Mercurial > repos > bgruening > peptideshaker
changeset 28:dfb3c79df8e9 draft
Deleted selected files
| author | iracooke |
|---|---|
| date | Mon, 15 Dec 2014 20:53:31 -0500 |
| parents | f1ea11b045d5 |
| children | ea975ed155a1 |
| files | macros.xml peptide_shaker.xml repository_dependencies.xml searchgui.xml searchgui_mods.loc.sample tool_dependencies.xml |
| diffstat | 6 files changed, 0 insertions(+), 1320 deletions(-) [+] |
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--- a/macros.xml Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,104 +0,0 @@ -<macros> - <xml name="stdio"> - <stdio> - <exit_code range="1:" level="fatal" description="Job Failed" /> - <regex match="java.*Exception" level="fatal" description="Java Exception"/> - <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> - </stdio> - </xml> - <token name="@GENERAL_PARAMETERS@"> - -frag_tol "${fragment_tol}" - -prec_tol "${precursor_ion_tol}" - -prec_ppm "${precursor_ion_tol_units}" - -enzyme "${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 - -min_charge $min_charge - -max_charge $max_charge - -mc $missed_cleavages - -fi $forward_ion - -ri $reverse_ion - </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"> - <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."/> - <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> - </xml> - - <xml name="citations"> - <citations> - <citation type="doi">10.1186/1471-2105-12-70</citation> - <citation type="doi">10.1002/pmic.201000595</citation> - </citations> - </xml> - -</macros>
--- a/peptide_shaker.xml Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,650 +0,0 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.35.0"> - <description> - Perform protein identification using various search engines based on results from SearchGUI - </description> - <requirements> - <requirement type="package" version="0.35">peptide_shaker</requirement> - </requirements> - - <expand macro="stdio" /> - <command> -<![CDATA[ - - ######################################################### - ## generate IdentificationParameters for PeptideShaker ## - ######################################################### - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI - -out PEPTIDESHAKER_IdentificationParameters.parameters - - @GENERAL_PARAMETERS@ - - -db input_database.fasta - - 2>> $temp_stderr) - && - - ###################### - ## PeptideShakerCLI ## - ###################### - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI - -temp_folder `pwd` - -experiment '${exp_str}' - -sample '${samp_str}' - -replicate 1 - -spectrum_files \$cwd - -identification_files \$cwd/output - -out \$cwd/peptide_shaker_output.cps - -id_params PEPTIDESHAKER_IdentificationParameters.parameters - - -threads "\${GALAXY_SLOTS:-12}" - - ##Optional gene annotation parameter - #if $species_type.species_type_selector != 'no_species_type': - -species_type "${species_type.species_type_selector}" - -species "${species_type.species}" - #end if - - ##Optional processing parameters: - #if $processing_options.processing_options_selector == "yes" - -protein_FDR "${processing_options.protein_fdr}" - -peptide_FDR "${processing_options.peptide_fdr}" - -psm_FDR "${processing_options.psm_fdr}" - -ptm_score "${processing_options.ptm_score.ptm_score_selector}" - #if $processing_options.ptm_score.ptm_score_selector == 1 - -score_neutral_losses "${processing_options.ptm_score.neutral_losses}" - #if str($processing_options.ptm_score.ptm_threshold) != '' - -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" - #end if - #end if - -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" - #end if - - ##Optional filtering parameters: - #if $filtering_options.filtering_options_selector == "yes": - -min_peptide_length "${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 "${filtering_options.max_omssa_e}" - -max_mascot_e "${filtering_options.max_mascot_e}" - -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" - #end if - - 2>> $temp_stderr) - && - - ################################## - ## PeptideShaker Report options ## - ################################## - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI - -temp_folder `pwd` - -in \$cwd/peptide_shaker_output.cps - -out_reports \$cwd/output_reports - #set $cleaned_list = str($outputs).split(',') - #if 'cps' in $cleaned_list: - #silent $cleaned_list.remove('cps') - #end if - #if 'mzidentML' in $cleaned_list: - #silent $cleaned_list.remove('mzidentML') - #end if - -reports #echo ','.join($cleaned_list)# - - 2>> $temp_stderr) - && - - #if 'mzidentML' in str($outputs).split(','): - java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI - -in \$cwd/peptide_shaker_output.cps - -output_file output.mzid - -contact_first_name 'Proteomics' - -contact_last_name 'Galaxy' - -contact_email 'galaxyp@umn.edu' - -contact_address 'galaxyp@umn.edu' - -organization_name 'University of Minnesota' - -organization_email 'galaxyp@umn.edu' - -organization_address 'Minneapolis, MN 55455, Vereinigte Staaten' - ; - #end if - #if '0' in str($outputs).split(','): - find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; - ; - #end if - #if '2' in str($outputs).split(','): - find \$cwd/output_reports -name '*PSM*' -exec bash -c 'mv "$0" "psm.txt"' {} \; - ; - #end if - #if '3' in str($outputs).split(','): - find \$cwd/output_reports -name '*Peptide*' -exec bash -c 'mv "$0" "peptides.txt"' {} \; - ; - #end if - #if '4' in str($outputs).split(','): - find \$cwd/output_reports -name '*Protein*' -exec bash -c 'mv "$0" "proteins.txt"' {} \; - ; - #end if - #if '1' in str($outputs).split(','): - find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \; - ; - #end if - - exit_code_for_galaxy=\$?; - cat $temp_stderr 2>&1; - (exit \$exit_code_for_galaxy) -]]> - </command> - <inputs> - <param format="fasta" name="input_database" type="data" label="Protein Database" - help="Select FASTA database from history"/> - - <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" help="Selecting this option will help PeptideShaker calculate FDR values" /> - - <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" - help="Select appropriate MGF dataset(s) from history" /> - - <expand macro="general_options"/> - - <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" - help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> - <option value="0">no correction</option> - <option value="1" selected="True">rename spectra</option> - <option value="2">delete spectra</option> - </param> - - <param name="missing_titles" label="Add missing spectrum titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" help="(-missing_titles)"/> - - <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" - help="Choose a smaller value if you are running on a machine with limited memory"/> - <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" - help="Choose a smaller value if you are running on a machine with limited memory"/> - - <conditional name="species_type"> - <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" - help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results"> - <option value="Fungi">Fungi</option> - <option value="Plants">Plants</option> - <option value="Metazoa">Metazoa</option> - <option value="Vertebrates">Vertebrates</option> - <option value="Protists">Protists</option> - <option value="no_species_type" selected="true">No species restriction</option> - </param> - <when value="Protists"> - <param name="species" type="select" label="The species to use for the gene annotation" - help=""> - <option value="Albugo laibachii">Albugo laibachii</option> - <option value="Dictyostelium discoideum">Dictyostelium discoideum</option> - <option value="Entamoeba histolytica">Entamoeba histolytica</option> - <option value="Giardia lamblia">Giardia lamblia</option> - <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option> - <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option> - <option value="Leishmania major">Leishmania major</option> - <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option> - <option value="Phytophthora infestans">Phytophthora infestans</option> - <option value="Phytophthora ramorum">Phytophthora ramorum</option> - <option value="Phytophthora sojae">Phytophthora sojae</option> - <option value="Plasmodium berghei">Plasmodium berghei</option> - <option value="Plasmodium chabaudi">Plasmodium chabaudi</option> - <option value="Plasmodium falciparum">Plasmodium falciparum</option> - <option value="Plasmodium knowlesi">Plasmodium knowlesi</option> - <option value="Plasmodium vivax">Plasmodium vivax</option> - <option value="Pythium ultimum">Pythium ultimum</option> - <option value="Tetrahymena thermophila">Tetrahymena thermophila</option> - <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option> - <option value="Toxoplasma gondii">Toxoplasma gondii</option> - <option value="Trypanosoma brucei">Trypanosoma brucei</option> - </param> - </when> - <when value="Plants"> - <param name="species" type="select" label="The species to use for the gene annotation" - help=""> - <option value="Arabidopsis lyrata">Arabidopsis lyrata</option> - <option value="Arabidopsis thaliana">Arabidopsis thaliana</option> - <option value="Brachypodium distachyon">Brachypodium distachyon</option> - <option value="Brassica rapa genes">Brassica rapa genes</option> - <option value="Chlamydomonas reinhardtii">Chlamydomonas reinhardtii</option> - <option value="Cyanidioschyzon merolae">Cyanidioschyzon merolae</option> - <option value="Glycine max">Glycine max</option> - <option value="Hordeum vulgare">Hordeum vulgare</option> - <option value="Medicago truncatula">Medicago truncatula</option> - <option value="Musa acuminata">Musa acuminata</option> - <option value="Oryza brachyantha">Oryza brachyantha</option> - <option value="Oryza glaberrima">Oryza glaberrima</option> - <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option> - <option value="Oryza sativa">Oryza sativa</option> - <option value="Physcomitrella patens">Physcomitrella patens</option> - <option value="Populus trichocarpa">Populus trichocarpa</option> - <option value="Selaginella moellendorffii">Selaginella moellendorffii</option> - <option value="Setaria italica">Setaria italica</option> - <option value="Solanum lycopersicum">Solanum lycopersicum</option> - <option value="Solanum tuberosum">Solanum tuberosum</option> - <option value="Sorghum bicolor">Sorghum bicolor</option> - <option value="Vitis vinifera">Vitis vinifera</option> - <option value="Zea mays">Zea mays</option> - </param> - </when> - <when value="Metazoa"> - <param name="species" type="select" label="The species to use for the gene annotation" - help=""> - <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option> - <option value="Aedes aegypti">Aedes aegypti</option> - <option value="Amphimedon queenslandica">Amphimedon queenslandica</option> - <option value="Anopheles darlingi">Anopheles darlingi</option> - <option value="Anopheles gambiae">Anopheles gambiae</option> - <option value="Apis mellifera">Apis mellifera</option> - <option value="Atta cephalotes">Atta cephalotes</option> - <option value="Bombyx mori">Bombyx mori</option> - <option value="Brugia malayi">Brugia malayi</option> - <option value="Caenorhabditis brenneri">Caenorhabditis brenneri</option> - <option value="Caenorhabditis briggsae">Caenorhabditis briggsae</option> - <option value="Caenorhabditis elegans">Caenorhabditis elegans</option> - <option value="Caenorhabditis japonica">Caenorhabditis japonica</option> - <option value="Caenorhabditis remanei">Caenorhabditis remanei</option> - <option value="Culex quinquefasciatus">Culex quinquefasciatus</option> - <option value="Danaus plexippus">Danaus plexippus</option> - <option value="Daphnia pulex">Daphnia pulex</option> - <option value="Drosophila ananassae">Drosophila ananassae</option> - <option value="Drosophila erecta">Drosophila erecta</option> - <option value="Drosophila grimshawi">Drosophila grimshawi</option> - <option value="Drosophila melanogaster">Drosophila melanogaster</option> - <option value="Drosophila mojavensis">Drosophila mojavensis</option> - <option value="Drosophila persimilis">Drosophila persimilis</option> - <option value="Drosophila pseudoobscura">Drosophila pseudoobscura</option> - <option value="Drosophila sechellia">Drosophila sechellia</option> - <option value="Drosophila simulans">Drosophila simulans</option> - <option value="Drosophila virilis">Drosophila virilis</option> - <option value="Drosophila willistoni">Drosophila willistoni</option> - <option value="Drosophila yakuba">Drosophila yakuba</option> - <option value="Heliconius melpomene">Heliconius melpomene</option> - <option value="Ixodes scapularis">Ixodes scapularis</option> - <option value="Loa loa">Loa loa</option> - <option value="Megaselia scalaris">Megaselia scalaris</option> - <option value="Nasonia vitripennis">Nasonia vitripennis</option> - <option value="Nematostella vectensis">Nematostella vectensis</option> - <option value="Pediculus humanus">Pediculus humanus</option> - <option value="Pristionchus pacificus">Pristionchus pacificus</option> - <option value="Schistosoma mansoni">Schistosoma mansoni</option> - <option value="Strigamia maritima">Strigamia maritima</option> - <option value="Strongylocentrotus purpuratus">Strongylocentrotus purpuratus</option> - <option value="Tribolium castaneum">Tribolium castaneum</option> - <option value="Trichinella spiralis">Trichinella spiralis</option> - <option value="Trichoplax adhaerens">Trichoplax adhaerens</option> - </param> - </when> - <when value="Fungi"> - <param name="species" type="select" label="The species to use for the gene annotation" - help=""> - <option value="Ashbya gossypii">Ashbya gossypii</option> - <option value="Aspergillus clavatus">Aspergillus clavatus</option> - <option value="Aspergillus flavus">Aspergillus flavus</option> - <option value="Aspergillus fumigatus">Aspergillus fumigatus</option> - <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option> - <option value="Aspergillus nidulans">Aspergillus nidulans</option> - <option value="Aspergillus niger">Aspergillus niger</option> - <option value="Aspergillus oryzae">Aspergillus oryzae</option> - <option value="Aspergillus terreus">Aspergillus terreus</option> - <option value="Botryotinia fuckeliana">Botryotinia fuckeliana</option> - <option value="Cryptococcus neoformans">Cryptococcus neoformans</option> - <option value="Fusarium oxysporum">Fusarium oxysporum</option> - <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option> - <option value="Gibberella moniliformis">Gibberella moniliformis</option> - <option value="Gibberella zeae">Gibberella zeae</option> - <option value="Glomerella graminicola">Glomerella graminicola</option> - <option value="Komagataella pastoris">Komagataella pastoris</option> - <option value="Leptosphaeria maculans">Leptosphaeria maculans</option> - <option value="Magnaporthe oryzae">Magnaporthe oryzae</option> - <option value="Magnaporthe poae">Magnaporthe poae</option> - <option value="Melampsora larici-populina">Melampsora larici-populina</option> - <option value="Nectria haematococca">Nectria haematococca</option> - <option value="Neosartorya fischeri">Neosartorya fischeri</option> - <option value="Neurospora crassa">Neurospora crassa</option> - <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option> - <option value="Puccinia graminis">Puccinia graminis</option> - <option value="Puccinia triticina">Puccinia triticina</option> - <option value="Pyrenophora teres">Pyrenophora teres</option> - <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option> - <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option> - <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option> - <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option> - <option value="Sporisorium reilianum">Sporisorium reilianum</option> - <option value="Trichoderma reesei">Trichoderma reesei</option> - <option value="Trichoderma virens">Trichoderma virens</option> - <option value="Tuber melanosporum">Tuber melanosporum</option> - <option value="Ustilago maydis">Ustilago maydis</option> - <option value="Yarrowia lipolytica">Yarrowia lipolytica</option> - <option value="Zymoseptoria tritici">Zymoseptoria tritici</option> - </param> - </when> - <when value="Vertebrates"> - <param name="species" type="select" label="The species to use for the gene annotation" - help=""> - <option value="Ailuropoda melanoleuca">Ailuropoda melanoleuca</option> - <option value="Anolis carolinensis">Anolis carolinensis</option> - <option value="Bos taurus">Bos taurus</option> - <option value="Caenorhabditis elegans">Caenorhabditis elegans</option> - <option value="Callithrix jacchus">Callithrix jacchus</option> - <option value="Canis familiaris">Canis familiaris</option> - <option value="Cavia porcellus">Cavia porcellus</option> - <option value="Choloepus hoffmanni">Choloepus hoffmanni</option> - <option value="Ciona intestinalis">Ciona intestinalis</option> - <option value="Ciona savignyi">Ciona savignyi</option> - <option value="Danio rerio">Danio rerio</option> - <option value="Dasypus novemcinctus">Dasypus novemcinctus</option> - <option value="Dipodomys ordii">Dipodomys ordii</option> - <option value="Drosophila melanogaster">Drosophila melanogaster</option> - <option value="Echinops telfairi">Echinops telfairi</option> - <option value="Equus caballus">Equus caballus</option> - <option value="Erinaceus europaeus">Erinaceus europaeus</option> - <option value="Felis catus">Felis catus</option> - <option value="Gallus gallus">Gallus gallus</option> - <option value="Gasterosteus aculeatus">Gasterosteus aculeatus</option> - <option value="Gorilla gorilla">Gorilla gorilla</option> - <option value="Homo sapiens">Homo sapiens</option> - <option value="Ictidomys tridecemlineatus">Ictidomys tridecemlineatus</option> - <option value="Latimeria chalumnae">Latimeria chalumnae</option> - <option value="Loxodonta africana">Loxodonta africana</option> - <option value="Macaca mulatta">Macaca mulatta</option> - <option value="Macropus eugenii">Macropus eugenii</option> - <option value="Meleagris gallopavo">Meleagris gallopavo</option> - <option value="Microcebus murinus">Microcebus murinus</option> - <option value="Monodelphis domestica">Monodelphis domestica</option> - <option value="Mus musculus">Mus musculus</option> - <option value="Mustela putorius furo">Mustela putorius furo</option> - <option value="Myotis lucifugus">Myotis lucifugus</option> - <option value="Nomascus leucogenys">Nomascus leucogenys</option> - <option value="Ochotona princeps">Ochotona princeps</option> - <option value="Oreochromis niloticus">Oreochromis niloticus</option> - <option value="Ornithorhynchus anatinus">Ornithorhynchus anatinus</option> - <option value="Oryctolagus cuniculus">Oryctolagus cuniculus</option> - <option value="Oryzias latipes">Oryzias latipes</option> - <option value="Otolemur garnettii">Otolemur garnettii</option> - <option value="Pan troglodytes">Pan troglodytes</option> - <option value="Petromyzon marinus">Petromyzon marinus</option> - <option value="Pelodiscus sinensis">Pelodiscus sinensis</option> - <option value="Pongo abelii">Pongo abelii</option> - <option value="Procavia capensis">Procavia capensis</option> - <option value="Pteropus vampyrus">Pteropus vampyrus</option> - <option value="Rattus norvegicus">Rattus norvegicus</option> - <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option> - <option value="Sarcophilus harrisii">Sarcophilus harrisii</option> - <option value="Sorex araneus">Sorex araneus</option> - <option value="Sus scrofa">Sus scrofa</option> - <option value="Taeniopygia guttata">Taeniopygia guttata</option> - <option value="Takifugu rubripes">Takifugu rubripes</option> - <option value="Tarsius syrichta">Tarsius syrichta</option> - <option value="Tetraodon nigroviridis">Tetraodon nigroviridis</option> - <option value="Tupaia belangeri">Tupaia belangeri</option> - <option value="Tursiops truncatus">Tursiops truncatus</option> - <option value="Vicugna pacos">Vicugna pacos</option> - <option value="Xenopus tropicalis">Xenopus tropicalis</option> - <option value="Xiphophorus maculatus">Xiphophorus maculatus</option> - </param> - </when> - </conditional> - - <conditional name="processing_options"> - <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options"> - <option value="no" selected="True">Default Processing Options</option> - <option value="yes">Advanced Processing Options</option> - </param> - <when value="no" /> - <when value="yes"> - <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="protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="" type="float" - help="default 95%: '95.0'" /> - <conditional name="ptm_score"> - <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> - <option value="0" selected="True">A-score</option> - <option value="1">PhosphoRS</option> - </param> - <when value="0" /> - <when value="1"> - <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> - <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float" - help="Automatic mode will be used if not set" /> - </when> - </conditional> - <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> - </when> - </conditional> - <conditional name="filtering_options"> - <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options" - help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s"> - <option value="no" selected="True">Default Filtering Options</option> - <option value="yes">Advanced Processing Options</option> - </param> - <when value="no" /> - <when value="yes"> - <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="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /> - <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - </when> - </conditional> - - <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> - <option value="mzidentML" selected="True">mzidentML File</option> - <option value="3" selected="True">Peptide Report</option> - <option value="4" selected="True">Protein Report</option> - <option value="2">PSM Report</option> - <option value="0">Certificate of Analysis</option> - <option value="1">Hierarchical Report</option> - <option value="cps">CPS file</option> - <validator type="no_options" message="Please select at least one output file" /> - </param> - </inputs> - <outputs> - <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file"> - <filter>'mzidentML' in outputs</filter> - </data> - <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file"> - <filter>'cps' in outputs</filter> - </data> - <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> - <filter>'0' in outputs</filter> - </data> - <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> - <filter>'2' in outputs</filter> - </data> - <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> - <filter>'3' in outputs</filter> - </data> - <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> - <filter>'4' in outputs</filter> - </data> - <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> - <filter>'1' in outputs</filter> - </data> - </outputs> - <tests> - <test> - <param name="input_database" value="tinydb.fasta"/> - <param name="peak_lists" value="tinyspectra.mgf"/> - <param name="precursor_ion_tol" value="100"/> - <param name="fixed_modifications" value="carbamidomethyl c"/> - <param name="variable_modifications" value="oxidation of m"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="3"/> - <param name="species_type_selector" value="no_species_type"/> - <param name="processing_options_selector" value="no"/> - <param name="filtering_options_selector" value="no"/> - <!--param name="xtandem_selector" value="no"/>--> - <param name="xtandem_selector" value="yes"/> - <param name="xtandem_selector.xtandem_refine_selector" value="yes"/> - - <param name="omssa_selector" value="no"/> - <param name="msgf_selector" value="yes"/> - <param name="ms_amanda_selector" value="no"/> - - <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" /> - </test> - </tests> - <help> -**What it does** - -Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results. - -https://code.google.com/p/peptide-shaker/ - -https://code.google.com/p/searchgui/ - ----- - -Reports -======= - - -PSM Report ----------- - -* Protein(s): Protein(s) to which the peptide can be attached -* Sequence: Sequence of the peptide -* Variable Modifications: The variable modifications -* D-score: D-score for variable PTM localization -* probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. -* Localization Confidence: The confidence in variable PTM localization. -* Fixed Modifications: The fixed modifications. -* Spectrum File: The spectrum file. -* Spectrum Title: The title of the spectrum. -* Spectrum Scan Number: The spectrum scan number. -* RT: Retention time -* m/z: Measured m/z -* Measured Charge: The charge as given in the spectrum file. -* Identification Charge: The charge as inferred by the search engine. -* Theoretical Mass: The theoretical mass of the peptide. -* Isotope Number: The isotope number targetted by the instrument. -* Precursor m/z Error: The precursor m/z matching error. -* Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). -* Confidence: Confidence in percent associated to the retained PSM. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - -Protein Report --------------- - -* Main Accession: Main accession of the protein group. -* Description: Description of the protein designed by the main accession. -* Gene Name: The gene names of the Ensembl gene ID associated to the main accession. -* Chromosome: The chromosome of the Ensembl gene ID associated to the main accession. -* PI: Protein Inference status of the protein group. -* Secondary Accessions: Other accessions in the protein group (alphabetical order). -* Protein Group: The complete protein group (alphabetical order). -* #Peptides: Total number of peptides. -* #Validated Peptides: Number of validated peptides. -* #Unique: Total number of peptides unique to this protein group. -* #PSMs: Number of PSMs -* #Validated PSMs: Number of validated PSMs -* Coverage (%): Sequence coverage in percent of the protein designed by the main accession. -* Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. -* MW (kDa): Molecular Weight. -* Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) -* Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) -* Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized. -* Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized. -* Score: Score of the protein group. -* Confidence: Confidence in percent associated to the protein group. -* Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - -Peptide Report --------------- - - -* Protein(s): Protein(s) to which this peptide can be attached. -* AAs Before: The amino-acids before the sequence. -* Sequence: Sequence of the peptide. -* AAs After: The amino-acids after the sequence. -* Modified Sequence: The peptide sequence annotated with variable modifications. -* Variable Modifications: The variable modifications. -* Localization Confidence: The confidence in PTMs localization. -* Fixed Modifications: The fixed modifications. -* #Validated PSMs: Number of validated PSMs. -* #PSMs: Number of PSMs. -* Score: Score of the peptide. -* Confidence: Confidence in percent associated to the peptide. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - -Hierachical Report ------------------- - -* Main Accession: Main accession of the protein group. -* Description: Description of the protein designed by the main accession. -* PI: Protein Inference status of the protein group. -* Secondary Accessions: Other accessions in the protein group (alphabetical order). -* Protein Group: The complete protein group (alphabetical order). -* #Peptides: Total number of peptides. -* #Validated Peptides: Number of validated peptides. -* #Unique: Total number of peptides unique to this protein group. -* #PSMs: Number of PSMs -* #Validated PSMs: Number of validated PSMs -* Coverage (%): Sequence coverage in percent of the protein designed by the main accession. -* Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. -* MW (kDa): Molecular Weight. -* Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) -* Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) -* Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized. -* Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized. -* Score: Score of the protein group. -* Confidence: Confidence in percent associated to the protein group. -* Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. -* Protein(s): Protein(s) to which this peptide can be attached. -* AAs Before: The amino-acids before the sequence. -* Sequence: Sequence of the peptide. -* AAs After: The amino-acids after the sequence. -* Variable Modifications: The variable modifications. -* Localization Confidence: The confidence in PTMs localization. -* Fixed Modifications: The fixed modifications. -* #Validated PSMs: Number of validated PSMs. -* #PSMs: Number of PSMs. -* Score: Score of the peptide. -* Confidence: Confidence in percent associated to the peptide. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. -* Protein(s): Protein(s) to which the peptide can be attached. -* Sequence: Sequence of the peptide. -* Modified Sequence: The peptide sequence annotated with variable modifications. -* Variable Modifications: The variable modifications. -* D-score: D-score for variable PTM localization. -* probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. -* Localization Confidence: The confidence in variable PTM localization. -* Fixed Modifications: The fixed modifications. -* Spectrum File: The spectrum file. -* Spectrum Title: The title of the spectrum. -* Spectrum Scan Number: The spectrum scan number. -* RT: Retention time -* m/z: Measured m/z -* Measured Charge: The charge as given in the spectrum file. -* Identification Charge: The charge as inferred by the search engine. -* Theoretical Mass: The theoretical mass of the peptide. -* Isotope Number: The isotope number targetted by the instrument. -* Precursor m/z Error: The precursor m/z matching error. -* Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). -* Confidence: Confidence in percent associated to the retained PSM. -* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). -* Validation: Indicates the validation level of the protein group. - - - - ------- - -**Citation** - -To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com - -If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker - </help> - <expand macro="citations" /> -</tool>
--- a/repository_dependencies.xml Mon Dec 15 19:56:40 2014 -0500 +++ /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="9cfabf0b942d" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> -</repositories>
--- a/searchgui.xml Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,343 +0,0 @@ -<tool id="search_gui" name="Search GUI" version="1.23.0"> - <description> - Perform protein identification using various search engines and prepare results for input to Peptide Shaker - </description> - <requirements> - <requirement type="package" version="1.23">searchgui</requirement> - </requirements> - - <expand macro="stdio" /> - <command> -<![CDATA[ - #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") - #set $temp_stderr = 'macs2_stderr' - - mkdir output; - mkdir output_reports; - cwd=`pwd`; - #for $mgf in $peak_lists: - #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" - ln -s '${mgf}' '${input_name}'; - #end for - ##ln -s "${input_database}" input_database.fasta; - cp "${input_database}" input_database.fasta; - - ########################################### - #### Creating decoy database #### - ########################################### - #if $create_decoy: - echo "Creating decoy database."; - java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy; - rm input_database.fasta; - cp input_database_concatenated_target_decoy.fasta input_database.fasta; - ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; - #end if - - ##################################################### - ## generate IdentificationParameters for SearchGUI ## - ##################################################### - - (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI - -out SEARCHGUI_IdentificationParameters.parameters - - @GENERAL_PARAMETERS@ - - -db input_database.fasta - - #if $advanced.advanced_type_selector == "advanced": - - #if $advanced.xtandem.xtandem_selector == "yes" - - -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks} - -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks} - -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz} - -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass} - -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr} - - #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes" - -xtandem_refine 1 - -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc} - -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi} - -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut} - -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps} - -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt} - #end if - #end if - - #if $advanced.omssa.omssa_selector == "yes" - -omssa_hitlist_length ${advanced.omssa.hitlist_length} - -omssa_remove_prec ${advanced.omssa.remove_precursor} - -omssa_scale_prec ${advanced.omssa.scale_precursor} - -omssa_estimate_charge ${advanced.omssa.estimate_charge} - #end if - - #if $advanced.msgf.msgf_selector == "yes" - -msgf_decoy ${advanced.msgf.msgf_decoy} - -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length} - -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length} - -msgf_termini ${advanced.msgf.msgf_termini} - -msgf_num_ptms ${advanced.msgf.msgf_num_ptms} - #end if - - ##if $advanced.ms_amanda.ms_amanda_selector == "yes" - ##end if - - #end if - - 2> $temp_stderr) - && - - ################ - ## Search CLI ## - ################ - (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI - -temp_folder `pwd` - -spectrum_files \$cwd - -output_folder \$cwd/output - -id_params SEARCHGUI_IdentificationParameters.parameters - - -threads "\${GALAXY_SLOTS:-12}" - -correct_titles "${correct_titles}" - $missing_titles - -mgf_splitting "${mgf_splitting}" - -mgf_spectrum_count "${mgf_spectrum_count}" - - ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created - ## the tree is generated afterwards in PeptideShaker - -protein_index 0 - - ##-makeblastdb_folder \$BLAST_ROOT_DIR - - #if $advanced.advanced_type_selector == "advanced": - - #if $advanced.xtandem.xtandem_selector == "yes" - -xtandem 1 - #else - -xtandem 0 - #end if - - #if $advanced.omssa.omssa_selector == "yes" - -omssa 1 - #else - -omssa 0 - #end if - - #if $advanced.msgf.msgf_selector == "yes" - -msgf 1 - #else - -msgf 0 - #end if - - #if $advanced.ms_amanda.ms_amanda_selector == "yes" - -ms_amanda 1 - #else - -ms_amanda 0 - #end if - - #if $advanced.myrimatch.myrimatch_selector == "yes" - -myrimatch 1 - #else - -myrimatch 0 - #end if - - #if $advanced.comet.comet_selector == "yes" - -comet 1 - #else - -comet 0 - #end if - - #else - -ms_amanda 0 - #end if - - ## single zip file - -output_option 0 - - 2>> $temp_stderr) - - && - - exit_code_for_galaxy=\$?; - cat $temp_stderr 2>&1; - (exit \$exit_code_for_galaxy) -]]> - </command> - <inputs> - <param format="fasta" name="input_database" type="data" label="Protein Database" - help="Select FASTA database from history"/> - - <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true" - label="Create a concatenated target/decoy database before running PeptideShaker" - help="Selecting this option will help PeptideShaker calculate FDR values" /> - - <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" - help="Select appropriate MGF dataset(s) from history" /> - - <expand macro="general_options"/> - - <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" - help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> - <option value="0">no correction</option> - <option value="1" selected="True">rename spectra</option> - <option value="2">delete spectra</option> - </param> - - <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" - label="Add missing spectrum titles" help="(-missing_titles)"/> - - <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" - help="Choose a smaller value if you are running on a machine with limited memory"/> - - <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" - help="Choose a smaller value if you are running on a machine with limited memory"/> - - <conditional name="advanced"> - <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options"> - <option value="basic" selected="True">Basic</option> - <option value="advanced">Advanced</option> - </param> - <when value="basic" /> - <when value="advanced"> - <conditional name="xtandem"> - <param name="xtandem_selector" type="select" label="Run X!Tandem search"> - <option value="yes" selected="True">Search with X!Tandem</option> - <option value="no">No X!Tandem search</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/> - <param name="xtandem_min_peaks" type="integer" value="15" - label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> - <param name="xtandem_min_frag_mz" type="integer" value="200" - label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> - <param name="xtandem_min_prec_mass" label="X!Tandem: Min Precursor Mass" type="integer" value="200" help="Minimum mass of 1+ mass of parent ion to be considered"/> - <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/> - - <conditional name="xtandem_refine"><!-- -xtandem_refine --> - <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> - <option value="no" selected="True">Don't refine</option> - <option value="yes" >Use refinement</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" - label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> - <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" - label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/> - <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" - label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/> - <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" - label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/> - <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" - label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/> - </when> - </conditional> - </when> - </conditional> - - <conditional name="omssa"> - <param name="omssa_selector" type="select" label="Run OMSSA search"> - <option value="yes" selected="True">Search with OMSSA</option> - <option value="no">No OMSSA search</option> - </param> - <when value="no" /> - <when value="yes"> - <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> - - <conditional name="msgf"> - <param name="msgf_selector" type="select" label="Run MSGF search"> - <option value="yes" selected="True">Search with MSGF</option> - <option value="no">No MSGF search</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" - label="Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> - <param name="msgf_min_pep_length" type="integer" value="6" - label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> - <param name="msgf_max_pep_length" type="integer" value="30" - label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> - <param name="msgf_termini" type="select" format="text" - label="Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> - <option value="0">0 (ie non-specific cleavage)</option> - <option value="1">1 (ie semi-tryptic cleavage)</option> - <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> - </param> - <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/> - </when> - </conditional> - - <conditional name="ms_amanda"> - <param name="ms_amanda_selector" type="select" label="Run MS Amanda search"> - <option value="yes">Search with MS Amanda</option> - <option value="no" selected="True">No MS Amanda search</option> - </param> - <when value="no" /> - <when value="yes"> - </when> - </conditional> - - <conditional name="myrimatch"> - <param name="myrimatch_selector" type="select" label="Run MyriMatch search"> - <option value="yes">Search with MyriMatch</option> - <option value="no" selected="True">No MyriMatch search</option> - </param> - <when value="no" /> - <when value="yes"> - </when> - </conditional> - - <conditional name="comet"> - <param name="comet_selector" type="select" label="Run Comet search"> - <option value="yes">Search with Comet</option> - <option value="no" selected="True">No Comet search</option> - </param> - <when value="no" /> - <when value="yes"> - </when> - </conditional> - - </when> - </conditional> - - </inputs> - <outputs> - <data format="bgzip" name="searchgui_results" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> - </outputs> - <tests> - <test> - <param name="input_database" value="tinydb.fasta"/> - <param name="peak_lists" value="tinyspectra.mgf"/> - <param name="precursor_ion_tol" value="100"/> - <param name="fixed_modifications" value="carbamidomethyl c"/> - <param name="variable_modifications" value="oxidation of m"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="3"/> - <param name="advanced_type_selector" value="advanced"/> - <!--param name="xtandem_selector" value="no"/>--> - <param name="xtandem_selector" value="yes"/> - <param name="xtandem_selector.xtandem_refine_selector" value="yes"/> - - <param name="omssa_selector" value="no"/> - <param name="msgf_selector" value="yes"/> - <param name="ms_amanda_selector" value="no"/> - - <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" /> - </test> - </tests> - <help> -**What it does** - -Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI. - - - </help> - <expand macro="citations" /> -</tool>
--- a/searchgui_mods.loc.sample Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,210 +0,0 @@ -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
--- a/tool_dependencies.xml Mon Dec 15 19:56:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="searchgui" version="1.23"> - <repository changeset_revision="c3f36ea6ecd8" name="package_searchgui_1_23" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="peptide_shaker" version="0.35"> - <repository changeset_revision="51996a518b20" name="package_peptideshaker_0_35" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>