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_