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annotate tool-data/msgfplus_mods_var.loc.sample @ 9:827f19088303 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:01:22 -0400
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827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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1 #This file lists the names of inbuilt chemical modifications accepted by msgfplus
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iracooke
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2 #Each entry consists of 4 tab separated fields like this
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3 #<Displayed Name> <DBKey> <Modification String> <DBKey>
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iracooke
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4 #
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iracooke
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5 #Modification strings should conform to the standard MSGFPlus syntax with the following exception
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iracooke
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6 #The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods
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iracooke
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7 #May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType
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iracooke
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8 #value
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9 #
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10 #Standard MSGFPlus syntax is
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11 #
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12 # To input a modification, use the following command:
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iracooke
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13 # Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required).
827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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14 # CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num])
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15 # - C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed.
827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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16 # - Atom can be omitted. The sequence of atoms must be followed.
827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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17 # - Negative numbers are allowed.
827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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18 # - E.g. C2H2O1 (valid), H2C1O1 (invalid)
827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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19 # Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient).
827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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20 # - E.g. 15.994915
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21 # Residues: affected amino acids (must be upper letters)
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22 # - Must be uppor letters or *
827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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23 # - Use * if this modification is applicable to any residue.
827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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24 # - * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.)
827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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25 # - E.g. NQ, *
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iracooke
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26 # ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive)
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iracooke
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27 # Position: position in the peptide where the modification can be attached.
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28 # - One of the following five values should be used:
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29 # - any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term)
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30 # - Case insensitive
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31 # - "-" can be omitted
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32 # - E.g. any, Any, Prot-n-Term, ProtNTerm => all valid
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33 # Name: name of the modification (Unimod PSI-MS name)
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34 # - For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name
827f19088303 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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35 # - E.g. Phospho, Acetyl
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36 #C2H3N1O1,C,fix,any,Carbamidomethyl # Fixed Carbamidomethyl C
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37 # Variable Modifications (default: none)
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38 #O1,M,opt,any,Oxidation # Oxidation M
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39 #15.994915,M,opt,any,Oxidation # Oxidation M (mass is used instead of CompositionStr)
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40 #H-1N-1O1,NQ,opt,any,Deamidated # Negative numbers are allowed.
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41 #C2H3NO,*,opt,N-term,Carbamidomethyl # Variable Carbamidomethyl N-term
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42 #H-2O-1,E,opt,N-term,Pyro_glu # Pyro-glu from E
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43 #H-3N-1,Q,opt,N-term,Pyro-glu # Pyro-glu from Q
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44 #C2H2O,*,opt,Prot-N-term,Acetyl # Acetylation Protein N-term
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45 #C2H2O1,K,opt,any,Acetyl # Acetylation K
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46 #CH2,K,opt,any,Methy # Methylation K
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47 #HO3P,STY,opt,any,Phospho # Phosphorylation STY
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48
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49 Oxidation M oxidation_m_ O1,M,opt,any,Oxidation oxidation_m_
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50 Acetylation Protein N-term acetyl_nterm_ C2H2O,*,opt,Prot-N-term,Acetyl acetyl_nterm_
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51 Deamidation NQ deamidation_nq_ H-1N-1O1,NQ,opt,any,Deamidated deamidation_nq_
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52 Acetylation K acetyl_k_ C2H2O1,K,opt,any,Acetyl acetyl_k_
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53 Methylation K methyl_k_ CH2,K,opt,any,Methy methyl_k_
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54 Phosphorylation STY phospho_sty_ HO3P,STY,opt,any,Phospho phospho_sty_
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55 Carbamidomethyl N-term carbamidomethyl_nterm_ C2H3NO,*,opt,N-term,Carbamidomethyl carbamidomethyl_nterm_