Mercurial > repos > iracooke > omssa
changeset 0:5e1594a15956
Uploaded
| author | iracooke |
|---|---|
| date | Sun, 06 Jan 2013 20:03:20 -0500 |
| parents | |
| children | 21cede3cfb9b |
| files | omssa.xml tool-data/omssa_mods.loc.sample tool-data/pepxml_databases.loc.sample |
| diffstat | 3 files changed, 355 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omssa.xml Sun Jan 06 20:03:20 2013 -0500 @@ -0,0 +1,161 @@ +<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.0"> + <requirements> + <requirement type="package">protkgem</requirement> + </requirements> + + <description>Run an OMSSA MS/MS Search</description> + + <command>#if $database.source_select=="built_in": + omssa_search.rb -d $database.dbkey + #else #omssa_search.rb -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 + + </command> + + + <inputs> + <conditional name="database"> + <param name="source_select" type="select" label="Database source"> + <option value="built_in">Built-In</option> + <option value="input_ref">Uploaded fasta file</option> + </param> + <when value="built_in"> + <param name="dbkey" type="select" format="text" > + <label>Database</label> + <options from_file="pepxml_databases.loc"> + <column name="name" index="0" /> + <column name="value" index="2" /> + </options> + </param> + </when> + <when value="input_ref"> + <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> + </when> + </conditional> + + <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/> + + <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while + clicking to select multiple items"> + <options from_file="omssa_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="2" /> + </options> + </param> + + <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while + clicking to select multiple items"> + <options from_file="omssa_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="2" /> + </options> + </param> + + + <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> + <label>Missed Cleavages Allowed</label> + <option value="0">0</option> + <option value="1">1</option> + <option value="2">2</option> + </param> + + <param name="enzyme" type="select" format="text"> + <label>Enzyme</label> + <option value="0">Trypsin</option> + <option value="1">Arg-C</option> + <option value="2">CNBr</option> + <option value="3">Chymotrypsin (FYWL)</option> + <option value="4">Formic Acid</option> + <option value="5">Lys-C</option> + <option value="6">Lys-C, no P rule</option> + <option value="7">Pepsin A</option> + <option value="8">Trypsin+CNBr</option> + <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option> + <option value="10">Trypsin, no P rule</option> + <option value="11">Whole protein</option> + <option value="12">Asp-N</option> + <option value="13">Glu-C</option> + <option value="14">Asp-N+Glu-C</option> + <option value="15">Top-Down</option> + <option value="16">Semi-Tryptic</option> + <option value="17">No Enzyme</option> + <option value="18">Chymotrypsin, no P rule (FYWL)</option> + <option value="19">Asp-N (DE)</option> + <option value="20">Glu-C (DE)</option> + <option value="21">Lys-N (K)</option> + <option value="22">Thermolysin, no P rule</option> + <option value="23">Semi-Chymotrypsin (FYWL)</option> + <option value="24">Semi-Glu-C</option> + </param> + + <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/> + <param name="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="1.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he--> + <param name="intensity_cut_off" help="Peak intensity cut-off as a fraction of maximum peak intensity" type="float" value="0.0005" min="0" max="1" label="Peak intensity cut-off"/><!-- -ci--> + + + <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> + <param name="precursor_tolu" type="select" format="text"> + <label>Precursor Ion Tolerance Units</label> + <option value="ppm">ppm</option> + <option value="Da">Da</option> + </param> + + <param name="use_average_mass" type="boolean" label="Use average precursor masses" help="Match precursor to average mass of the parent ion instead of its monoisotopic mass" truevalue="-a average" falsevalue=""/> + <param name="respect_precursor_charges" type="boolean" label="Respect precursor charges" help="Use precursor charge information in input file rather than OMSSA's inferred value" truevalue="--respect-charges" falsevalue=""/> + + <param name="multi_isotope" type="select" format="text" help="Include this many neighbouring peaks when searching for a match to the precursor mass. Only used when doing monoisotopic search"> + <label>Multi-isotope search.</label> + <option value="0">0</option> + <option value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + <option value="4">4</option> + </param> + + <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help=""> + <option selected="true" value="0">a</option> + <option selected="true" value="1">b</option> + <option value="2">c</option> + <option selected="true" value="3">x</option> + <option selected="true" value="4">y</option> + <option value="5">zdot</option> + <option value="10">adot</option> + <option value="11">x-CO2</option> + <option value="12">adot-CO2</option> + </param> + + </inputs> + + <outputs> + <data format="raw_pepxml" name="output" metadata_source="input_file" label="omssa_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.pepXML"/> + </outputs> + + <help> +**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). + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/omssa_mods.loc.sample Sun Jan 06 20:03:20 2013 -0500 @@ -0,0 +1,181 @@ +#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_
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pepxml_databases.loc.sample Sun Jan 06 20:03:20 2013 -0500 @@ -0,0 +1,13 @@ +#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_