# HG changeset patch # User iracooke # Date 1402783284 14400 # Node ID a9c27818f417c485cd9252491110dd84c8300726 # Parent 54b870eaca8d3c8cb8d83ce8ecc720fe6cf06672 Uploaded diff -r 54b870eaca8d -r a9c27818f417 ._.DS_Store Binary file ._.DS_Store has changed diff -r 54b870eaca8d -r a9c27818f417 README --- a/README Sun Jun 09 08:18:30 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -This package installs wrapper scripts for running OMSSA MS/MS searches - -Requirements: -This package depends on the galaxy_protk, protk_omssa and protk_blast packages -Please see instructions for those packages before installing diff -r 54b870eaca8d -r a9c27818f417 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sat Jun 14 18:01:24 2014 -0400 @@ -0,0 +1,8 @@ +## What is it? +Galaxy tool definition file and wrapper scripts for the [OMSSA search engine](http://pubchem.ncbi.nlm.nih.gov/omssa/). + +## Installation +Install from the main galaxy toolshed at http://toolshed.g2.bx.psu.edu/ + +Depends on command-line scripts and databases available in the [protk ruby gem](https://bitbucket.org/iracooke/protk). + diff -r 54b870eaca8d -r a9c27818f417 omssa.xml --- a/omssa.xml Sun Jun 09 08:18:30 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,189 +0,0 @@ - - - - galaxy_protk - omssa - blast - - - - Run an OMSSA MS/MS Search - - rvm 1.9.3@protk-1.2.2 do omssa_search.rb - - #if $database.source_select=="built_in": - -d $database.dbkey - #else - -d $database.fasta_file - #end if - - --var-mods=' - $variable_mods - ' - - --fix-mods=' - $fixed_mods - ' - - --searched-ions=' - $searched_ions - ' - - $input_file - -o $output - -r - - --enzyme=$enzyme - - --precursor-ion-tol-units=$precursor_tolu - - -v $missed_cleavages - - -f $fragment_ion_tol - - -p $precursor_ion_tol - - --num-peaks-for-multi-isotope-search $multi_isotope - - $use_average_mass - $respect_precursor_charges - - --max-hit-expect $max_hit_expect - - --intensity-cut-off $intensity_cut_off - - - - - - - - - - - - - Database - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Missed Cleavages Allowed - - - - - - - Enzyme - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Precursor Ion Tolerance Units - - - - - - - - - Multi-isotope search. - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -Runs an MS/MS database search using the OMSSA search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. - ----- - -**Citation** - -If you use this tool please read and cite the paper describing OMSSA. - -Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004). - - - diff -r 54b870eaca8d -r a9c27818f417 repository_dependencies.xml --- a/repository_dependencies.xml Sun Jun 09 08:18:30 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ - - - - - - - - - - - - diff -r 54b870eaca8d -r a9c27818f417 tool-data/omssa_mods.loc.sample --- a/tool-data/omssa_mods.loc.sample Sun Jun 09 08:18:30 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,181 +0,0 @@ -#This file lists the names of chemical modifications accepted by OMMSA -# -# -2-amino-3-oxo-butanoic acid T 2-amino-3-oxo-butanoicacidt_ 23 2-amino-3-oxo-butanoicacidt_ -Asparagine HexNAc asparaginehexnac_ 182 asparaginehexnac_ -Asparagine dHexHexNAc asparaginedhexhexnac_ 183 asparaginedhexhexnac_ -CAMthiopropanoyl K camthiopropanoylk_ 131 camthiopropanoylk_ -CHD2-di-methylation of K chd2-di-methylationofk_ 189 chd2-di-methylationofk_ -CHD2-di-methylation of peptide n-term chd2-di-methylationofpeptiden-term_ 190 chd2-di-methylationofpeptiden-term_ -ICAT heavy icatheavy_ 130 icatheavy_ -ICAT light icatlight_ 129 icatlight_ -M cleavage from protein n-term mcleavagefromproteinn-term_ 9 mcleavagefromproteinn-term_ -MMTS on C mmtsonc_ 179 mmtsonc_ -Maleimide-PEO2-Biotin of C maleimide-peo2-biotinofc_ 191 maleimide-peo2-biotinofc_ -NEM C nemc_ 83 nemc_ -NIPCAM nipcam_ 84 nipcam_ -O18 on peptide n-term o18onpeptiden-term_ 87 o18onpeptiden-term_ -PNGasF in O18 water pngasfino18water_ 139 pngasfino18water_ -SeMet semet_ 113 semet_ -Serine HexNAc serinehexnac_ 184 serinehexnac_ -TMT 6-plex on K tmt6-plexonk_ 198 tmt6-plexonk_ -TMT 6-plex on n-term peptide tmt6-plexonn-termpeptide_ 199 tmt6-plexonn-termpeptide_ -Threonine HexNAc threoninehexnac_ 185 threoninehexnac_ -Uniblue A on K uniblueaonk_ 195 uniblueaonk_ -acetylation of K acetylationofk_ 24 acetylationofk_ -acetylation of protein n-term acetylationofproteinn-term_ 10 acetylationofproteinn-term_ -amidation of peptide c-term amidationofpeptidec-term_ 25 amidationofpeptidec-term_ -arginine to ornithine argininetoornithine_ 163 argininetoornithine_ -beta elimination of S betaeliminationofs_ 140 betaeliminationofs_ -beta elimination of T betaeliminationoft_ 141 betaeliminationoft_ -beta methythiolation of D betamethythiolationofd_ 13 betamethythiolationofd_ -beta-carboxylation of D beta-carboxylationofd_ 47 beta-carboxylationofd_ -beta-methylthiolation of D (duplicate of 13) beta-methylthiolationofd_duplicateof13__ 26 beta-methylthiolationofd_duplicateof13__ -carbamidomethyl C carbamidomethylc_ 3 carbamidomethylc_ -carbamylation of K carbamylationofk_ 31 carbamylationofk_ -carbamylation of n-term peptide carbamylationofn-termpeptide_ 32 carbamylationofn-termpeptide_ -carboxyamidomethylation of D carboxyamidomethylationofd_ 29 carboxyamidomethylationofd_ -carboxyamidomethylation of E carboxyamidomethylationofe_ 30 carboxyamidomethylationofe_ -carboxyamidomethylation of H carboxyamidomethylationofh_ 28 carboxyamidomethylationofh_ -carboxyamidomethylation of K carboxyamidomethylationofk_ 27 carboxyamidomethylationofk_ -carboxykynurenin of W carboxykynureninofw_ 165 carboxykynureninofw_ -carboxymethyl C carboxymethylc_ 2 carboxymethylc_ -carboxymethylated selenocysteine carboxymethylatedselenocysteine_ 207 carboxymethylatedselenocysteine_ -citrullination of R citrullinationofr_ 33 citrullinationofr_ -deamidation of N deamidationofn_ 196 deamidationofn_ -deamidation of N and Q deamidationofnandq_ 4 deamidationofnandq_ -dehydro of S and T dehydroofsandt_ 164 dehydroofsandt_ -di-O18 on peptide n-term di-o18onpeptiden-term_ 88 di-o18onpeptiden-term_ -di-iodination of Y di-iodinationofy_ 35 di-iodinationofy_ -di-methylation of K di-methylationofk_ 36 di-methylationofk_ -di-methylation of R di-methylationofr_ 37 di-methylationofr_ -di-methylation of peptide n-term di-methylationofpeptiden-term_ 38 di-methylationofpeptiden-term_ -farnesylation of C farnesylationofc_ 42 farnesylationofc_ -fluorophenylalanine fluorophenylalanine_ 46 fluorophenylalanine_ -formylation of K formylationofk_ 43 formylationofk_ -formylation of peptide n-term formylationofpeptiden-term_ 44 formylationofpeptiden-term_ -formylation of protein n-term formylationofproteinn-term_ 82 formylationofproteinn-term_ -gamma-carboxylation of E gamma-carboxylationofe_ 48 gamma-carboxylationofe_ -gammathiopropionylation of K gammathiopropionylationofk_ 40 gammathiopropionylationofk_ -gammathiopropionylation of peptide n-term gammathiopropionylationofpeptiden-term_ 41 gammathiopropionylationofpeptiden-term_ -geranyl-geranyl geranyl-geranyl_ 49 geranyl-geranyl_ -glucuronylation of protein n-term glucuronylationofproteinn-term_ 50 glucuronylationofproteinn-term_ -glutathione disulfide glutathionedisulfide_ 51 glutathionedisulfide_ -guanidination of K guanidinationofk_ 53 guanidinationofk_ -heavy arginine-13C6 heavyarginine-13c6_ 136 heavyarginine-13c6_ -heavy arginine-13C6-15N4 heavyarginine-13c6-15n4_ 137 heavyarginine-13c6-15n4_ -heavy lysine - 13C6 15N2 heavylysine-13c615n2_ 181 heavylysine-13c615n2_ -heavy lysine - 2H4 heavylysine-2h4_ 180 heavylysine-2h4_ -heavy lysine-13C6 heavylysine-13c6_ 138 heavylysine-13c6_ -homoserine homoserine_ 56 homoserine_ -homoserine lactone homoserinelactone_ 57 homoserinelactone_ -hydroxylation of Y hydroxylationofy_ 64 hydroxylationofy_ -hydroxylation of D hydroxylationofd_ 59 hydroxylationofd_ -hydroxylation of F hydroxylationoff_ 63 hydroxylationoff_ -hydroxylation of K hydroxylationofk_ 60 hydroxylationofk_ -hydroxylation of N hydroxylationofn_ 61 hydroxylationofn_ -hydroxylation of P hydroxylationofp_ 62 hydroxylationofp_ -iTRAQ114 on K itraq114onk_ 168 itraq114onk_ -iTRAQ114 on Y itraq114ony_ 169 itraq114ony_ -iTRAQ114 on nterm itraq114onnterm_ 167 itraq114onnterm_ -iTRAQ115 on K itraq115onk_ 171 itraq115onk_ -iTRAQ115 on Y itraq115ony_ 172 itraq115ony_ -iTRAQ115 on nterm itraq115onnterm_ 170 itraq115onnterm_ -iTRAQ116 on K itraq116onk_ 174 itraq116onk_ -iTRAQ116 on Y itraq116ony_ 175 itraq116ony_ -iTRAQ116 on nterm itraq116onnterm_ 173 itraq116onnterm_ -iTRAQ117 on K itraq117onk_ 177 itraq117onk_ -iTRAQ117 on Y itraq117ony_ 178 itraq117ony_ -iTRAQ117 on nterm itraq117onnterm_ 176 itraq117onnterm_ -iTRAQ8plex itraq8plex_ 204 itraq8plex_ -iTRAQ8plex itraq8plex_ 205 itraq8plex_ -iTRAQ8plex itraq8plex_ 203 itraq8plex_ -iTRAQ8plex itraq8plex_ 201 itraq8plex_ -iTRAQ8plex itraq8plex_ 202 itraq8plex_ -iTRAQ8plex itraq8plex_ 200 itraq8plex_ -iodination of Y iodinationofy_ 65 iodinationofy_ -lipoyl K lipoylk_ 67 lipoylk_ -methyl C methylc_ 73 methylc_ -methyl H methylh_ 74 methylh_ -methyl N methyln_ 75 methyln_ -methyl R methylr_ 77 methylr_ -methyl ester of D methylesterofd_ 69 methylesterofd_ -methyl ester of E (duplicate of 17) methylesterofe_duplicateof17__ 70 methylesterofe_duplicateof17__ -methyl ester of S methylesterofs_ 71 methylesterofs_ -methyl ester of Y methylesterofy_ 72 methylesterofy_ -methyl ester of peptide c-term (duplicate of 18) methylesterofpeptidec-term_duplicateof18__ 68 methylesterofpeptidec-term_duplicateof18__ -methylation of D methylationofd_ 16 methylationofd_ -methylation of E methylationofe_ 17 methylationofe_ -methylation of K methylationofk_ 0 methylationofk_ -methylation of Q methylationofq_ 14 methylationofq_ -methylation of peptide c-term methylationofpeptidec-term_ 18 methylationofpeptidec-term_ -methylation of peptide n-term methylationofpeptiden-term_ 76 methylationofpeptiden-term_ -methylation of protein n-term methylationofproteinn-term_ 11 methylationofproteinn-term_ -myristoleylation of G myristoleylationofg_ 78 myristoleylationofg_ -myristoyl-4H of G myristoyl-4hofg_ 79 myristoyl-4hofg_ -myristoylation of K myristoylationofk_ 81 myristoylationofk_ -myristoylation of peptide n-term G myristoylationofpeptiden-termg_ 80 myristoylationofpeptiden-termg_ -n-acyl diglyceride cysteine n-acyldiglyceridecysteine_ 118 n-acyldiglyceridecysteine_ -n-formyl met addition n-formylmetaddition_ 22 n-formylmetaddition_ -oxidation of C oxidationofc_ 193 oxidationofc_ -oxidation of C to cysteic acid oxidationofctocysteicacid_ 34 oxidationofctocysteicacid_ -oxidation of C to sulfinic acid oxidationofctosulfinicacid_ 162 oxidationofctosulfinicacid_ -oxidation of F to dihydroxyphenylalanine oxidationofftodihydroxyphenylalanine_ 39 oxidationofftodihydroxyphenylalanine_ -oxidation of H oxidationofh_ 89 oxidationofh_ -oxidation of H to D oxidationofhtod_ 55 oxidationofhtod_ -oxidation of H to N oxidationofhton_ 54 oxidationofhton_ -oxidation of M oxidationofm_ 1 oxidationofm_ -oxidation of P to pyroglutamic acid oxidationofptopyroglutamicacid_ 111 oxidationofptopyroglutamicacid_ -oxidation of W oxidationofw_ 90 oxidationofw_ -oxidation of W to formylkynurenin oxidationofwtoformylkynurenin_ 45 oxidationofwtoformylkynurenin_ -oxidation of W to hydroxykynurenin oxidationofwtohydroxykynurenin_ 58 oxidationofwtohydroxykynurenin_ -oxidation of W to kynurenin oxidationofwtokynurenin_ 66 oxidationofwtokynurenin_ -oxidation of W to nitro oxidationofwtonitro_ 85 oxidationofwtonitro_ -oxidation of Y (duplicate of 64) oxidationofy_duplicateof64__ 194 oxidationofy_duplicateof64__ -oxidation of Y to nitro oxidationofytonitro_ 86 oxidationofytonitro_ -palmitoleyl of C palmitoleylofc_ 187 palmitoleylofc_ -palmitoleyl of S palmitoleylofs_ 186 palmitoleylofs_ -palmitoleyl of T palmitoleyloft_ 188 palmitoleyloft_ -palmitoylation of C palmitoylationofc_ 92 palmitoylationofc_ -palmitoylation of K palmitoylationofk_ 93 palmitoylationofk_ -palmitoylation of S palmitoylationofs_ 94 palmitoylationofs_ -palmitoylation of T palmitoylationoft_ 95 palmitoylationoft_ -phosphopantetheine S phosphopantetheines_ 91 phosphopantetheines_ -phosphorylation of H phosphorylationofh_ 192 phosphorylationofh_ -phosphorylation of S phosphorylationofs_ 6 phosphorylationofs_ -phosphorylation of S with ETD loss phosphorylationofswithetdloss_ 134 phosphorylationofswithetdloss_ -phosphorylation of S with prompt loss phosphorylationofswithpromptloss_ 96 phosphorylationofswithpromptloss_ -phosphorylation of T phosphorylationoft_ 7 phosphorylationoft_ -phosphorylation of T with ETD loss phosphorylationoftwithetdloss_ 135 phosphorylationoftwithetdloss_ -phosphorylation of T with prompt loss phosphorylationoftwithpromptloss_ 97 phosphorylationoftwithpromptloss_ -phosphorylation of Y phosphorylationofy_ 8 phosphorylationofy_ -phosphorylation with neutral loss on C phosphorylationwithneutrallossonc_ 99 phosphorylationwithneutrallossonc_ -phosphorylation with neutral loss on D phosphorylationwithneutrallossond_ 100 phosphorylationwithneutrallossond_ -phosphorylation with neutral loss on H phosphorylationwithneutrallossonh_ 101 phosphorylationwithneutrallossonh_ -phosphorylation with neutral loss on S phosphorylationwithneutrallossons_ 132 phosphorylationwithneutrallossons_ -phosphorylation with neutral loss on T phosphorylationwithneutrallossont_ 133 phosphorylationwithneutrallossont_ -phosphorylation with prompt loss on Y phosphorylationwithpromptlossony_ 98 phosphorylationwithpromptlossony_ -propionamide C propionamidec_ 5 propionamidec_ -propionyl heavy K propionylheavyk_ 104 propionylheavyk_ -propionyl heavy peptide n-term propionylheavypeptiden-term_ 105 propionylheavypeptiden-term_ -propionyl light K propionyllightk_ 102 propionyllightk_ -propionyl light on peptide n-term propionyllightonpeptiden-term_ 103 propionyllightonpeptiden-term_ -pyridyl K pyridylk_ 106 pyridylk_ -pyridyl peptide n-term pyridylpeptiden-term_ 107 pyridylpeptiden-term_ -pyro-cmC pyro-cmc_ 108 pyro-cmc_ -pyro-glu from n-term E pyro-glufromn-terme_ 109 pyro-glufromn-terme_ -pyro-glu from n-term Q pyro-glufromn-termq_ 110 pyro-glufromn-termq_ -s-pyridylethylation of C s-pyridylethylationofc_ 112 s-pyridylethylationofc_ -selenocysteine selenocysteine_ 206 selenocysteine_ -sulfation of Y sulfationofy_ 114 sulfationofy_ -sulphone of M sulphoneofm_ 115 sulphoneofm_ -sumoylation of K sumoylationofk_ 166 sumoylationofk_ -tri-deuteromethylation of D tri-deuteromethylationofd_ 19 tri-deuteromethylationofd_ -tri-deuteromethylation of E tri-deuteromethylationofe_ 20 tri-deuteromethylationofe_ -tri-deuteromethylation of peptide c-term tri-deuteromethylationofpeptidec-term_ 21 tri-deuteromethylationofpeptidec-term_ -tri-iodination of Y tri-iodinationofy_ 116 tri-iodinationofy_ -tri-methylation of K tri-methylationofk_ 15 tri-methylationofk_ -tri-methylation of R tri-methylationofr_ 117 tri-methylationofr_ -tri-methylation of protein n-term tri-methylationofproteinn-term_ 12 tri-methylationofproteinn-term_ -trideuteration of L (SILAC) trideuterationofl_silac__ 197 trideuterationofl_silac__ -ubiquitinylation residue ubiquitinylationresidue_ 52 ubiquitinylationresidue_ diff -r 54b870eaca8d -r a9c27818f417 tool-data/pepxml_databases.loc.sample --- a/tool-data/pepxml_databases.loc.sample Sun Jun 09 08:18:30 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#This file lists the names of protein databases installed locally in protk. -# These are used by omssa and x!tandem as well as the "mascot to pepxml" tool -# In order to combine search results with Interprophet searches must be run against an identical database -# -# Entries should follow the be structured as follows -# Display_name omssa_tandem_dbname dbkey -# -# -Swissprot spall_ spall spall_ -Combined PlasmboDB (falciparum) and Swissprot Human plasmodb_pfalciparum_sphuman_ plasmodb_pfalciparum_sphuman plasmodb_pfalciparum_sphuman_ -Swissprot Human sphuman_ sphuman sphuman_ -Combined Swissprot/TRembl Human sptrhuman_ sptrhuman sptrhuman_ -Swissprot Mouse spmouse_ spmouse spmouse_ diff -r 54b870eaca8d -r a9c27818f417 tool_dependencies.xml --- a/tool_dependencies.xml Sun Jun 09 08:18:30 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - - - - - - - - - - - - - - - - - -