Mercurial > repos > bgruening > peptideshaker
changeset 1:149d652fc9f5 draft
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 01 May 2014 17:41:16 -0400 |
| parents | d833f714faa6 |
| children | e873824c4198 |
| files | 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 reverse.py reverse.xml tool_dependencies.xml |
| diffstat | 9 files changed, 456 insertions(+), 390 deletions(-) [+] |
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--- a/dbtoolkit-4.2/LICENSE-2.0.txt Sat Apr 12 11:50:34 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,202 +0,0 @@ - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. Definitions. - - "License" shall mean the terms and conditions for use, reproduction, - and distribution as defined by Sections 1 through 9 of this document. - - "Licensor" shall mean the copyright owner or entity authorized by - the copyright owner that is granting the License. - - "Legal Entity" shall mean the union of the acting entity and all - other entities that control, are controlled by, or are under common - control with that entity. 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--- a/dbtoolkit-4.2/lib/jargs-1.0.jar Sat Apr 12 11:50:34 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -<?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>
--- a/peptide_shaker.xml Sat Apr 12 11:50:34 2014 -0400 +++ b/peptide_shaker.xml Thu May 01 17:41:16 2014 -0400 @@ -3,6 +3,7 @@ <requirements> <requirement type="package" version="0.28.0">peptide_shaker</requirement> <requirement type="package" version="1.18.0">searchgui</requirement> + <!--<requirement type="package" version="2.2.29">blast+</requirement>--> </requirements> <description> Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. @@ -19,12 +20,25 @@ #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" ln -s '$mgf' 'spectra/$input_name'; #end for + ln -s $input_database input_database.fasta; - java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI - ##SearchCLI - -spectrum_files \$cwd/spectra - -output_folder \$cwd/output - -ppm $precursor_ion_tol_units + ########################################### + #### 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 input_database_decoy.fasta -temp_folder `pwd`; + ln -sf input_database_decoy.fasta input_database.fasta; + #end if + + ##################################################### + ## generate IdentificationParameters for SearchGUI ## + ##################################################### + + java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI + -temp_folder `pwd` + -out SEARCHGUI_IdentificationParameters.parameters + -prec_ppm $precursor_ion_tol_units -prec_tol $precursor_ion_tol -frag_tol $fragment_tol -enzyme '$enzyme' @@ -36,61 +50,157 @@ #if $variable_mods_str -variable_mods "$variable_mods_str" #end if + -min_charge $min_charge + -max_charge $max_charge -mc $missed_cleavages - #if $advanced.specify: - -xtandem $advanced.xtandem - #if $advanced.omssa.run_omssa - #set $omssa = 1 + -fi $forward_ion + -ri $reverse_ion + -db input_database.fasta + + #if $advanced.advanced_type_selector == "advanced": + + ##if $advanced.xtandem.xtandem_selector == "yes" + ##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" + ##end if + + ##if $advanced.ms_amanda.ms_amanda_selector == "yes" + ##end if + + #end if + ; + + ################ + ## Search CLI ## + ################ + java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI + -temp_folder `pwd` + -spectrum_files \$cwd/spectra + -output_folder \$cwd/output + -id_params SEARCHGUI_IdentificationParameters.parameters + + -threads "\${GALAXY_SLOTS:-12}" + -correct_titles $correct_titles + -mgf_splitting $mgf_splitting + -mgf_spectrum_count $mgf_spectrum_count + + #if $advanced.advanced_type_selector == "advanced": + + #if $advanced.xtandem.xtandem_selector == "yes" + -xtandem 1 #else - #set $omssa = 0 + -xtandem 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} + #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 + #end if - -db $input_database; + ; + ######################################################### + ## generate IdentificationParameters for PeptideShaker ## + ######################################################### + java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI + -temp_folder `pwd` + -out PEPTIDESHAKER_IdentificationParameters.parameters + -prec_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 + -min_charge $min_charge + -max_charge $max_charge + -mc $missed_cleavages + -fi $forward_ion + -ri $reverse_ion + -db input_database.fasta + ; + ###################### + ## PeptideShakerCLI ## + ###################### java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI - ##PeptideShakerCLI + -temp_folder `pwd` -experiment '$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 + -out \$cwd/output.cps + -id_params PEPTIDESHAKER_IdentificationParameters.parameters + + ##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} - -psm_FLR ${processing_options.psm_flr} - #if str($processing_options.a_score.use) == "1" - #set $a_score = 1 - #else - #set $a_score = 0 + -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 - -a_score $a_score - #if str($a_score) == "1" - -a_score_neutral_losses ${processing_options.a_score.neutral_losses} - #end if + -protein_fraction_mw_confidence $processing_options.protein_fraction_mw_confidence #end if - #if $filtering_options.specify + + + ##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 - -out \$cwd/output.cps ; + + ##Optional output parameters: + ##Output folder for text summary - format 1 (three files: proteins, peptides and psms, soon deprecated). + -out_txt_1 \$cwd/output_reports + + ; + cp -R ./* /home/bag/test/foo; mv output_reports/*peptides.txt peptides.txt ; mv output_reports/*psms.txt psms.txt ; mv output_reports/*proteins.txt proteins.txt @@ -101,6 +211,9 @@ <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 name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" /> + <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" @@ -138,8 +251,244 @@ <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> + <option value="Semi-Glu-C">Semi-Glu-C</option> + </param> + + <param name="correct_titles" type="select" label="Correct for duplicate spectrum titles" + help="(-correct_titles)"> + <option value="0">no correction</option> + <option value="1" selected="True">rename spectra</option> + <option value="2">delete spectra</option> </param> + + <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" + help="(-mgf_splitting)"/> + <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" + help="(-mgf_spectrum_count)"/> + + <conditional name="species_type"> + <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" + help="(-species_type)"> + <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="(-species)"> + <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="(-species)"> + <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="(-species)"> + <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="(-species)"> + <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="(-species)"> + <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> + <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" @@ -169,50 +518,94 @@ <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="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"> <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + + <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"> + </when> + </conditional> + <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="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"> + </when> + </conditional> + + <conditional name="ms_amanda"> + <param name="ms_amanda_selector" type="select" label="Run MS Amanda search"> + <option value="yes" selected="True">Search with MSGF</option> + <option value="no">No MS Amanda search</option> + </param> + <when value="no" /> + <when value="yes"> + </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="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="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" /> + <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' (-protein_fraction_mw_confidence)" /> + <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="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> + <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="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="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)." /> @@ -220,8 +613,9 @@ <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_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="(-max_mascot_e)" /> <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> </when> </conditional>
--- a/reverse.py Sat Apr 12 11:50:34 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -#!/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()
--- a/reverse.xml Sat Apr 12 11:50:34 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -<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='$output' - --script_path \$PEPTIDESHAKER_SCRIPT_PATH - </command> - <inputs> - <param format="fasta" name="input" type="data" label="FASTA Input" /> - </inputs> - <outputs> - <data format="fasta" name="output" /> - </outputs> - <help> -**What it does** - -Given an input database, this tool will produce a target-decoy -database in the format required by PeptideShaker using dbtoolkit. - ------- - -**Citation** - -For the underlying tool, please cite `Martens et al. DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics (2005) vol. 21 (17) pp. 3584-5`. - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/peptideshaker . - - </help> -</tool>
--- a/tool_dependencies.xml Sat Apr 12 11:50:34 2014 -0400 +++ b/tool_dependencies.xml Thu May 01 17:41:16 2014 -0400 @@ -4,9 +4,12 @@ <environment_variable action="set_to" name="PEPTIDESHAKER_SCRIPT_PATH">$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" /> + <repository changeset_revision="dacab27c8ed9" 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" /> + <repository changeset_revision="dc40b31c1d5b" name="package_peptideshaker_0_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> + <!--<package name="blast+" version="2.2.29"> + <repository name="package_blast_plus_2_2_29" owner="iuc" /> + </package>--> </tool_dependency>