Mercurial > repos > galaxyp > metanovo

view macros_modifications.xml @ 3:4a851c02f558 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 420ef6b0ee91e44ed354366a55575c1aa504e380"
author galaxyp
date Tue, 29 Mar 2022 20:53:42 +0000
parents 9025f297a511
children
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<macros>
  <!-- Although the options for fixed and variable modifications are the same, two macros are used to set different default options -->
  <xml name="fixed_modifications">
    <option value="18O(1) of peptide C-term">18O(1) of peptide C-term</option>
    <option value="18O(2) of peptide C-term">18O(2) of peptide C-term</option>
    <option value="4-Hydroxyproline">4-Hydroxyproline</option>
    <option value="Acetaldehyde +26">Acetaldehyde +26</option>
    <option value="Acetylation of K">Acetylation of K</option>
    <option value="Acetylation of peptide N-term">Acetylation of peptide N-term</option>
    <option value="Acetylation of protein N-term">Acetylation of protein N-term</option>
    <option value="Amidation of the peptide C-term">Amidation of the peptide C-term</option>
    <option value="Amidation of the protein C-term">Amidation of the protein C-term</option>
    <option value="Arginine 13C(6)">Arginine 13C(6)</option>
    <option value="Arginine 13C(6) 15N(4)">Arginine 13C(6) 15N(4)</option>
    <option value="Carbamidomethylation of C" selected="true">Carbamidomethylation of C</option>
    <option value="Carbamidomethylation of E">Carbamidomethylation of E</option>
    <option value="Carbamidomethylation of K">Carbamidomethylation of K</option>
    <option value="Carbamilation of K">Carbamilation of K</option>
    <option value="Carbamilation of protein N-term">Carbamilation of protein N-term</option>
    <option value="Carboxymethylation of C">Carboxymethylation of C</option>
    <option value="Citrullination of R">Citrullination of R</option>
    <option value="Deamidation of N">Deamidation of N</option>
    <option value="Deamidation of N 18O">Deamidation of N 18O</option>
    <option value="Deamidation of Q">Deamidation of Q</option>
    <option value="Dehydration of S">Dehydration of S</option>
    <option value="Dehydration of T">Dehydration of T</option>
    <option value="Didehydro of T">Didehydro of T</option>
    <option value="Diiodination of Y">Diiodination of Y</option>
    <option value="Dimethylation of K">Dimethylation of K</option>
    <option value="Dimethylation of K 2H(4)">Dimethylation of K 2H(4)</option>
    <option value="Dimethylation of K 2H(6)">Dimethylation of K 2H(6)</option>
    <option value="Dimethylation of K 2H(6) 13C(2)">Dimethylation of K 2H(6) 13C(2)</option>
    <option value="Dimethylation of R">Dimethylation of R</option>
    <option value="Dimethylation of peptide N-term">Dimethylation of peptide N-term</option>
    <option value="Dimethylation of peptide N-term 2H(4)">Dimethylation of peptide N-term 2H(4)</option>
    <option value="Dimethylation of peptide N-term 2H(6)">Dimethylation of peptide N-term 2H(6)</option>
    <option value="Dimethylation of peptide N-term 2H(6) 13C(2)">Dimethylation of peptide N-term 2H(6) 13C(2)</option>
    <option value="Dioxidation of M">Dioxidation of M</option>
    <option value="Dioxidation of W">Dioxidation of W</option>
    <option value="Farnesylation of C">Farnesylation of C</option>
    <option value="FormylMet of protein N-term">FormylMet of protein N-term</option>
    <option value="Formylation of K">Formylation of K</option>
    <option value="Formylation of S">Formylation of S</option>
    <option value="Formylation of T">Formylation of T</option>
    <option value="Formylation of peptide N-term">Formylation of peptide N-term</option>
    <option value="Formylation of protein N-term">Formylation of protein N-term</option>
    <option value="Geranyl-geranyl of C">Geranyl-geranyl of C</option>
    <option value="Glutathione of C">Glutathione of C</option>
    <option value="Guanidination of K">Guanidination of K</option>
    <option value="Guanidination of peptide N-term">Guanidination of peptide N-term</option>
    <option value="Hex(1)NAc(1) of S">Hex(1)NAc(1) of S</option>
    <option value="Hex(1)NAc(1) of T">Hex(1)NAc(1) of T</option>
    <option value="Hex(5) HexNAc(4) NeuAc(2) Na of N">Hex(5) HexNAc(4) NeuAc(2) Na of N</option>
    <option value="Hex(5) HexNAc(4) NeuAc(2) of N">Hex(5) HexNAc(4) NeuAc(2) of N</option>
    <option value="HexNAc of S">HexNAc of S</option>
    <option value="HexNAc of T">HexNAc of T</option>
    <option value="Hexose of K">Hexose of K</option>
    <option value="Homoserine lactone of peptide C-term M">Homoserine lactone of peptide C-term M</option>
    <option value="Homoserine of peptide C-term M">Homoserine of peptide C-term M</option>
    <option value="ICAT-9">ICAT-9</option>
    <option value="ICAT-O">ICAT-O</option>
    <option value="ICPL0 of K">ICPL0 of K</option>
    <option value="ICPL0 of peptide N-term">ICPL0 of peptide N-term</option>
    <option value="ICPL10 of K">ICPL10 of K</option>
    <option value="ICPL10 of peptide N-term">ICPL10 of peptide N-term</option>
    <option value="ICPL4 of K">ICPL4 of K</option>
    <option value="ICPL4 of peptide N-term">ICPL4 of peptide N-term</option>
    <option value="ICPL6 of K">ICPL6 of K</option>
    <option value="ICPL6 of peptide N-term">ICPL6 of peptide N-term</option>
    <option value="Isoleucine 13C(6) 15N(1)">Isoleucine 13C(6) 15N(1)</option>
    <option value="Label of K 2H(4)">Label of K 2H(4)</option>
    <option value="Leucine 13C(6) 15N(1)">Leucine 13C(6) 15N(1)</option>
    <option value="Lipoyl of K">Lipoyl of K</option>
    <option value="Lysine 13C(6)">Lysine 13C(6)</option>
    <option value="Lysine 13C(6) 15N(2)">Lysine 13C(6) 15N(2)</option>
    <option value="Lysine 2H(4)">Lysine 2H(4)</option>
    <option value="Methylation of C">Methylation of C</option>
    <option value="Methylation of D">Methylation of D</option>
    <option value="Methylation of E">Methylation of E</option>
    <option value="Methylation of K">Methylation of K</option>
    <option value="Methylation of R">Methylation of R</option>
    <option value="Methylation of S">Methylation of S</option>
    <option value="Methylthio of C">Methylthio of C</option>
    <option value="Methylthio of D">Methylthio of D</option>
    <option value="Methylthio of N">Methylthio of N</option>
    <option value="NIPCAM of C">NIPCAM of C</option>
    <option value="Nethylmaleimide of C">Nethylmaleimide of C</option>
    <option value="Oxidation of C">Oxidation of C</option>
    <option value="Oxidation of K">Oxidation of K</option>
    <option value="Oxidation of M">Oxidation of M</option>
    <option value="Oxidation of P">Oxidation of P</option>
    <option value="Palmitoylation of C">Palmitoylation of C</option>
    <option value="Palmitoylation of K">Palmitoylation of K</option>
    <option value="Palmitoylation of S">Palmitoylation of S</option>
    <option value="Palmitoylation of T">Palmitoylation of T</option>
    <option value="Palmitoylation of protein N-term">Palmitoylation of protein N-term</option>
    <option value="Phosphorylation of S">Phosphorylation of S</option>
    <option value="Phosphorylation of T">Phosphorylation of T</option>
    <option value="Phosphorylation of Y">Phosphorylation of Y</option>
    <option value="Proline 13C(5)">Proline 13C(5)</option>
    <option value="Propionamide of C">Propionamide of C</option>
    <option value="Propionamide of K">Propionamide of K</option>
    <option value="Propionamide of peptide N-term">Propionamide of peptide N-term</option>
    <option value="Propionyl of K heavy">Propionyl of K heavy</option>
    <option value="Propionyl of K light">Propionyl of K light</option>
    <option value="Propionyl of peptide N-term heavy">Propionyl of peptide N-term heavy</option>
    <option value="Propionyl of peptide N-term light">Propionyl of peptide N-term light</option>
    <option value="Pyridylethyl of C">Pyridylethyl of C</option>
    <option value="Pyrolidone from E">Pyrolidone from E</option>
    <option value="Pyrolidone from Q">Pyrolidone from Q</option>
    <option value="Pyrolidone from carbamidomethylated C">Pyrolidone from carbamidomethylated C</option>
    <option value="SUMO-2/3 Q87R">SUMO-2/3 Q87R</option>
    <option value="Sodium adduct to D">Sodium adduct to D</option>
    <option value="Sodium adduct to E">Sodium adduct to E</option>
    <option value="Sulfation of S">Sulfation of S</option>
    <option value="Sulfation of T">Sulfation of T</option>
    <option value="Sulfation of Y">Sulfation of Y</option>
    <option value="TMT 10-plex of K">TMT 10-plex of K</option>
    <option value="TMT 10-plex of peptide N-term">TMT 10-plex of peptide N-term</option>
    <option value="TMT 2-plex of K">TMT 2-plex of K</option>
    <option value="TMT 2-plex of peptide N-term">TMT 2-plex of peptide N-term</option>
    <option value="TMT 6-plex of K">TMT 6-plex of K</option>
    <option value="TMT 6-plex of peptide N-term">TMT 6-plex of peptide N-term</option>
    <option value="Thioacyl of peptide N-term">Thioacyl of peptide N-term</option>
    <option value="Trideuterated Methyl Ester of D">Trideuterated Methyl Ester of D</option>
    <option value="Trideuterated Methyl Ester of E">Trideuterated Methyl Ester of E</option>
    <option value="Trideuterated Methyl Ester of K">Trideuterated Methyl Ester of K</option>
    <option value="Trideuterated Methyl Ester of R">Trideuterated Methyl Ester of R</option>
    <option value="Trideuterated Methyl Ester of peptide C-term">Trideuterated Methyl Ester of peptide C-term</option>
    <option value="Trimethylation of K">Trimethylation of K</option>
    <option value="Trimethylation of R">Trimethylation of R</option>
    <option value="Trimethylation of protein N-term A">Trimethylation of protein N-term A</option>
    <option value="Trioxidation of C">Trioxidation of C</option>
    <option value="Ubiquitination of K">Ubiquitination of K</option>
    <option value="iTRAQ 4-plex of K">iTRAQ 4-plex of K</option>
    <option value="iTRAQ 4-plex of Y">iTRAQ 4-plex of Y</option>
    <option value="iTRAQ 4-plex of peptide N-term">iTRAQ 4-plex of peptide N-term</option>
    <option value="iTRAQ 8-plex of K">iTRAQ 8-plex of K</option>
    <option value="iTRAQ 8-plex of Y">iTRAQ 8-plex of Y</option>
    <option value="iTRAQ 8-plex of peptide N-term">iTRAQ 8-plex of peptide N-term</option>
    <option value="mTRAQ of 13C(6) 15N(2)">mTRAQ of 13C(6) 15N(2)</option>
    <option value="mTRAQ of K 13C(3) 15N">mTRAQ of K 13C(3) 15N</option>
    <option value="mTRAQ of K light">mTRAQ of K light</option>
    <option value="mTRAQ of peptide N-term 13C(3) 15N">mTRAQ of peptide N-term 13C(3) 15N</option>
    <option value="mTRAQ of peptide N-term 13C(6) 15N(2)">mTRAQ of peptide N-term 13C(6) 15N(2)</option>
    <option value="mTRAQ of peptide N-term light">mTRAQ of peptide N-term light</option>
  </xml>
  <xml name="variable_modifications">
    <option value="18O(1) of peptide C-term">18O(1) of peptide C-term</option>
    <option value="18O(2) of peptide C-term">18O(2) of peptide C-term</option>
    <option value="4-Hydroxyproline">4-Hydroxyproline</option>
    <option value="Acetaldehyde +26">Acetaldehyde +26</option>
    <option value="Acetylation of K">Acetylation of K</option>
    <option value="Acetylation of peptide N-term">Acetylation of peptide N-term</option>
    <option value="Acetylation of protein N-term">Acetylation of protein N-term</option>
    <option value="Amidation of the peptide C-term">Amidation of the peptide C-term</option>
    <option value="Amidation of the protein C-term">Amidation of the protein C-term</option>
    <option value="Arginine 13C(6)">Arginine 13C(6)</option>
    <option value="Arginine 13C(6) 15N(4)">Arginine 13C(6) 15N(4)</option>
    <option value="Carbamidomethylation of C">Carbamidomethylation of C</option>
    <option value="Carbamidomethylation of E">Carbamidomethylation of E</option>
    <option value="Carbamidomethylation of K">Carbamidomethylation of K</option>
    <option value="Carbamilation of K">Carbamilation of K</option>
    <option value="Carbamilation of protein N-term">Carbamilation of protein N-term</option>
    <option value="Carboxymethylation of C">Carboxymethylation of C</option>
    <option value="Citrullination of R">Citrullination of R</option>
    <option value="Deamidation of N">Deamidation of N</option>
    <option value="Deamidation of N 18O">Deamidation of N 18O</option>
    <option value="Deamidation of Q">Deamidation of Q</option>
    <option value="Dehydration of S">Dehydration of S</option>
    <option value="Dehydration of T">Dehydration of T</option>
    <option value="Didehydro of T">Didehydro of T</option>
    <option value="Diiodination of Y">Diiodination of Y</option>
    <option value="Dimethylation of K">Dimethylation of K</option>
    <option value="Dimethylation of K 2H(4)">Dimethylation of K 2H(4)</option>
    <option value="Dimethylation of K 2H(6)">Dimethylation of K 2H(6)</option>
    <option value="Dimethylation of K 2H(6) 13C(2)">Dimethylation of K 2H(6) 13C(2)</option>
    <option value="Dimethylation of R">Dimethylation of R</option>
    <option value="Dimethylation of peptide N-term">Dimethylation of peptide N-term</option>
    <option value="Dimethylation of peptide N-term 2H(4)">Dimethylation of peptide N-term 2H(4)</option>
    <option value="Dimethylation of peptide N-term 2H(6)">Dimethylation of peptide N-term 2H(6)</option>
    <option value="Dimethylation of peptide N-term 2H(6) 13C(2)">Dimethylation of peptide N-term 2H(6) 13C(2)</option>
    <option value="Dioxidation of M">Dioxidation of M</option>
    <option value="Dioxidation of W">Dioxidation of W</option>
    <option value="Farnesylation of C">Farnesylation of C</option>
    <option value="FormylMet of protein N-term">FormylMet of protein N-term</option>
    <option value="Formylation of K">Formylation of K</option>
    <option value="Formylation of S">Formylation of S</option>
    <option value="Formylation of T">Formylation of T</option>
    <option value="Formylation of peptide N-term">Formylation of peptide N-term</option>
    <option value="Formylation of protein N-term">Formylation of protein N-term</option>
    <option value="Geranyl-geranyl of C">Geranyl-geranyl of C</option>
    <option value="Glutathione of C">Glutathione of C</option>
    <option value="Guanidination of K">Guanidination of K</option>
    <option value="Guanidination of peptide N-term">Guanidination of peptide N-term</option>
    <option value="Hex(1)NAc(1) of S">Hex(1)NAc(1) of S</option>
    <option value="Hex(1)NAc(1) of T">Hex(1)NAc(1) of T</option>
    <option value="Hex(5) HexNAc(4) NeuAc(2) Na of N">Hex(5) HexNAc(4) NeuAc(2) Na of N</option>
    <option value="Hex(5) HexNAc(4) NeuAc(2) of N">Hex(5) HexNAc(4) NeuAc(2) of N</option>
    <option value="HexNAc of S">HexNAc of S</option>
    <option value="HexNAc of T">HexNAc of T</option>
    <option value="Hexose of K">Hexose of K</option>
    <option value="Homoserine lactone of peptide C-term M">Homoserine lactone of peptide C-term M</option>
    <option value="Homoserine of peptide C-term M">Homoserine of peptide C-term M</option>
    <option value="ICAT-9">ICAT-9</option>
    <option value="ICAT-O">ICAT-O</option>
    <option value="ICPL0 of K">ICPL0 of K</option>
    <option value="ICPL0 of peptide N-term">ICPL0 of peptide N-term</option>
    <option value="ICPL10 of K">ICPL10 of K</option>
    <option value="ICPL10 of peptide N-term">ICPL10 of peptide N-term</option>
    <option value="ICPL4 of K">ICPL4 of K</option>
    <option value="ICPL4 of peptide N-term">ICPL4 of peptide N-term</option>
    <option value="ICPL6 of K">ICPL6 of K</option>
    <option value="ICPL6 of peptide N-term">ICPL6 of peptide N-term</option>
    <option value="Isoleucine 13C(6) 15N(1)">Isoleucine 13C(6) 15N(1)</option>
    <option value="Label of K 2H(4)">Label of K 2H(4)</option>
    <option value="Leucine 13C(6) 15N(1)">Leucine 13C(6) 15N(1)</option>
    <option value="Lipoyl of K">Lipoyl of K</option>
    <option value="Lysine 13C(6)">Lysine 13C(6)</option>
    <option value="Lysine 13C(6) 15N(2)">Lysine 13C(6) 15N(2)</option>
    <option value="Lysine 2H(4)">Lysine 2H(4)</option>
    <option value="Methylation of C">Methylation of C</option>
    <option value="Methylation of D">Methylation of D</option>
    <option value="Methylation of E">Methylation of E</option>
    <option value="Methylation of K">Methylation of K</option>
    <option value="Methylation of R">Methylation of R</option>
    <option value="Methylation of S">Methylation of S</option>
    <option value="Methylthio of C">Methylthio of C</option>
    <option value="Methylthio of D">Methylthio of D</option>
    <option value="Methylthio of N">Methylthio of N</option>
    <option value="NIPCAM of C">NIPCAM of C</option>
    <option value="Nethylmaleimide of C">Nethylmaleimide of C</option>
    <option value="Oxidation of C">Oxidation of C</option>
    <option value="Oxidation of K">Oxidation of K</option>
    <option value="Oxidation of M" selected="true">Oxidation of M</option>
    <option value="Oxidation of P">Oxidation of P</option>
    <option value="Palmitoylation of C">Palmitoylation of C</option>
    <option value="Palmitoylation of K">Palmitoylation of K</option>
    <option value="Palmitoylation of S">Palmitoylation of S</option>
    <option value="Palmitoylation of T">Palmitoylation of T</option>
    <option value="Palmitoylation of protein N-term">Palmitoylation of protein N-term</option>
    <option value="Phosphorylation of S">Phosphorylation of S</option>
    <option value="Phosphorylation of T">Phosphorylation of T</option>
    <option value="Phosphorylation of Y">Phosphorylation of Y</option>
    <option value="Proline 13C(5)">Proline 13C(5)</option>
    <option value="Propionamide of C">Propionamide of C</option>
    <option value="Propionamide of K">Propionamide of K</option>
    <option value="Propionamide of peptide N-term">Propionamide of peptide N-term</option>
    <option value="Propionyl of K heavy">Propionyl of K heavy</option>
    <option value="Propionyl of K light">Propionyl of K light</option>
    <option value="Propionyl of peptide N-term heavy">Propionyl of peptide N-term heavy</option>
    <option value="Propionyl of peptide N-term light">Propionyl of peptide N-term light</option>
    <option value="Pyridylethyl of C">Pyridylethyl of C</option>
    <option value="Pyrolidone from E">Pyrolidone from E</option>
    <option value="Pyrolidone from Q">Pyrolidone from Q</option>
    <option value="Pyrolidone from carbamidomethylated C">Pyrolidone from carbamidomethylated C</option>
    <option value="SUMO-2/3 Q87R">SUMO-2/3 Q87R</option>
    <option value="Sodium adduct to D">Sodium adduct to D</option>
    <option value="Sodium adduct to E">Sodium adduct to E</option>
    <option value="Sulfation of S">Sulfation of S</option>
    <option value="Sulfation of T">Sulfation of T</option>
    <option value="Sulfation of Y">Sulfation of Y</option>
    <option value="TMT 10-plex of K">TMT 10-plex of K</option>
    <option value="TMT 10-plex of peptide N-term">TMT 10-plex of peptide N-term</option>
    <option value="TMT 2-plex of K">TMT 2-plex of K</option>
    <option value="TMT 2-plex of peptide N-term">TMT 2-plex of peptide N-term</option>
    <option value="TMT 6-plex of K">TMT 6-plex of K</option>
    <option value="TMT 6-plex of peptide N-term">TMT 6-plex of peptide N-term</option>
    <option value="Thioacyl of peptide N-term">Thioacyl of peptide N-term</option>
    <option value="Trideuterated Methyl Ester of D">Trideuterated Methyl Ester of D</option>
    <option value="Trideuterated Methyl Ester of E">Trideuterated Methyl Ester of E</option>
    <option value="Trideuterated Methyl Ester of K">Trideuterated Methyl Ester of K</option>
    <option value="Trideuterated Methyl Ester of R">Trideuterated Methyl Ester of R</option>
    <option value="Trideuterated Methyl Ester of peptide C-term">Trideuterated Methyl Ester of peptide C-term</option>
    <option value="Trimethylation of K">Trimethylation of K</option>
    <option value="Trimethylation of R">Trimethylation of R</option>
    <option value="Trimethylation of protein N-term A">Trimethylation of protein N-term A</option>
    <option value="Trioxidation of C">Trioxidation of C</option>
    <option value="Ubiquitination of K">Ubiquitination of K</option>
    <option value="iTRAQ 4-plex of K">iTRAQ 4-plex of K</option>
    <option value="iTRAQ 4-plex of Y">iTRAQ 4-plex of Y</option>
    <option value="iTRAQ 4-plex of peptide N-term">iTRAQ 4-plex of peptide N-term</option>
    <option value="iTRAQ 8-plex of K">iTRAQ 8-plex of K</option>
    <option value="iTRAQ 8-plex of Y">iTRAQ 8-plex of Y</option>
    <option value="iTRAQ 8-plex of peptide N-term">iTRAQ 8-plex of peptide N-term</option>
    <option value="mTRAQ of 13C(6) 15N(2)">mTRAQ of 13C(6) 15N(2)</option>
    <option value="mTRAQ of K 13C(3) 15N">mTRAQ of K 13C(3) 15N</option>
    <option value="mTRAQ of K light">mTRAQ of K light</option>
    <option value="mTRAQ of peptide N-term 13C(3) 15N">mTRAQ of peptide N-term 13C(3) 15N</option>
    <option value="mTRAQ of peptide N-term 13C(6) 15N(2)">mTRAQ of peptide N-term 13C(6) 15N(2)</option>
    <option value="mTRAQ of peptide N-term light">mTRAQ of peptide N-term light</option>
  </xml>
</macros>