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README.md |
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._.DS_Store 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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| diff -r 54b870eaca8d -r a9c27818f417 ._.DS_Store |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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). + |
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| 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 |
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| @@ -1,189 +0,0 @@ -<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1"> - - <requirements> - <requirement type="package" version="1.2.2">galaxy_protk</requirement> - <requirement type="package" version="2.1.9">omssa</requirement> - <requirement type="package" version="2.2.27">blast</requirement> - </requirements> - - - <description>Run an OMSSA MS/MS Search</description> - - <command>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 - - </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 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 |
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| @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Proteomics datatypes, omssa and blast executables"> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="e34365cd29fa"/> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="8f3813e7b0a6"/> - -</repositories> |
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| 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 |
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| b'@@ -1,181 +0,0 @@\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 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 |
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| @@ -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_ |
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| 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 |
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| @@ -1,18 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - - <package name="galaxy_protk" version="1.2.2"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/> - </package> - - <package name="blast" version="2.2.27"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="e34365cd29fa"/> - </package> - - <package name="omssa" version="2.1.9"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="8f3813e7b0a6"/> - </package> - - - -</tool_dependency> |