Mercurial > repos > bgruening > peptideshaker
changeset 0:d833f714faa6 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 12 Apr 2014 11:50:34 -0400 |
| parents | |
| children | 149d652fc9f5 |
| files | COPYING README.md datatypes_conf.xml dbtoolkit-4.2/LICENSE-2.0.txt dbtoolkit-4.2/dbtoolkit-4.2.jar dbtoolkit-4.2/lib/jargs-1.0.jar dbtoolkit-4.2/lib/log4j-1.2.12.jar dbtoolkit-4.2/lib/utilities-3.8.7.jar peptide_shaker.xml repository_dependencies.xml reverse.py reverse.xml searchgui_mods.loc.sample tool_dependencies.xml |
| diffstat | 14 files changed, 995 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Sat Apr 12 11:50:34 2014 -0400 @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sat Apr 12 11:50:34 2014 -0400 @@ -0,0 +1,63 @@ +GalaxyP - PeptideShaker +======================= + +* Home: <https://bitbucket.org/galaxyp/peptideshaker> +* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> +* Tool ID: `peptideshaker` +* Tool Type: `default` + + +Description +----------- + +Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. + +Tool wrapper for SearchGUI and PeptideShaker. This tool takes any number of mgf files and performs X! Tandem and OMSSA searches on these via SearchGUI and merges the results using PeptideShaker. + +Note: + +- SearchGUI requires a version greater than 1.12.2 which contained several bugs preventing this from working on the command-line and via Linux. + +- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. + +See: + +* <https://code.google.com/p/peptide-shaker/> +* <https://code.google.com/p/searchgui/> + + +GalaxyP Community +----------------- + +Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: + +<https://bitbucket.org/galaxyp/galaxyp> + + +License +------- + +Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. + +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. + +You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. + + +Contributing +------------ + +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out. + + +Authors +------- + +Authors and contributors: + +* Cody Wang +* Fred Sadler +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Sat Apr 12 11:50:34 2014 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<datatypes> + <registration> + <datatype extension="cps" type="galaxy.datatypes.binary:Binary" subclass="True" display_in_upload="true" /> + </registration> +</datatypes>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dbtoolkit-4.2/lib/jargs-1.0.jar Sat Apr 12 11:50:34 2014 -0400 @@ -0,0 +1,48 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="SearchGUI" version="1.13.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://searchgui.googlecode.com/files/SearchGUI-1.13.1_mac_and_linux.zip</action> + <action type="shell_command">tar -xf $DIR_NAME/*.tar</action> + <action type="shell_command">cd $DIR_NAME</action> + <action type="shell_command">chmod -R $DIR_NAME/*resources</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/</destination_directory> + </action> + <action type="shell_command">mkdir -p $BIN_DIR</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + This package downloads and installs the SearchGUI scripts develped as part of the Peptideshaker tool. + (https://github.com/jmchilton/peptide-shaker). + + </readme> + </package> + + <package name="PeptideShaker" version="0.20.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://peptide-shaker.googlecode.com/files/PeptideShaker-0.20.1.zip</action> + <action type="shell_command">chmod -R o+w resources</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/</destination_directory> + </action> + <action type="shell_command">mkdir -p $BIN_DIR</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + This package downloads and installs the peptideshaker tool as a part of the peptideshaker framework. + (https://github.com/jmchilton/peptide-shaker). + + </readme> + </package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptide_shaker.xml Sat Apr 12 11:50:34 2014 -0400 @@ -0,0 +1,248 @@ +<tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0"> + <!-- TODO: Set defaults for weights correctly --> + <requirements> + <requirement type="package" version="0.28.0">peptide_shaker</requirement> + <requirement type="package" version="1.18.0">searchgui</requirement> + </requirements> + <description> + Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. + </description> + <command> + #from datetime import datetime + #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s") + #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s") + mkdir spectra; + mkdir output; + mkdir output_reports; + cwd=`pwd`; + #for $mgf in $peak_lists: + #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" + ln -s '$mgf' 'spectra/$input_name'; + #end for + + java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI + ##SearchCLI + -spectrum_files \$cwd/spectra + -output_folder \$cwd/output + -ppm $precursor_ion_tol_units + -prec_tol $precursor_ion_tol + -frag_tol $fragment_tol + -enzyme '$enzyme' + #set $fixed_mods_str = $fixed_modifications or '' + #set $variable_mods_str = $variable_modifications or '' + #if $fixed_mods_str + -fixed_mods "$fixed_mods_str" + #end if + #if $variable_mods_str + -variable_mods "$variable_mods_str" + #end if + -mc $missed_cleavages + #if $advanced.specify: + -xtandem $advanced.xtandem + #if $advanced.omssa.run_omssa + #set $omssa = 1 + #else + #set $omssa = 0 + #end if + -omssa $omssa + + #if $omssa == 1 + -hitlist_length ${advanced.omssa.hitlist_length} + -remove_prec ${advanced.omssa.remove_precursor} + -scale_prec ${advanced.omssa.scale_precursor} + -estimate_charge ${advanced.omssa.estimate_charge} + #end if + #end if + -db $input_database; + + + java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI + ##PeptideShakerCLI + -experiment '$exp_str' + -sample '$samp_str' + -replicate 1 + -spectrum_files \$cwd/spectra + -identification_files \$cwd/output + -search_params \$cwd/output/SearchGUI.parameters + -out_txt_1 \$cwd/output_reports + #if $processing_options.specify + -protein_FDR ${processing_options.protein_fdr} + -peptide_FDR ${processing_options.peptide_fdr} + -psm_FDR ${processing_options.psm_fdr} + -psm_FLR ${processing_options.psm_flr} + #if str($processing_options.a_score.use) == "1" + #set $a_score = 1 + #else + #set $a_score = 0 + #end if + -a_score $a_score + #if str($a_score) == "1" + -a_score_neutral_losses ${processing_options.a_score.neutral_losses} + #end if + #end if + #if $filtering_options.specify + -min_peptide_length ${filtering_options.min_peptide_length} + -max_peptide_length ${filtering_options.max_peptide_length} + -max_precursor_error ${filtering_options.max_precursor_error} + -max_precursor_error_type ${filtering_options.max_precursor_error_type} + -max_xtandem_e ${filtering_options.max_xtandem_e} + -max_omssa_e ${filtering_options.max_omssa_e} + -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} + #end if + -out \$cwd/output.cps ; + + mv output_reports/*peptides.txt peptides.txt ; + mv output_reports/*psms.txt psms.txt ; + mv output_reports/*proteins.txt proteins.txt + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Job Failed" /> + </stdio> + <inputs> + <param format="fasta" name="input_database" type="data" label="Protein Database" + help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/> + <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" + help="Select appropriate MGF dataset(s) from history" /> + <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" + help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> + <option value="1">Parts per million (ppm)</option> + <option value="0">Daltons</option> + </param> + <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" + help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> + <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" + help="Provide error value for fragment ions, based on instrument used"/> + <param name="enzyme" type="select" label="Enzyme" + help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> + <option value="Trypsin">Trypsin</option> + <option value="Arg-C">Arg-C</option> + <option value="CNBr">CNBr</option> + <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> + <option value="Formic Acid">Formic Acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-C, no P rule">Lys-C, no P rule</option> + <option value="Pepsin A">Pepsin A</option> + <option value="Trypsin + CNBr">Trypsin + CNBr</option> + <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> + <option value="Trypsin, no P rule">Trypsin, no P rule</option> + <option value="whole protein">whole protein</option> + <option value="Asp-N">Asp-N</option> + <option value="Glu-C">Glu-C</option> + <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> + <option value="Top-Down">Top-Down</option> + <option value="Semi-Tryptic">Semi-Tryptic</option> + <option value="No enzyme">No enzyme</option> + <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> + <option value="Asp-N (DE)">Asp-N (DE)</option> + <option value="Glu-C (DE)">Glu-C (DE)</option> + <option value="Lys-N (K)">Lys-N (K)</option> + <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> + <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> + <option value="Semi-Glu-C">Semi-Glu-C</option> + </param> + <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" + help="Allow peptides to contain up to this many missed enzyme cleavage sites. 2 is the recommended value"/> + <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" + help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" + help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> + <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> + <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> + <option value="a">a</option> + <option value="b" selected="true">b</option> + <option value="c">c</option> + </param> + <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> + <option value="x">x</option> + <option value="y" selected="true">y</option> + <option value="z">z</option> + </param> + <conditional name="advanced"> + <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" + help=" Run X! Tandem, OMSSA, or both and provide options for OMSSA search"/> + <when value="false" /> + <when value="true"> + <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <conditional name="omssa"> + <param name="run_omssa" label="Run OMSSA" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <when value="0" /> + <when value="1"> + <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" /> + <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/> + <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> + <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + </when> + </conditional> + </when> + </conditional> + <conditional name="processing_options"> + <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" + help="Select and provide False Discovery Rate (FDR) levels at the peptide, protein, + and peptide-spectral match (PSM) levels, as well as False Loss Rate (FLR) for PSM’s and A score options for post-translational modifications (PTM’s). See this link_ for more details + .. _link: http://peptide-shaker.googlecode.com/svn-history/r1267/wiki/tutorial/6_ptm_analysis.docx" /> + <when value="false" /> + <when value="true"> + <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> + <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> + <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> + <param name="psm_flr" label="FLR at the PSM level" value="1" type="float" + help="In percent (default 1% FLR: '1'). Percent for peptides with different potential modification sites and one variable modification." /> + <conditional name="a_score"> + <param name="use" label="Calculate A Score" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <when value="0" /> + <when value="1"> + <param name="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> + </when> + </conditional> + <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> + </when> + </conditional> + <conditional name="filtering_options"> + <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" + help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s"/> + <when value="false" /> + <when value="true"> + <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" /> + <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" /> + <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." /> + <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> + <option value="0">ppm</option> + <option value="1">Daltons</option> + </param> + <param name="max_xtandem_e" label="Maximum X! Tandem E Value" value="100" type="float" help="" /> + <param name="max_omssa_e" label="Maximum OMSSA E Value" value="100" type="float" help="" /> + <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="cps" name="output" from_work_dir="output.cps" label="PeptideShaker CPS results for ${on_string}" /> + <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="PeptideShaker Peptide Report for ${on_string}" /> + <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="PeptideShaker Protein Report for ${on_string}" /> + <data format="tabular" name="output_psms" from_work_dir="psms.txt" label="PeptideShaker PSM Report for ${on_string}" /> + </outputs> + <help> +**What it does** + +Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results. + +------ + +**Citation** + +For the underlying tool, please cite `TODO` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/peptideshaker + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Sat Apr 12 11:50:34 2014 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Required proteomics dependencies."> + <repository changeset_revision="25f42af5b73d" name="proteomics_datatypes" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reverse.py Sat Apr 12 11:50:34 2014 -0400 @@ -0,0 +1,48 @@ +#!/usr/bin/env python +from os.path import join +import sys +from optparse import OptionParser +from ConfigParser import SafeConfigParser +import subprocess + +DEBUG = False + +def main(): + (options, args) = _parse_args() + _run_shell("cat '%s' > '%s'" % (options.input, options.output)) + _run_dbtoolkit("com.compomics.dbtoolkit.toolkit.ReverseFASTADB", "'%s' | head --lines -4 >> '%s'" % (options.input, options.output), options) + + +def _run_shell(command): + if DEBUG: + print "Running shell command %s" % command + _exec(command) + + +def _run_dbtoolkit(java_class, command, args): + command_prefix = "java -cp %s" % _dbtoolkit_jar_path( args.script_path ) + _exec("%s %s %s" % (command_prefix, java_class, command)) + + +def _dbtoolkit_jar_path( script_path ): + jar_path = join(script_path, "dbtoolkit-4.2", "dbtoolkit-4.2.jar") + return jar_path + +def _exec(command): + proc = subprocess.Popen(args=command, shell=True) + return_code = proc.wait() + if return_code != 0: + print "Error executing command [%s], return code is %d" % (command, return_code) + sys.exit(return_code) + + +def _parse_args(): + parser = OptionParser() + parser.add_option("-i", "--input") + parser.add_option("-o", "--output") + parser.add_option("-s", "--script_path") + return parser.parse_args() + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reverse.xml Sat Apr 12 11:50:34 2014 -0400 @@ -0,0 +1,33 @@ +<tool id="compomics_reverse" name="Create Target-Decoy Database" version="0.1.0"> + <description>Creates a target-decoy database for use with Peptide Shaker</description> + <requirements> + <requirement type="set_environment">PEPTIDESHAKER_SCRIPT_PATH</requirement> + </requirements> + <command interpreter="python"> + reverse.py + --input='$input' + --output='$output' + --script_path \$PEPTIDESHAKER_SCRIPT_PATH + </command> + <inputs> + <param format="fasta" name="input" type="data" label="FASTA Input" /> + </inputs> + <outputs> + <data format="fasta" name="output" /> + </outputs> + <help> +**What it does** + +Given an input database, this tool will produce a target-decoy +database in the format required by PeptideShaker using dbtoolkit. + +------ + +**Citation** + +For the underlying tool, please cite `Martens et al. DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics (2005) vol. 21 (17) pp. 3584-5`. + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/peptideshaker . + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui_mods.loc.sample Sat Apr 12 11:50:34 2014 -0400 @@ -0,0 +1,210 @@ +methylation of k +oxidation of m +carboxymethyl c +carbamidomethyl c +deamidation of n and q +propionamide c +phosphorylation of s +phosphorylation of t +phosphorylation of y +m cleavage from protein n-term +acetylation of protein n-term +methylation of protein n-term +tri-methylation of protein n-term +beta methythiolation of d +methylation of q +tri-methylation of k +methylation of d +methylation of e +methylation of peptide c-term +tri-deuteromethylation of d +tri-deuteromethylation of e +tri-deuteromethylation of peptide c-term +n-formyl met addition +2-amino-3-oxo-butanoic acid t +acetylation of k +amidation of peptide c-term +beta-methylthiolation of d (duplicate of 13) +carboxyamidomethylation of k +carboxyamidomethylation of h +carboxyamidomethylation of d +carboxyamidomethylation of e +carbamylation of k +carbamylation of n-term peptide +citrullination of r +oxidation of c to cysteic acid +di-iodination of y +di-methylation of k +di-methylation of r +di-methylation of peptide n-term +oxidation of f to dihydroxyphenylalanine +gammathiopropionylation of k +gammathiopropionylation of peptide n-term +farnesylation of c +formylation of k +formylation of peptide n-term +oxidation of w to formylkynurenin +fluorophenylalanine +beta-carboxylation of d +gamma-carboxylation of e +geranyl-geranyl +glucuronylation of protein n-term +glutathione disulfide +ubiquitinylation residue +guanidination of k +oxidation of h to n +oxidation of h to d +homoserine +homoserine lactone +oxidation of w to hydroxykynurenin +hydroxylation of d +hydroxylation of k +hydroxylation of n +hydroxylation of p +hydroxylation of f +hydroxylation of y +iodination of y +oxidation of w to kynurenin +lipoyl k +methyl ester of peptide c-term (duplicate of 18) +methyl ester of d +methyl ester of e (duplicate of 17) +methyl ester of s +methyl ester of y +methyl c +methyl h +methyl n +methylation of peptide n-term +methyl r +myristoleylation of g +myristoyl-4h of g +myristoylation of peptide n-term g +myristoylation of k +formylation of protein n-term +nem c +nipcam +oxidation of w to nitro +oxidation of y to nitro +o18 on peptide n-term +di-o18 on peptide n-term +oxidation of h +oxidation of w +phosphopantetheine s +palmitoylation of c +palmitoylation of k +palmitoylation of s +palmitoylation of t +phosphorylation of s with prompt loss +phosphorylation of t with prompt loss +phosphorylation with prompt loss on y +phosphorylation with neutral loss on c +phosphorylation with neutral loss on d +phosphorylation with neutral loss on h +propionyl light k +propionyl light on peptide n-term +propionyl heavy k +propionyl heavy peptide n-term +pyridyl k +pyridyl peptide n-term +pyro-cmc +pyro-glu from n-term e +pyro-glu from n-term q +oxidation of p to pyroglutamic acid +s-pyridylethylation of c +semet +sulfation of y +sulphone of m +tri-iodination of y +tri-methylation of r +n-acyl diglyceride cysteine +icat light +icat heavy +camthiopropanoyl k +phosphorylation with neutral loss on s +phosphorylation with neutral loss on t +phosphorylation of s with etd loss +phosphorylation of t with etd loss +heavy arginine-13c6 +heavy arginine-13c6-15n4 +heavy lysine-13c6 +pngasf in o18 water +beta elimination of s +beta elimination of t +oxidation of c to sulfinic acid +arginine to ornithine +dehydro of s and t +carboxykynurenin of w +sumoylation of k +itraq114 on nterm +itraq114 on k +itraq114 on y +itraq115 on nterm +itraq115 on k +itraq115 on y +itraq116 on nterm +itraq116 on k +itraq116 on y +itraq117 on nterm +itraq117 on k +itraq117 on y +mmts on c +heavy lysine - 2h4 +heavy lysine - 13c6 15n2 +asparagine hexnac +asparagine dhexhexnac +serine hexnac +threonine hexnac +palmitoleyl of s +palmitoleyl of c +palmitoleyl of t +chd2-di-methylation of k +chd2-di-methylation of peptide n-term +maleimide-peo2-biotin of c +phosphorylation of h +oxidation of c +oxidation of y (duplicate of 64) +uniblue a on k +deamidation of n +trideuteration of l (silac) +tmt duplex on k +tmt duplex on n-term peptide +tmt 6-plex on k +tmt 6-plex on n-term peptide +itraq8plex:13c(7)15n(1) on nterm +itraq8plex:13c(7)15n(1) on k +itraq8plex:13c(7)15n(1) on y +itraq8plex:13c(6)15n(2) on nterm +itraq8plex:13c(6)15n(2) on k +itraq8plex:13c(6)15n(2) on y +selenocysteine +carboxymethylated selenocysteine +dimethyl 2d n-terminus +dimethyl 2d k +gtp desthiobiotinc12 +gtp desthiobiotinc13 +user modification 5 +user modification 6 +user modification 7 +user modification 8 +user modification 9 +user modification 10 +user modification 11 +user modification 12 +user modification 13 +user modification 14 +user modification 15 +user modification 16 +user modification 17 +user modification 18 +user modification 19 +user modification 20 +user modification 21 +user modification 22 +user modification 23 +user modification 24 +user modification 25 +user modification 26 +user modification 27 +user modification 28 +user modification 29 +user modification 30
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Apr 12 11:50:34 2014 -0400 @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable action="set_to" name="PEPTIDESHAKER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="searchgui" version="1.18.0"> + <repository changeset_revision="3bcfc0d7275b" name="package_searchgui_1_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="peptide_shaker" version="0.28.0"> + <repository changeset_revision="aa0a836dfaa9" name="package_peptideshaker_0_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>