Mercurial > repos > galaxyp > peptideshaker
changeset 24:815f93bb3e1b draft
Uploaded
| author | galaxyp |
|---|---|
| date | Fri, 06 Nov 2015 15:33:34 -0500 |
| parents | 913dbf2b83e0 |
| children | 0986f68fb410 |
| files | README.rst macros.xml peptide_shaker.xml repository_dependencies.xml searchgui.xml searchgui_mods.loc.sample tool_dependencies.xml |
| diffstat | 7 files changed, 240 insertions(+), 227 deletions(-) [+] |
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--- a/README.rst Mon Aug 10 18:25:37 2015 -0400 +++ b/README.rst Fri Nov 06 15:33:34 2015 -0500 @@ -42,6 +42,8 @@ Note ---- +- Requires Galaxy release v15.10 or later, which fixes the installation of package_peptideshaker_1_1 and provides a searchgui_archive datatype that includes a version + - PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. See: @@ -50,6 +52,14 @@ * <https://code.google.com/p/searchgui/> +Search GUI - Fixed and Variable Modifications +------------------------------------------- + + - Options for modifications are read from local data file: searchgui_mods.loc + This is copied from searchgui_mods.loc.sample on the first installation. + +The modifications are from: https://github.com/compomics/compomics-utilities/blob/master/src/main/java/com/compomics/util/experiment/identification/search_parameters_cli/IdentificationParametersInputBean.java + GalaxyP Community -----------------
--- a/macros.xml Mon Aug 10 18:25:37 2015 -0400 +++ b/macros.xml Fri Nov 06 15:33:34 2015 -0500 @@ -25,7 +25,8 @@ -fi $forward_ion -ri $reverse_ion </token> - + <token name="@SEARCHGUI_MAJOR_VERSION@">2</token> + <token name="@SEARCHGUI_VERSION@">2.1</token> <xml name="general_options"> <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
--- a/peptide_shaker.xml Mon Aug 10 18:25:37 2015 -0400 +++ b/peptide_shaker.xml Fri Nov 06 15:33:34 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="0.40.0"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.1.1"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> @@ -6,7 +6,7 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.40">peptide_shaker</requirement> + <requirement type="package" version="1.1">peptide_shaker</requirement> </requirements> <expand macro="stdio" /> <command> @@ -33,7 +33,7 @@ -sample '$samp_str' -replicate 1 -identification_files \$cwd/searchgui_input.zip - -out \$cwd/peptideshaker_output.cps + -out \$cwd/peptideshaker_output.cpsx -zip \$cwd/peptideshaker_output.zip -threads "\${GALAXY_SLOTS:-12}" @@ -166,7 +166,12 @@ </command> <inputs> <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" - help="SearchGUI Results from History"/> + help="SearchGUI Results from History"> + <options options_filter_attribute="metadata.searchgui_major_version" > + <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" /> + </options> + <validator type="expression" message="This version of PeptideShaker will only work with SearchGUI version: @SEARCHGUI_MAJOR_VERSION@ .">value is not None and value.metadata.searchgui_major_version == "@SEARCHGUI_MAJOR_VERSION@"</validator> + </param> <conditional name="species_type"> <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" @@ -178,6 +183,7 @@ <option value="Protists">Protists</option> <option value="no_species_type" selected="true">No species restriction</option> </param> + <when value="no_species_type"/> <when value="Protists"> <param name="species" type="select" label="The species to use for the gene annotation" help="">
--- a/repository_dependencies.xml Mon Aug 10 18:25:37 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Required proteomics dependencies."> - <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories>
--- a/searchgui.xml Mon Aug 10 18:25:37 2015 -0400 +++ b/searchgui.xml Fri Nov 06 15:33:34 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="1.28.0"> +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -6,7 +6,7 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="1.28">searchgui</requirement> + <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> <environment_variable name="LC_ALL" action="set_to">C</environment_variable> </requirements> <expand macro="stdio" /> @@ -22,6 +22,9 @@ cwd=`pwd`; export HOME=\$cwd; + ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present + echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties; + cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin; tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`; @@ -48,7 +51,7 @@ ##################################################### (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI - -out SEARCHGUI_IdentificationParameters.parameters + -out SEARCHGUI_IdentificationParameters.par @GENERAL_PARAMETERS@ @@ -168,6 +171,27 @@ -myrimatch_max_peak ${myrimatch.myrimatch_max_peak} #end if + #* + #if $andromeda.andromeda_advanced == "yes" + -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass} + -andromeda_max_comb ${andromeda.andromeda_max_comb} + -andromeda_top_peaks ${andromeda.andromeda_top_peaks} + -andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window} + -andromeda_incl_water ${andromeda.andromeda_incl_water} + -andromeda_incl_ammonia ${andromeda.andromeda_incl_ammonia} + -andromeda_neutral_losses ${andromeda.andromeda_neutral_losses} + -andromeda_fragment_all ${andromeda.andromeda_fragment_all} + -andromeda_emp_correction ${andromeda.andromeda_emp_correction} + -andromeda_higher_charge ${andromeda.andromeda_higher_charge} + -andromeda_equal_il ${andromeda.andromeda_equal_il} + -andromeda_frag_method ${andromeda.andromeda_frag_method} + -andromeda_max_mods ${andromeda.andromeda_max_mods} + -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length} + -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length} + -andromeda_max_psms ${andromeda.andromeda_max_psms} + #end if + *# + #if $tide.tide_advanced == "yes" -tide_num_ptms ${tide.tide_num_ptms} -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type} @@ -256,7 +280,7 @@ -temp_folder `pwd` -spectrum_files \$cwd -output_folder \$cwd/output - -id_params SEARCHGUI_IdentificationParameters.parameters + -id_params SEARCHGUI_IdentificationParameters.par -threads "\${GALAXY_SLOTS:-12}" @@ -316,6 +340,12 @@ -ms_amanda 0 #end if + #if 'Andromeda' in $engines_list: + -andromeda 1 + #else + -andromeda 0 + #end if + ## single zip file -output_option 0 @@ -330,6 +360,10 @@ && + (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr) + + && + exit_code_for_galaxy=\$?; cat $temp_stderr 2>&1; (exit \$exit_code_for_galaxy) @@ -357,6 +391,9 @@ <option value="OMSSA" selected="True">OMSSA</option> <option value="Comet">Comet</option> <option value="Tide">Tide</option> + <!-- Windows only + <option value="Andromeda">Andromeda</option> + --> <validator type="no_options" message="Please select at least one output file" /> </param> @@ -780,6 +817,39 @@ </when> </conditional> + <!-- Andromeda ADVANCED PARAMETERS --> + <!-- Windows only + <conditional name="andromeda"> + <param name="andromeda_advanced" type="select" label="Andromeda Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" /> + <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" /> + <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" /> + <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" /> + <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" /> + <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" /> + <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" /> + <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" /> + <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" /> + <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" /> + <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" /> + <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." > + <option value="CID" selected="true">CID</option> + <option value="HCD">HCD</option> + <option value="EDT">EDT</option> + </param> + <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" /> + <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" /> + <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" /> + <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" /> + </when> + </conditional> + --> + <!-- Comet ADVANCED PARAMETERS --> <conditional name="comet"> <param name="comet_advanced" type="select" label="Comet Options">
--- a/searchgui_mods.loc.sample Mon Aug 10 18:25:37 2015 -0400 +++ b/searchgui_mods.loc.sample Fri Nov 06 15:33:34 2015 -0500 @@ -1,210 +1,140 @@ -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 +18O(1) of peptide C-term +18O(2) of peptide C-term +4-Hydroxyproline +Acetaldehyde +26 +Acetylation of K +Acetylation of peptide N-term +Acetylation of protein N-term +Amidation of the peptide C-term +Amidation of the protein C-term +Arginine 13C(6) +Arginine 13C(6) 15N(4) +Carbamidomethylation of C +Carbamidomethylation of E +Carbamidomethylation of K +Carbamilation of K +Carbamilation of protein N-term +Carboxymethylation of C +Deamidation of N +Deamidation of N 18O +Deamidation of Q +Dehydration of S +Dehydration of T +Didehydro of T +Diiodination of Y +Dimethylation of K +Dimethylation of K 2H(4) +Dimethylation of K 2H(6) +Dimethylation of R +Dimethylation of peptide N-term 2H(6) +Dimethylation of peptide N-term 2H(6) 13C(2) +Dimethylation of peptide N-term K +Dimethylation of peptide N-term K 2H(4) +Dioxidation of M +Dioxidation of W +Farnesylation of C +FormylMet of protein N-term +Formylation of K +Formylation of S +Formylation of T +Formylation of peptide N-term +Formylation of protein N-term +Geranyl-geranyl of C +Glutathione of C +Guanidination of K +Guanidination of peptide N-term +Hex(1)NAc(1) of S +Hex(1)NAc(1) of T +Hex(5) HexNAc(4) NeuAc(2) Na of N +Hex(5) HexNAc(4) NeuAc(2) of N +HexNAc of S +HexNAc of T +Hexose of K +Homoserine lactone of peptide C-term M +Homoserine of peptide C-term M +ICAT-9 +ICAT-O +ICPL0 of K +ICPL0 of peptide N-term +ICPL10 of K +ICPL10 of peptide N-term +ICPL4 of K +ICPL4 of peptide N-term +ICPL6 of K +ICPL6 of peptide N-term +Isoleucine 13C(6) 15N(1) +Leucine 13C(6) 15N(1) +Lipoyl of K +Lysine 13C(6) +Lysine 13C(6) 15N(2) +Lysine 2H(4) +Methylation of C +Methylation of D +Methylation of E +Methylation of K +Methylation of R +Methylation of S +Methylthio of C +Methylthio of D +Methylthio of N +NIPCAM of C +Nethylmaleimide of C +Oxidation of C +Oxidation of K +Oxidation of M +Oxidation of P +Palmitoylation of C +Palmitoylation of K +Palmitoylation of S +Palmitoylation of T +Palmitoylation of protein N-term +Phosphorylation of S +Phosphorylation of T +Phosphorylation of Y +Proline 13C(5) +Propionamide of C +Propionamide of K +Propionamide of peptide N-term +Propionyl of K heavy +Propionyl of K light +Propionyl of peptide N-term heavy +Propionyl of peptide N-term light +Pyridylethyl of C +Pyrolidone from E +Pyrolidone from Q +Pyrolidone from carbamidomethylated C +SUMO-2/3 Q87R +Sodium adduct to D +Sodium adduct to E +Sulfonation of S +Sulfonation of T +Sulfonation of Y +TMT 10-plex of K +TMT 10-plex of peptide N-term +TMT 2-plex of K +TMT 2-plex of peptide N-term +TMT 6-plex of K +TMT 6-plex of peptide N-term +Thioacyl of peptide N-term +Trideuterated Methyl Ester of D +Trideuterated Methyl Ester of E +Trideuterated Methyl Ester of K +Trideuterated Methyl Ester of R +Trideuterated Methyl Ester of peptide C-term +Trimethylation of K +Trimethylation of R +Trimethylation of protein N-term A +Trioxidation of C +Ubiquitination of K +iTRAQ 4-plex of K +iTRAQ 4-plex of Y +iTRAQ 4-plex of peptide N-term +iTRAQ 8-plex of K +iTRAQ 8-plex of Y +iTRAQ 8-plex of peptide N-term +mTRAQ of 13C(6) 15N(2) +mTRAQ of K 13C(3) 15N +mTRAQ of K light +mTRAQ of peptide N-term 13C(3) 15N +mTRAQ of peptide N-term 13C(6) 15N(2) +mTRAQ of peptide N-term light
--- a/tool_dependencies.xml Mon Aug 10 18:25:37 2015 -0400 +++ b/tool_dependencies.xml Fri Nov 06 15:33:34 2015 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="searchgui" version="1.28"> - <repository changeset_revision="0d8bbd52ae42" name="package_searchgui_1_28" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="searchgui" version="2.1"> + <repository changeset_revision="42249a2266ba" name="package_searchgui_2_1" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="peptide_shaker" version="0.40"> - <repository changeset_revision="9a4d33da1cce" name="package_peptideshaker_0_40" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="peptide_shaker" version="1.1"> + <repository changeset_revision="d96500b8f698" name="package_peptideshaker_1_1" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>