Mercurial > repos > galaxyp > peptideshaker
changeset 16:c353378140ca draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb474693831a3375db79755e88641ad32b3b4e6-dirty
| author | galaxyp |
|---|---|
| date | Sun, 21 Feb 2016 11:17:39 -0500 |
| parents | 3fa49ed11f3d |
| children | 2f8e9d0351a8 |
| files | README.rst peptide_shaker.xml repository_dependencies.xml searchgui_mods.loc.sample tool_dependencies.xml |
| diffstat | 5 files changed, 153 insertions(+), 217 deletions(-) [+] |
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--- a/README.rst Wed Oct 21 15:13:17 2015 -0400 +++ b/README.rst Sun Feb 21 11:17:39 2016 -0500 @@ -42,6 +42,8 @@ Note ---- +- Requires Galaxy release v15.10 or later, which fixes the installation of package_peptideshaker_1_1 and provides a searchgui_archive datatype that includes a version + - PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. See: @@ -50,6 +52,14 @@ * <https://code.google.com/p/searchgui/> +Search GUI - Fixed and Variable Modifications +------------------------------------------- + + - Options for modifications are read from local data file: searchgui_mods.loc + This is copied from searchgui_mods.loc.sample on the first installation. + +The modifications are from: https://github.com/compomics/compomics-utilities/blob/master/src/main/java/com/compomics/util/experiment/identification/search_parameters_cli/IdentificationParametersInputBean.java + GalaxyP Community -----------------
--- a/peptide_shaker.xml Wed Oct 21 15:13:17 2015 -0400 +++ b/peptide_shaker.xml Sun Feb 21 11:17:39 2016 -0500 @@ -473,7 +473,7 @@ <when value="0" /> <when value="1"> <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> - <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float" + <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float" help="Automatic mode will be used if not set" /> </when> </conditional>
--- a/repository_dependencies.xml Wed Oct 21 15:13:17 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Required proteomics dependencies."> - <repository changeset_revision="349af9298ff1" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> -</repositories>
--- a/searchgui_mods.loc.sample Wed Oct 21 15:13:17 2015 -0400 +++ b/searchgui_mods.loc.sample Sun Feb 21 11:17:39 2016 -0500 @@ -1,210 +1,140 @@ -methylation of k -oxidation of m -carboxymethyl c -carbamidomethyl c -deamidation of n and q -propionamide c -phosphorylation of s -phosphorylation of t -phosphorylation of y -m cleavage from protein n-term -acetylation of protein n-term -methylation of protein n-term -tri-methylation of protein n-term -beta methythiolation of d -methylation of q -tri-methylation of k -methylation of d -methylation of e -methylation of peptide c-term -tri-deuteromethylation of d -tri-deuteromethylation of e -tri-deuteromethylation of peptide c-term -n-formyl met addition -2-amino-3-oxo-butanoic acid t -acetylation of k -amidation of peptide c-term -beta-methylthiolation of d (duplicate of 13) -carboxyamidomethylation of k -carboxyamidomethylation of h -carboxyamidomethylation of d -carboxyamidomethylation of e -carbamylation of k -carbamylation of n-term peptide -citrullination of r -oxidation of c to cysteic acid -di-iodination of y -di-methylation of k -di-methylation of r -di-methylation of peptide n-term -oxidation of f to dihydroxyphenylalanine -gammathiopropionylation of k -gammathiopropionylation of peptide n-term -farnesylation of c -formylation of k -formylation of peptide n-term -oxidation of w to formylkynurenin -fluorophenylalanine -beta-carboxylation of d -gamma-carboxylation of e -geranyl-geranyl -glucuronylation of protein n-term -glutathione disulfide -ubiquitinylation residue -guanidination of k -oxidation of h to n -oxidation of h to d -homoserine -homoserine lactone -oxidation of w to hydroxykynurenin -hydroxylation of d -hydroxylation of k -hydroxylation of n -hydroxylation of p -hydroxylation of f -hydroxylation of y -iodination of y -oxidation of w to kynurenin -lipoyl k -methyl ester of peptide c-term (duplicate of 18) -methyl ester of d -methyl ester of e (duplicate of 17) -methyl ester of s -methyl ester of y -methyl c -methyl h -methyl n -methylation of peptide n-term -methyl r -myristoleylation of g -myristoyl-4h of g -myristoylation of peptide n-term g -myristoylation of k -formylation of protein n-term -nem c -nipcam -oxidation of w to nitro -oxidation of y to nitro -o18 on peptide n-term -di-o18 on peptide n-term -oxidation of h -oxidation of w -phosphopantetheine s -palmitoylation of c -palmitoylation of k -palmitoylation of s -palmitoylation of t -phosphorylation of s with prompt loss -phosphorylation of t with prompt loss -phosphorylation with prompt loss on y -phosphorylation with neutral loss on c -phosphorylation with neutral loss on d -phosphorylation with neutral loss on h -propionyl light k -propionyl light on peptide n-term -propionyl heavy k -propionyl heavy peptide n-term -pyridyl k -pyridyl peptide n-term -pyro-cmc -pyro-glu from n-term e -pyro-glu from n-term q -oxidation of p to pyroglutamic acid -s-pyridylethylation of c -semet -sulfation of y -sulphone of m -tri-iodination of y -tri-methylation of r -n-acyl diglyceride cysteine -icat light -icat heavy -camthiopropanoyl k -phosphorylation with neutral loss on s -phosphorylation with neutral loss on t -phosphorylation of s with etd loss -phosphorylation of t with etd loss -heavy arginine-13c6 -heavy arginine-13c6-15n4 -heavy lysine-13c6 -pngasf in o18 water -beta elimination of s -beta elimination of t -oxidation of c to sulfinic acid -arginine to ornithine -dehydro of s and t -carboxykynurenin of w -sumoylation of k -itraq114 on nterm -itraq114 on k -itraq114 on y -itraq115 on nterm -itraq115 on k -itraq115 on y -itraq116 on nterm -itraq116 on k -itraq116 on y -itraq117 on nterm -itraq117 on k -itraq117 on y -mmts on c -heavy lysine - 2h4 -heavy lysine - 13c6 15n2 -asparagine hexnac -asparagine dhexhexnac -serine hexnac -threonine hexnac -palmitoleyl of s -palmitoleyl of c -palmitoleyl of t -chd2-di-methylation of k -chd2-di-methylation of peptide n-term -maleimide-peo2-biotin of c -phosphorylation of h -oxidation of c -oxidation of y (duplicate of 64) -uniblue a on k -deamidation of n -trideuteration of l (silac) -tmt duplex on k -tmt duplex on n-term peptide -tmt 6-plex on k -tmt 6-plex on n-term peptide -itraq8plex:13c(7)15n(1) on nterm -itraq8plex:13c(7)15n(1) on k -itraq8plex:13c(7)15n(1) on y -itraq8plex:13c(6)15n(2) on nterm -itraq8plex:13c(6)15n(2) on k -itraq8plex:13c(6)15n(2) on y -selenocysteine -carboxymethylated selenocysteine -dimethyl 2d n-terminus -dimethyl 2d k -gtp desthiobiotinc12 -gtp desthiobiotinc13 -user modification 5 -user modification 6 -user modification 7 -user modification 8 -user modification 9 -user modification 10 -user modification 11 -user modification 12 -user modification 13 -user modification 14 -user modification 15 -user modification 16 -user modification 17 -user modification 18 -user modification 19 -user modification 20 -user modification 21 -user modification 22 -user modification 23 -user modification 24 -user modification 25 -user modification 26 -user modification 27 -user modification 28 -user modification 29 -user modification 30 +18O(1) of peptide C-term +18O(2) of peptide C-term +4-Hydroxyproline +Acetaldehyde +26 +Acetylation of K +Acetylation of peptide N-term +Acetylation of protein N-term +Amidation of the peptide C-term +Amidation of the protein C-term +Arginine 13C(6) +Arginine 13C(6) 15N(4) +Carbamidomethylation of C +Carbamidomethylation of E +Carbamidomethylation of K +Carbamilation of K +Carbamilation of protein N-term +Carboxymethylation of C +Deamidation of N +Deamidation of N 18O +Deamidation of Q +Dehydration of S +Dehydration of T +Didehydro of T +Diiodination of Y +Dimethylation of K +Dimethylation of K 2H(4) +Dimethylation of K 2H(6) +Dimethylation of R +Dimethylation of peptide N-term 2H(6) +Dimethylation of peptide N-term 2H(6) 13C(2) +Dimethylation of peptide N-term K +Dimethylation of peptide N-term K 2H(4) +Dioxidation of M +Dioxidation of W +Farnesylation of C +FormylMet of protein N-term +Formylation of K +Formylation of S +Formylation of T +Formylation of peptide N-term +Formylation of protein N-term +Geranyl-geranyl of C +Glutathione of C +Guanidination of K +Guanidination of peptide N-term +Hex(1)NAc(1) of S +Hex(1)NAc(1) of T +Hex(5) HexNAc(4) NeuAc(2) Na of N +Hex(5) HexNAc(4) NeuAc(2) of N +HexNAc of S +HexNAc of T +Hexose of K +Homoserine lactone of peptide C-term M +Homoserine of peptide C-term M +ICAT-9 +ICAT-O +ICPL0 of K +ICPL0 of peptide N-term +ICPL10 of K +ICPL10 of peptide N-term +ICPL4 of K +ICPL4 of peptide N-term +ICPL6 of K +ICPL6 of peptide N-term +Isoleucine 13C(6) 15N(1) +Leucine 13C(6) 15N(1) +Lipoyl of K +Lysine 13C(6) +Lysine 13C(6) 15N(2) +Lysine 2H(4) +Methylation of C +Methylation of D +Methylation of E +Methylation of K +Methylation of R +Methylation of S +Methylthio of C +Methylthio of D +Methylthio of N +NIPCAM of C +Nethylmaleimide of C +Oxidation of C +Oxidation of K +Oxidation of M +Oxidation of P +Palmitoylation of C +Palmitoylation of K +Palmitoylation of S +Palmitoylation of T +Palmitoylation of protein N-term +Phosphorylation of S +Phosphorylation of T +Phosphorylation of Y +Proline 13C(5) +Propionamide of C +Propionamide of K +Propionamide of peptide N-term +Propionyl of K heavy +Propionyl of K light +Propionyl of peptide N-term heavy +Propionyl of peptide N-term light +Pyridylethyl of C +Pyrolidone from E +Pyrolidone from Q +Pyrolidone from carbamidomethylated C +SUMO-2/3 Q87R +Sodium adduct to D +Sodium adduct to E +Sulfonation of S +Sulfonation of T +Sulfonation of Y +TMT 10-plex of K +TMT 10-plex of peptide N-term +TMT 2-plex of K +TMT 2-plex of peptide N-term +TMT 6-plex of K +TMT 6-plex of peptide N-term +Thioacyl of peptide N-term +Trideuterated Methyl Ester of D +Trideuterated Methyl Ester of E +Trideuterated Methyl Ester of K +Trideuterated Methyl Ester of R +Trideuterated Methyl Ester of peptide C-term +Trimethylation of K +Trimethylation of R +Trimethylation of protein N-term A +Trioxidation of C +Ubiquitination of K +iTRAQ 4-plex of K +iTRAQ 4-plex of Y +iTRAQ 4-plex of peptide N-term +iTRAQ 8-plex of K +iTRAQ 8-plex of Y +iTRAQ 8-plex of peptide N-term +mTRAQ of 13C(6) 15N(2) +mTRAQ of K 13C(3) 15N +mTRAQ of K light +mTRAQ of peptide N-term 13C(3) 15N +mTRAQ of peptide N-term 13C(6) 15N(2) +mTRAQ of peptide N-term light
--- a/tool_dependencies.xml Wed Oct 21 15:13:17 2015 -0400 +++ b/tool_dependencies.xml Sun Feb 21 11:17:39 2016 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="searchgui" version="2.1"> - <repository changeset_revision="c3e018747db9" name="package_searchgui_2_1" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="996169901942" name="package_searchgui_2_1" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="peptide_shaker" version="1.1"> - <repository changeset_revision="a21a8f32bb5b" name="package_peptideshaker_1_1" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a639559a8e83" name="package_peptideshaker_1_1" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>