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README mascot.xml mascot_to_pepxml.xml repository_dependencies.xml tool-data/mascot_databases.loc.sample tool-data/mascot_mods.loc.sample tool-data/pepxml_databases.loc.sample tool-data/tandem_mods.loc.sample tool_dependencies.xml |
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| diff -r 327b2d99d4c5 -r f36b84d1ac09 README --- a/README Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ -This includes tools for running Mascot MS/MS searches - -Running this tool requires a working installation of Mascot (commercial software). -Mascot is available from http://www.matrixscience.com/ - -Requirements: -This package depends on the galaxy_protk and protk_trans_proteomic_pipeline packages -Please see instructions for those packages before installing. In particular -you will need to install system package requirements for galaxy_protk and protk_trans_proteomic_pipeline -using your package manager |
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| diff -r 327b2d99d4c5 -r f36b84d1ac09 mascot.xml --- a/mascot.xml Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,186 +0,0 @@ -<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.1"> - - - <requirements> - <requirement type="package" version="1.2.2">galaxy_protk</requirement> - </requirements> - - <description>Mascot MS/MS Search</description> - - - <command>rvm 1.9.3@protk-1.2.2 do mascot_search.rb - - #if $database.source_select=="built_in": - -d $database.dbkey - #else - -d $database.custom_db - #end if - - -f $fragment_ion_tol - - -S $server $input_file - - -o $output - - -r - - ## Variable Mods - - --var-mods=' - $variable_mods - ' - - --fix-mods=' - $fixed_mods - ' - --allowed-charges=$allowed_charges - - --enzyme=$enzyme - - --instrument=$instrument - - --precursor-ion-tol-units=$precursor_tolu - - --email=$email - - -v $missed_cleavages - - #if $security.security_use - --use-security - --username $security.username - --password $security.password - #end if - - #if $proxy - --proxy $proxy - #end if - - </command> - - <inputs> - - <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/> - - <conditional name="database"> - <param name="source_select" type="select" label="Database Type"> - <option value="built_in">Built-In</option> - <option value="custom_defined">Custom</option> - </param> - <when value="built_in"> - <param name="dbkey" type="select" format="text" > - <label>Database</label> - <options from_file="mascot_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - </when> - <when value="custom_defined"> - <param name="custom_db" type="text" size="80" value="SwissProt" label="Database Name" help="Exact name of a database defined on the Mascot server (case-sensitive)"/> - </when> - </conditional> - - <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed"> - <options from_file="mascot_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="Multiple values allowed"> - <options from_file="mascot_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - - <param name="missed_cleavages" type="select" format="text"> - <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="Trypsin">Trypsin</option> - </param> - - <param name="allowed_charges" type="select" format="text"> - <label>Peptide Charge</label> - <option value="8-">8-</option> - <option value="7-">7-</option> - <option value="6-">6-</option> - <option value="5-">5-</option> - <option value="4-">4-</option> - <option value="3-">3-</option> - <option value="2-,3- and 4-">2-,3- and 4-</option> - <option value="2- and 3-">2- and 3-</option> - <option value="2-">2-</option> - <option value="1-,2- and 3-">1-,2- and 3-</option> - <option value="1-">1-</option> - <option value="Mr">Mr</option> - <option value="1+">1+</option> - <option value="1+, 2+ and 3+">1+,2+ and 3+</option> - <option value="2+">2+</option> - <option value="2+ and 3+">2+ and 3+</option> - <option value="2+,3+ and 4+">2+,3+ and 4+</option> - <option value="3+">3+</option> - <option value="4+">4+</option> - <option value="5+">5+</option> - <option value="6+">6+</option> - <option value="7+">7+</option> - <option value="8+">8+</option> - </param> - - <param name="instrument" type="select" format="text"> - <label>Instrument</label> - <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option> - <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option> - <option value="ESI-TRAP">ESI-TRAP</option> - <option value="ESI-QUAD">ESI-QUAD</option> - <option value="ESI-FTICR">ESI-FTICR</option> - <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option> - <option value="ESI-4SECTOR">ESI-4SECTOR</option> - <option value="FTMS-ECD">FTMS-ECD</option> - <option value="ETD-TRAP">ETD-TRAP</option> - <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option> - <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option> - <option value="MALDI-ISD">MALDI-ISD</option> - <option value="CID+ETD">CID+ETD</option> - </param> - - <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/> - - <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/> - <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="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/> - <param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/> - - <conditional name="security"> - <param name="security_use" type="boolean" label="Use Mascot Security?" help="Select this if you need to enter a username and password" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/> - <param name="password" type="text" label="Password" size="60" value="" help="Mascot Password. Password is encrypted when over the internet but is stored in clear-text on the Galaxy server"/> - </when> - </conditional> - <param name="email" type="text" label="Email " size="60" value="" help=""/> - - - - </inputs> - <outputs> - <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database.dbkey if $database.has_key('dbkey') else $database.custom_db}.${input_file.display_name}.mascotdat"/> - </outputs> - - <help> - Run a Mascot Search - </help> - -</tool> |
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| diff -r 327b2d99d4c5 -r f36b84d1ac09 mascot_to_pepxml.xml --- a/mascot_to_pepxml.xml Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,82 +0,0 @@ -<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.1"> - <requirements> - <requirement type="package" version="1.2.2">galaxy_protk</requirement> - <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> - </requirements> - - <description>Converts a mascot results file to pepXML</description> - -<command>rvm 1.9.3@protk-1.2.2 do mascot_to_pepxml.rb - $input_file - - -o $output - - #if $database.source_select=="built_in": - -d $database.dbkey - #else - -d $database.fasta_file - #end if - - #if $explicit_enzyme.explicit_enzyme_use - --enzyme $explicit_enzyme.enzyme - #end if - - $shortid - -</command> -<inputs> - - - <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/> - - <conditional name="database"> - <param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search"> - <option value="built_in">Built-In</option> - <option value="input_ref">Uploaded fasta file</option> - </param> - <when value="built_in"> - <param name="dbkey" type="select" format="text" > - <label>Database</label> - <options from_file="pepxml_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - </when> - <when value="input_ref"> - <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> - </when> - </conditional> - - <param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" /> - - <conditional name="explicit_enzyme"> - <param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/> - </when> - </conditional> - - - -</inputs> -<outputs> - <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> -</outputs> - - <tests> - <test> - <param name="source_select" value="input_ref"/> - <param name="fasta_file" value="bsa.fasta"/> - <param name="input_file" value="F002832.dat"/> - <output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" /> - </test> - - </tests> - -<help> - Convert mascot results from mascotdat to pepXML -</help> - -</tool> |
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| diff -r 327b2d99d4c5 -r f36b84d1ac09 repository_dependencies.xml --- a/repository_dependencies.xml Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Requires the Proteomics Datatypes package"> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/> - -</repositories> |
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| diff -r 327b2d99d4c5 -r f36b84d1ac09 tool-data/mascot_databases.loc.sample --- a/tool-data/mascot_databases.loc.sample Sun Jun 09 08:17:38 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 on Mascot -# -#In order to use interprophet to combine results from different search engines -#it is important that all searches are performed on the same database -#you should therefore ensure that each database installed on mascot has an equivalent -#database installed in the Protk databases directory (databases used by omssa and x!tandem) -#the mascot_to_pepxml tool will ask for this database when performing the conversion. -# -# Entries should follow the be structured as follows -# Display_name dbkey dbNameOnMascot dbkey -# -Swissprot spall_ SwissProt spall_ -Swissprot Human sphuman_ SPHuman sphuman_ \ No newline at end of file |
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| diff -r 327b2d99d4c5 -r f36b84d1ac09 tool-data/mascot_mods.loc.sample --- a/tool-data/mascot_mods.loc.sample Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,77 +0,0 @@ -#This file lists the names of chemical modifications acceptable for proteomics search engines -# -# -Acetyl (K) acetyl_k_ Acetyl (K) acetyl_k_ -Acetyl (N-term) acetyl_n-term_ Acetyl (N-term) acetyl_n-term_ -Acetyl (Protein N-term) acetyl_proteinn-term_ Acetyl (Protein N-term) acetyl_proteinn-term_ -Amidated (C-term) amidated_c-term_ Amidated (C-term) amidated_c-term_ -Amidated (Protein C-term) amidated_proteinc-term_ Amidated (Protein C-term) amidated_proteinc-term_ -Ammonia-loss (N-term C) ammonia-loss_n-termc_ Ammonia-loss (N-term C) ammonia-loss_n-termc_ -Biotin (K) biotin_k_ Biotin (K) biotin_k_ -Biotin (N-term) biotin_n-term_ Biotin (N-term) biotin_n-term_ -Carbamidomethyl (C) carbamidomethyl_c_ Carbamidomethyl (C) carbamidomethyl_c_ -Carbamyl (K) carbamyl_k_ Carbamyl (K) carbamyl_k_ -Carbamyl (N-term) carbamyl_n-term_ Carbamyl (N-term) carbamyl_n-term_ -Carboxymethyl (C) carboxymethyl_c_ Carboxymethyl (C) carboxymethyl_c_ -Cation:Na (C-term) cation_na_c-term_ Cation:Na (C-term) cation_na_c-term_ -Cation:Na (DE) cation_na_de_ Cation:Na (DE) cation_na_de_ -Deamidated (NQ) deamidated_nq_ Deamidated (NQ) deamidated_nq_ -Deamidated-N (N) deamidated-n_n_ Deamidated-N (N) deamidated-n_n_ -Dehydrated (N-term C) dehydrated_n-termc_ Dehydrated (N-term C) dehydrated_n-termc_ -Dehydro (C) dehydro_c_ Dehydro (C) dehydro_c_ -Dioxidation (M) dioxidation_m_ Dioxidation (M) dioxidation_m_ -Ethanolyl (C) ethanolyl_c_ Ethanolyl (C) ethanolyl_c_ -ExacTagAmine (K) exactagamine_k_ ExacTagAmine (K) exactagamine_k_ -ExacTagThiol (C) exactagthiol_c_ ExacTagThiol (C) exactagthiol_c_ -Formyl (N-term) formyl_n-term_ Formyl (N-term) formyl_n-term_ -Formyl (Protein N-term) formyl_proteinn-term_ Formyl (Protein N-term) formyl_proteinn-term_ -Gln->pyro-Glu (N-term Q) gln_pyro-glu_n-termq_ Gln->pyro-Glu (N-term Q) gln_pyro-glu_n-termq_ -Glu->pyro-Glu (N-term E) glu_pyro-glu_n-terme_ Glu->pyro-Glu (N-term E) glu_pyro-glu_n-terme_ -Guanidinyl (K) guanidinyl_k_ Guanidinyl (K) guanidinyl_k_ -ICAT-C (C) icat-c_c_ ICAT-C (C) icat-c_c_ -ICAT-C:13C(9) (C) icat-c_13c_9__c_ ICAT-C:13C(9) (C) icat-c_13c_9__c_ -ICPL (K) icpl_k_ ICPL (K) icpl_k_ -ICPL (Protein N-term) icpl_proteinn-term_ ICPL (Protein N-term) icpl_proteinn-term_ -ICPL:13C(6) (K) icpl_13c_6__k_ ICPL:13C(6) (K) icpl_13c_6__k_ -ICPL:13C(6) (Protein N-term) icpl_13c_6__proteinn-term_ ICPL:13C(6) (Protein N-term) icpl_13c_6__proteinn-term_ -ICPL:13C(6)2H(4) (K) icpl_13c_6_2h_4__k_ ICPL:13C(6)2H(4) (K) icpl_13c_6_2h_4__k_ -ICPL:13C(6)2H(4) (N-term) icpl_13c_6_2h_4__n-term_ ICPL:13C(6)2H(4) (N-term) icpl_13c_6_2h_4__n-term_ -ICPL:13C(6)2H(4) (Protein N-term) icpl_13c_6_2h_4__proteinn-term_ ICPL:13C(6)2H(4) (Protein N-term) icpl_13c_6_2h_4__proteinn-term_ -ICPL:2H(4) (K) icpl_2h_4__k_ ICPL:2H(4) (K) icpl_2h_4__k_ -ICPL:2H(4) (Protein N-term) icpl_2h_4__proteinn-term_ ICPL:2H(4) (Protein N-term) icpl_2h_4__proteinn-term_ -iTRAQ4plex (K) itraq4plex_k_ iTRAQ4plex (K) itraq4plex_k_ -iTRAQ4plex (N-term) itraq4plex_n-term_ iTRAQ4plex (N-term) itraq4plex_n-term_ -iTRAQ4plex (Y) itraq4plex_y_ iTRAQ4plex (Y) itraq4plex_y_ -iTRAQ8plex (K) itraq8plex_k_ iTRAQ8plex (K) itraq8plex_k_ -iTRAQ8plex (N-term) itraq8plex_n-term_ iTRAQ8plex (N-term) itraq8plex_n-term_ -iTRAQ8plex (Y) itraq8plex_y_ iTRAQ8plex (Y) itraq8plex_y_ -Label:18O(1) (C-term) label_18o_1__c-term_ Label:18O(1) (C-term) label_18o_1__c-term_ -Label:18O(2) (C-term) label_18o_2__c-term_ Label:18O(2) (C-term) label_18o_2__c-term_ -Met->Hse (C-term M) met_hse_c-termm_ Met->Hse (C-term M) met_hse_c-termm_ -Met->Hsl (C-term M) met_hsl_c-termm_ Met->Hsl (C-term M) met_hsl_c-termm_ -Methyl (C-term) methyl_c-term_ Methyl (C-term) methyl_c-term_ -Methyl (DE) methyl_de_ Methyl (DE) methyl_de_ -Methylthio (C) methylthio_c_ Methylthio (C) methylthio_c_ -mTRAQ (K) mtraq_k_ mTRAQ (K) mtraq_k_ -mTRAQ (N-term) mtraq_n-term_ mTRAQ (N-term) mtraq_n-term_ -mTRAQ (Y) mtraq_y_ mTRAQ (Y) mtraq_y_ -mTRAQ:13C(3)15N(1) (K) mtraq_13c_3_15n_1__k_ mTRAQ:13C(3)15N(1) (K) mtraq_13c_3_15n_1__k_ -mTRAQ:13C(3)15N(1) (N-term) mtraq_13c_3_15n_1__n-term_ mTRAQ:13C(3)15N(1) (N-term) mtraq_13c_3_15n_1__n-term_ -mTRAQ:13C(3)15N(1) (Y) mtraq_13c_3_15n_1__y_ mTRAQ:13C(3)15N(1) (Y) mtraq_13c_3_15n_1__y_ -NIPCAM (C) nipcam_c_ NIPCAM (C) nipcam_c_ -Oxidation (HW) oxidation_hw_ Oxidation (HW) oxidation_hw_ -Oxidation (M) oxidation_m_ Oxidation (M) oxidation_m_ -Phospho (ST) phospho_st_ Phospho (ST) phospho_st_ -Phospho (Y) phospho_y_ Phospho (Y) phospho_y_ -Propionamide (C) propionamide_c_ Propionamide (C) propionamide_c_ -Pyridylethyl (C) pyridylethyl_c_ Pyridylethyl (C) pyridylethyl_c_ -Pyro-carbamidomethyl (N-term C) pyro-carbamidomethyl_n-termc_ Pyro-carbamidomethyl (N-term C) pyro-carbamidomethyl_n-termc_ -Sulfo (S) sulfo_s_ Sulfo (S) sulfo_s_ -Sulfo (T) sulfo_t_ Sulfo (T) sulfo_t_ -Sulfo (Y) sulfo_y_ Sulfo (Y) sulfo_y_ -TMT (K) tmt_k_ TMT (K) tmt_k_ -TMT (N-term) tmt_n-term_ TMT (N-term) tmt_n-term_ -TMT2plex (K) tmt2plex_k_ TMT2plex (K) tmt2plex_k_ -TMT2plex (N-term) tmt2plex_n-term_ TMT2plex (N-term) tmt2plex_n-term_ -TMT6plex (K) tmt6plex_k_ TMT6plex (K) tmt6plex_k_ -TMT6plex (N-term) tmt6plex_n-term_ TMT6plex (N-term) tmt6plex_n-term_ |
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| diff -r 327b2d99d4c5 -r f36b84d1ac09 tool-data/pepxml_databases.loc.sample --- a/tool-data/pepxml_databases.loc.sample Sun Jun 09 08:17:38 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_ SwissProt 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 327b2d99d4c5 -r f36b84d1ac09 tool-data/tandem_mods.loc.sample --- a/tool-data/tandem_mods.loc.sample Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -#This file lists the names of inbuilt chemical modifications accepted by X!Tandem -# -# -Carbamidomethyl C carbamidomethyl_c_ 57.021464@C carbamidomethyl_c_ -Glycocapture-N glycocapture_n_ 0.998@N!{P}[ST] glycocapture_n_ -Oxidation M oxidation_m_ 15.994915@M oxidation_m_ \ No newline at end of file |
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| diff -r 327b2d99d4c5 -r f36b84d1ac09 tool_dependencies.xml --- a/tool_dependencies.xml Sun Jun 09 08:17:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +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="trans_proteomic_pipeline" version="4.6.1"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/> - </package> - -</tool_dependency> |