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README omssa.xml repository_dependencies.xml tool-data/omssa_mods.loc.sample tool-data/pepxml_databases.loc.sample tool_dependencies.xml |
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README.md |
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| diff -r a9c27818f417 -r ac9be1d4885d README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Sat Jun 14 18:01:42 2014 -0400 |
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| @@ -0,0 +1,5 @@ +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 |
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| diff -r a9c27818f417 -r ac9be1d4885d README.md --- a/README.md Sat Jun 14 18:01:24 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -## 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). - |
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| diff -r a9c27818f417 -r ac9be1d4885d omssa.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omssa.xml Sat Jun 14 18:01:42 2014 -0400 |
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| @@ -0,0 +1,189 @@ +<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1"> + + <requirements> + <requirement type="package" version="1.3">protk</requirement> + <requirement type="package" version="2.1.9">omssa</requirement> + <requirement type="package" version="2.2.29">blast+</requirement> + </requirements> + + + <description>Run an OMSSA MS/MS Search</description> + + <command>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 + + </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> |
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| diff -r a9c27818f417 -r ac9be1d4885d repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Sat Jun 14 18:01:42 2014 -0400 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Proteomics datatypes"> + <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + </repositories> |
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| diff -r a9c27818f417 -r ac9be1d4885d tool-data/omssa_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/omssa_mods.loc.sample Sat Jun 14 18:01:42 2014 -0400 |
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| b'@@ -0,0 +1,181 @@\n+#This file lists the names of chemical modifications accepted by OMMSA\n+#\n+#\n+2-amino-3-oxo-butanoic acid T\t2-amino-3-oxo-butanoicacidt_\t23\t2-amino-3-oxo-butanoicacidt_\n+Asparagine HexNAc\tasparaginehexnac_\t182\tasparaginehexnac_\n+Asparagine dHexHexNAc\tasparaginedhexhexnac_\t183\tasparaginedhexhexnac_\n+CAMthiopropanoyl K\tcamthiopropanoylk_\t131\tcamthiopropanoylk_\n+CHD2-di-methylation of K\tchd2-di-methylationofk_\t189\tchd2-di-methylationofk_\n+CHD2-di-methylation of peptide n-term\tchd2-di-methylationofpeptiden-term_\t190\tchd2-di-methylationofpeptiden-term_\n+ICAT heavy\ticatheavy_\t130\ticatheavy_\n+ICAT light\ticatlight_\t129\ticatlight_\n+M cleavage from protein n-term\tmcleavagefromproteinn-term_\t9\tmcleavagefromproteinn-term_\n+MMTS on C\tmmtsonc_\t179\tmmtsonc_\n+Maleimide-PEO2-Biotin of C\tmaleimide-peo2-biotinofc_\t191\tmaleimide-peo2-biotinofc_\n+NEM C\tnemc_\t83\tnemc_\n+NIPCAM\tnipcam_\t84\tnipcam_\n+O18 on peptide n-term\to18onpeptiden-term_\t87\to18onpeptiden-term_\n+PNGasF in O18 water\tpngasfino18water_\t139\tpngasfino18water_\n+SeMet\tsemet_\t113\tsemet_\n+Serine HexNAc\tserinehexnac_\t184\tserinehexnac_\n+TMT 6-plex on K\ttmt6-plexonk_\t198\ttmt6-plexonk_\n+TMT 6-plex on n-term peptide\ttmt6-plexonn-termpeptide_\t199\ttmt6-plexonn-termpeptide_\n+Threonine HexNAc\tthreoninehexnac_\t185\tthreoninehexnac_\n+Uniblue A on K\tuniblueaonk_\t195\tuniblueaonk_\n+acetylation of K\tacetylationofk_\t24\tacetylationofk_\n+acetylation of protein n-term\tacetylationofproteinn-term_\t10\tacetylationofproteinn-term_\n+amidation of peptide c-term\tamidationofpeptidec-term_\t25\tamidationofpeptidec-term_\n+arginine to ornithine\targininetoornithine_\t163\targininetoornithine_\n+beta elimination of S\tbetaeliminationofs_\t140\tbetaeliminationofs_\n+beta elimination of T\tbetaeliminationoft_\t141\tbetaeliminationoft_\n+beta methythiolation of D\tbetamethythiolationofd_\t13\tbetamethythiolationofd_\n+beta-carboxylation of D\tbeta-carboxylationofd_\t47\tbeta-carboxylationofd_\n+beta-methylthiolation of D (duplicate of 13)\tbeta-methylthiolationofd_duplicateof13__\t26\tbeta-methylthiolationofd_duplicateof13__\n+carbamidomethyl C\tcarbamidomethylc_\t3\tcarbamidomethylc_\n+carbamylation of K\tcarbamylationofk_\t31\tcarbamylationofk_\n+carbamylation of n-term peptide\tcarbamylationofn-termpeptide_\t32\tcarbamylationofn-termpeptide_\n+carboxyamidomethylation of D\tcarboxyamidomethylationofd_\t29\tcarboxyamidomethylationofd_\n+carboxyamidomethylation of E\tcarboxyamidomethylationofe_\t30\tcarboxyamidomethylationofe_\n+carboxyamidomethylation of H\tcarboxyamidomethylationofh_\t28\tcarboxyamidomethylationofh_\n+carboxyamidomethylation of K\tcarboxyamidomethylationofk_\t27\tcarboxyamidomethylationofk_\n+carboxykynurenin of W\tcarboxykynureninofw_\t165\tcarboxykynureninofw_\n+carboxymethyl C\tcarboxymethylc_\t2\tcarboxymethylc_\n+carboxymethylated selenocysteine\tcarboxymethylatedselenocysteine_\t207\tcarboxymethylatedselenocysteine_\n+citrullination of R\tcitrullinationofr_\t33\tcitrullinationofr_\n+deamidation of N\tdeamidationofn_\t196\tdeamidationofn_\n+deamidation of N and Q\tdeamidationofnandq_\t4\tdeamidationofnandq_\n+dehydro of S and T\tdehydroofsandt_\t164\tdehydroofsandt_\n+di-O18 on peptide n-term\tdi-o18onpeptiden-term_\t88\tdi-o18onpeptiden-term_\n+di-iodination of Y\tdi-iodinationofy_\t35\tdi-iodinationofy_\n+di-methylation of K\tdi-methylationofk_\t36\tdi-methylationofk_\n+di-methylation of R\tdi-methylationofr_\t37\tdi-methylationofr_\n+di-methylation of peptide n-term\tdi-methylationofpeptiden-term_\t38\tdi-methylationofpeptiden-term_\n+farnesylation of C\tfarnesylationofc_\t42\tfarnesylationofc_\n+fluorophenylalanine\tfluorophenylalanine_\t46\tfluorophenylalanine_\n+formylation of K\tformylationofk_\t43\tformylationofk_\n+formylation of peptide n-term\tformylationofpeptiden-term_\t44\tformylationofpeptiden-term_\n+formylation of protein n-term\tformylationofproteinn-term_\t82\tformylationofproteinn-term_\n+gamma-carboxylation of E\tgamma-carboxylationofe_\t48\tgamma-carboxylationofe_\n+gammathiopropionylation of K\tgammathiopropionylationofk_\t40\tgammathiopropionylationofk_\n+gammathiopropionylation of peptid'..b'enin\toxidationofwtoformylkynurenin_\t45\toxidationofwtoformylkynurenin_\n+oxidation of W to hydroxykynurenin\toxidationofwtohydroxykynurenin_\t58\toxidationofwtohydroxykynurenin_\n+oxidation of W to kynurenin\toxidationofwtokynurenin_\t66\toxidationofwtokynurenin_\n+oxidation of W to nitro\toxidationofwtonitro_\t85\toxidationofwtonitro_\n+oxidation of Y (duplicate of 64)\toxidationofy_duplicateof64__\t194\toxidationofy_duplicateof64__\n+oxidation of Y to nitro\toxidationofytonitro_\t86\toxidationofytonitro_\n+palmitoleyl of C\tpalmitoleylofc_\t187\tpalmitoleylofc_\n+palmitoleyl of S\tpalmitoleylofs_\t186\tpalmitoleylofs_\n+palmitoleyl of T\tpalmitoleyloft_\t188\tpalmitoleyloft_\n+palmitoylation of C\tpalmitoylationofc_\t92\tpalmitoylationofc_\n+palmitoylation of K\tpalmitoylationofk_\t93\tpalmitoylationofk_\n+palmitoylation of S\tpalmitoylationofs_\t94\tpalmitoylationofs_\n+palmitoylation of T\tpalmitoylationoft_\t95\tpalmitoylationoft_\n+phosphopantetheine S\tphosphopantetheines_\t91\tphosphopantetheines_\n+phosphorylation of H\tphosphorylationofh_\t192\tphosphorylationofh_\n+phosphorylation of S\tphosphorylationofs_\t6\tphosphorylationofs_\n+phosphorylation of S with ETD loss\tphosphorylationofswithetdloss_\t134\tphosphorylationofswithetdloss_\n+phosphorylation of S with prompt loss\tphosphorylationofswithpromptloss_\t96\tphosphorylationofswithpromptloss_\n+phosphorylation of T\tphosphorylationoft_\t7\tphosphorylationoft_\n+phosphorylation of T with ETD loss\tphosphorylationoftwithetdloss_\t135\tphosphorylationoftwithetdloss_\n+phosphorylation of T with prompt loss\tphosphorylationoftwithpromptloss_\t97\tphosphorylationoftwithpromptloss_\n+phosphorylation of Y\tphosphorylationofy_\t8\tphosphorylationofy_\n+phosphorylation with neutral loss on C\tphosphorylationwithneutrallossonc_\t99\tphosphorylationwithneutrallossonc_\n+phosphorylation with neutral loss on D\tphosphorylationwithneutrallossond_\t100\tphosphorylationwithneutrallossond_\n+phosphorylation with neutral loss on H\tphosphorylationwithneutrallossonh_\t101\tphosphorylationwithneutrallossonh_\n+phosphorylation with neutral loss on S\tphosphorylationwithneutrallossons_\t132\tphosphorylationwithneutrallossons_\n+phosphorylation with neutral loss on T\tphosphorylationwithneutrallossont_\t133\tphosphorylationwithneutrallossont_\n+phosphorylation with prompt loss on Y\tphosphorylationwithpromptlossony_\t98\tphosphorylationwithpromptlossony_\n+propionamide C\tpropionamidec_\t5\tpropionamidec_\n+propionyl heavy K\tpropionylheavyk_\t104\tpropionylheavyk_\n+propionyl heavy peptide n-term\tpropionylheavypeptiden-term_\t105\tpropionylheavypeptiden-term_\n+propionyl light K\tpropionyllightk_\t102\tpropionyllightk_\n+propionyl light on peptide n-term\tpropionyllightonpeptiden-term_\t103\tpropionyllightonpeptiden-term_\n+pyridyl K\tpyridylk_\t106\tpyridylk_\n+pyridyl peptide n-term\tpyridylpeptiden-term_\t107\tpyridylpeptiden-term_\n+pyro-cmC\tpyro-cmc_\t108\tpyro-cmc_\n+pyro-glu from n-term E\tpyro-glufromn-terme_\t109\tpyro-glufromn-terme_\n+pyro-glu from n-term Q\tpyro-glufromn-termq_\t110\tpyro-glufromn-termq_\n+s-pyridylethylation of C\ts-pyridylethylationofc_\t112\ts-pyridylethylationofc_\n+selenocysteine\tselenocysteine_\t206\tselenocysteine_\n+sulfation of Y\tsulfationofy_\t114\tsulfationofy_\n+sulphone of M\tsulphoneofm_\t115\tsulphoneofm_\n+sumoylation of K\tsumoylationofk_\t166\tsumoylationofk_\n+tri-deuteromethylation of D\ttri-deuteromethylationofd_\t19\ttri-deuteromethylationofd_\n+tri-deuteromethylation of E\ttri-deuteromethylationofe_\t20\ttri-deuteromethylationofe_\n+tri-deuteromethylation of peptide c-term\ttri-deuteromethylationofpeptidec-term_\t21\ttri-deuteromethylationofpeptidec-term_\n+tri-iodination of Y\ttri-iodinationofy_\t116\ttri-iodinationofy_\n+tri-methylation of K\ttri-methylationofk_\t15\ttri-methylationofk_\n+tri-methylation of R\ttri-methylationofr_\t117\ttri-methylationofr_\n+tri-methylation of protein n-term\ttri-methylationofproteinn-term_\t12\ttri-methylationofproteinn-term_\n+trideuteration of L (SILAC)\ttrideuterationofl_silac__\t197\ttrideuterationofl_silac__\n+ubiquitinylation residue\tubiquitinylationresidue_\t52\tubiquitinylationresidue_\n' |
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| diff -r a9c27818f417 -r ac9be1d4885d tool-data/pepxml_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pepxml_databases.loc.sample Sat Jun 14 18:01:42 2014 -0400 |
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| @@ -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_ |
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| diff -r a9c27818f417 -r ac9be1d4885d tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Jun 14 18:01:42 2014 -0400 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tool_dependency> + + <package name="blast+" version="2.2.29"> + <repository changeset_revision="a2ec897aac2c" name="package_blast_plus_2_2_29" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + +</tool_dependency> |