------------------+------------+-------------+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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324 |...| C2H6OS | IAZDPXIOMUYVGZ-UHFFFAOYSA-N | IAZDPXIOMUYVGZ | UHFFFAOYSA | N | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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325 +---+------------------+-----------------------------+------------------+------------+-------------+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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326 |...| ... | ... | ... | ... | ... | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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327 +---+------------------+-----------------------------+------------------+------------+-------------+ |
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328 |
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329 |
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330 |
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331 **\2b. MetFragDatabaseType MetChem** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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332 |
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333 MetChem is a modified PubChem database and can be used in replace of PubChem |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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334 for performing API calls to the public PubChem instance. |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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335 |
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336 **\3. Database Search Relative Mass Deviation - ppm** |
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337 |
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338 A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses. |
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339 |
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340 **\4. Fragment Peak Match Relative Mass Deviation - ppm** |
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341 |
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342 Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks. |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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343 |
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344 **\5. Fragment Peak Match Absolute Mass Deviation (Da)** |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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345 |
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346 Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks. |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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347 |
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348 **\6. Polarity** |
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349 |
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350 The polarity used for the mode of acquisition. |
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351 |
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352 **\7. Schema** |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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353 |
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354 The Schema used by the MSP file (e.g. generic MSP format or MassBank format) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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355 |
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356 **\8. Suspect list** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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357 |
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358 Choose whether to include a file containing a list of suspects. |
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359 |
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360 **\9. MetFrag Score Types** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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361 |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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362 The type of scores MetFrac is using for the calculations. Please do not change the values unless you know what you are doing! |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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363 |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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364 **\10. MetFrag Score Weights** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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365 |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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366 The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100%. |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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367 |
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368 **\11. MetFrag Database Type** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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369 |
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370 Database to choose from. |
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371 |
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372 **\12. minMSMSpeaks** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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373 |
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374 Minimum MS/MS peaks within a MS/MS spectra to be used for the MetFrag calculation |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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375 |
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376 **\13. PreProcessFilter** |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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377 |
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378 Various filters can be performed on the potential compounds prior to predicting the in silico spectra |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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379 |
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380 **\14. PostProcessFilter** |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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381 |
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382 To make the output more manageble results below certain criteria can be removed from the various filters can be |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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383 performed on the potential compounds prior to predicting the in silico spectra |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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384 |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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385 Output |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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386 ------- |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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387 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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388 These columns are derived from any metadata in the MSP input file (additional columns can included if they are recorded in the MSP file) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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389 |
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390 +-------------+--------------------------------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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391 | adduct | name |...| |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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392 +-------------+--------------------------------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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393 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...| |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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394 +-------------+--------------------------------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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395 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...| |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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396 +-------------+--------------------------------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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397 | ... | ... |...| |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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398 +-------------+--------------------------------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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399 |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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400 Table continued (these columns are derived from the MetFrag result): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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401 |
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402 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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403 |...| sample_name | ExplPeaks | FormulasOfExplPeaks | ... | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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404 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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405 |...| 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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406 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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407 |...| 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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408 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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409 |...| ... | ... | ... | ... | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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410 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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411 |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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412 |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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413 Table continued (columns are derived from the MetFrag result): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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414 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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415 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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416 |...| FragmenterScore | FragmenterScore_Values | FormulasOfExplPeaks | Identifier | InChI |...| |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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417 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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418 |...| 105.844569063138 | 696.0;1156.0;696.0;1156.0 | 6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 206 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H |...| |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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419 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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420 |...| 105.844569063138 | 696.0;1156.0;696.0;1156.0 | (3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 5793 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 |...| |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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421 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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422 |...| ... | ... | ... | ... | ... |...| |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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423 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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424 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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425 Table continued (columns are derived from the MetFrag result): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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426 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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427 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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428 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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429 |...| NoExplPeaks | NumberPeaksUsed | OfflineMetFusionScore | SMILES | Score | SuspectListScore | XlogP3 | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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430 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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431 |...| 4 | 5 | 2.84566828424078 | C(C1C(C(C(C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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432 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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433 |...| 4 | 5 | 2.84566828424078 | C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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434 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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435 |...| ... | ... | ... | ... | ... | ... | ... | |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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436 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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437 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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438 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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439 Additional notes |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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440 -------------------- |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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441 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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442 The following adducts (and format) are currently supported in the MSP file. The neutral mass is automatically |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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443 calculated for the precursor m/z by subtracting the adduct mass |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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444 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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445 - '[M+H]+': 1.007276, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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446 - '[M+NH4]+': 18.034374, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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447 - '[M+Na]+': 22.989218, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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448 - '[M+K]+': 38.963158, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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449 - '[M+CH3OH+H]+': 33.033489, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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450 - '[M+ACN+H]+': 42.033823, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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451 - '[M+ACN+Na]+': 64.015765, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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452 - '[M+2ACN+H]+': 83.06037, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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453 - '[M-H]-': -1.007276, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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454 - '[M+Cl]-': 34.969402, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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455 - '[M+HCOO]-': 44.99819, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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456 - '[M-H+HCOOH]-': 44.99819, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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457 - '[M+CH3COO]-': 59.01385, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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458 - '[M-H+CH3COOH]-': 59.01385 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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459 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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460 Developers and contributors |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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461 --------------------------- |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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462 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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463 - **Julien Saint-Vanne (julien.saint-vanne@sb-roscoff.fr) - ABiMS (France)** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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464 - **Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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465 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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466 - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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467 - **Payam Emami (payam.emami@medsci.uu.se) - Uppsala Universitet (Sweden)** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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468 - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)** |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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469 </help> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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470 <citations> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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471 <citation type="doi">10.1186/s13321-016-0115-9</citation> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
472 </citations> |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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473 </tool> |