Mercurial > repos > galaxyp > peptideshaker
view peptide_shaker.xml @ 29:78fad25eff17 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
| author | galaxyp |
|---|---|
| date | Fri, 10 Jun 2016 09:58:03 -0400 |
| parents | 432140bcc7fe |
| children | ad60446b1e93 |
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<tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="1.11">peptide_shaker</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 $temp_stderr = "peptideshaker_stderr" mkdir output_reports; cwd=`pwd`; cp -r "\${PEPTIDESHAKER_JAR_PATH%/*}" bin; tmp_peptideshaker_jar_path=`echo "\$cwd/bin/\${PEPTIDESHAKER_JAR_PATH\#\#/*/}"`; ln -s '$searchgui_input' searchgui_input.zip && ###################### ## PeptideShakerCLI ## ###################### (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.PeptideShakerCLI -temp_folder \$cwd/PeptideShakerCLI -experiment '$exp_str' -sample '$samp_str' -replicate 1 -identification_files \$cwd/searchgui_input.zip -out \$cwd/peptideshaker_output.cpsx -zip \$cwd/peptideshaker_output.zip -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}" -species_update 1 #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 "${processing_options.protein_fraction_mw_confidence}" -ptm_alignment "${processing_options.ptm_alignment}" #end if ##Optional filtering parameters: #if $filtering_options.filtering_options_selector == "yes": -import_peptide_length_min "${filtering_options.min_peptide_length}" -import_peptide_length_max "${filtering_options.max_peptide_length}" -import_precurosor_mz "${filtering_options.max_precursor_error}" -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}" ##-max_xtandem_e "${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>> $temp_stderr) && echo "Running Reports"; ################################## ## PeptideShaker Report options ## ################################## #if 'mzidentML' in str($outputs).split(','): echo "Generating mzIdentML"; (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.MzidCLI -in \$cwd/peptideshaker_output.zip -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" 2>> $temp_stderr) && #end if ## Generate Reports if the user has selected one of the 8 additional reports ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker ## and will not be passed to the command line #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.ReportCLI -temp_folder \$cwd/ReportCLI -in \$cwd/peptideshaker_output.zip -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 #if 'zip' in $cleaned_list: #silent $cleaned_list.remove('zip') #end if ## Only numbers are left over. These corresponds to different reports. -reports #echo ','.join($cleaned_list)# 2>> $temp_stderr) && #end if #if '0' in str($outputs).split(','): find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; ; #end if #if '1' in str($outputs).split(','): find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \; ; #end if #if '2' in str($outputs).split(','): find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \; ; #end if #if '3' in str($outputs).split(','): find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \; ; #end if #if '4' in str($outputs).split(','): find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \; ; #end if #if '5' in str($outputs).split(','): find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \; ; #end if #if '6' in str($outputs).split(','): find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \; ; #end if #if '7' in str($outputs).split(','): find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \; ; #end if exit_code_for_galaxy=\$?; cat $temp_stderr 2>&1; (exit \$exit_code_for_galaxy) ]]> </command> <inputs> <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" help="SearchGUI Results from History"> <options options_filter_attribute="metadata.searchgui_major_version" > <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" /> </options> </param> <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="no_species_type"/> <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="Bigelowiella natans">Bigelowiella natans</option> <option value="Dictyostelium discoideum">Dictyostelium discoideum</option> <option value="Emiliania huxleyi">Emiliania huxleyi</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="Paramecium tetraurelia">Paramecium tetraurelia</option> <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option> <option value="Phytophthora infestans">Phytophthora infestans</option> <option value="Phytophthora kernoviae">Phytophthora kernoviae</option> <option value="Phytophthora lateralis">Phytophthora lateralis</option> <option value="Phytophthora parasitica">Phytophthora parasitica</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 aphanidermatum">Pythium aphanidermatum</option> <option value="Pythium arrhenomanes">Pythium arrhenomanes</option> <option value="Pythium irregulare">Pythium irregulare</option> <option value="Pythium iwayamai">Pythium iwayamai</option> <option value="Pythium ultimum">Pythium ultimum</option> <option value="Pythium vexans">Pythium vexans</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="Amborella (Amborella trichopoda)">Amborella (Amborella trichopoda)</option> <option value="Arabidopsis lyrata (Lyrate rockcress)">Arabidopsis lyrata (Lyrate rockcress)</option> <option value="Arabidopsis thaliana (Thale-cress)">Arabidopsis thaliana (Thale-cress)</option> <option value="Brachypodium distachyon (False brome)">Brachypodium distachyon (False brome)</option> <option value="Brassica oleracea">Brassica oleracea</option> <option value="Brassica rapa genes (Field mustard)">Brassica rapa genes (Field mustard)</option> <option value="Chlamydomonas reinhardtii (Green algae)">Chlamydomonas reinhardtii (Green algae)</option> <option value="Cyanidioschyzon merolae (Red algae)">Cyanidioschyzon merolae (Red algae)</option> <option value="Glycine max (Soybean)">Glycine max (Soybean)</option> <option value="Hordeum vulgare (Barley)">Hordeum vulgare (Barley)</option> <option value="Leersia perrieri (Leersia)">Leersia perrieri (Leersia)</option> <option value="Medicago truncatula (Barrel medic)">Medicago truncatula (Barrel medic)</option> <option value="Musa acuminata (Banana)">Musa acuminata (Banana)</option> <option value="Oryza brachyantha">Oryza brachyantha</option> <option value="Oryza glumaepatula">Oryza glumaepatula</option> <option value="Oryza meridionalis">Oryza meridionalis</option> <option value="Oryza nivara">Oryza nivara</option> <option value="Oryza punctata">Oryza punctata</option> <option value="Oryza rufipogon (Common wild rice)">Oryza rufipogon (Common wild rice)</option> <option value="Oryza sativa (Indica rice)">Oryza sativa (Indica rice)</option> <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option> <option value="Oryza sativa Japonica (Japonica rice)">Oryza sativa Japonica (Japonica rice)</option> <option value="Ostreococcus lucimarinus (Green algae)">Ostreococcus lucimarinus (Green algae)</option> <option value="Physcomitrella patens">Physcomitrella patens</option> <option value="Physcomitrella patens (Moss)">Physcomitrella patens (Moss)</option> <option value="Populus trichocarpa">Populus trichocarpa</option> <option value="Populus trichocarpa (Western balsam poplar)">Populus trichocarpa (Western balsam poplar)</option> <option value="Prunus persica (Peach)">Prunus persica (Peach)</option> <option value="Selaginella moellendorffii (Spike moss)">Selaginella moellendorffii (Spike moss)</option> <option value="Setaria italica (Foxtail millet)">Setaria italica (Foxtail millet)</option> <option value="Solanum lycopersicum (Tomato)">Solanum lycopersicum (Tomato)</option> <option value="Solanum tuberosum (Potato)">Solanum tuberosum (Potato)</option> <option value="Sorghum bicolor (Sorghum)">Sorghum bicolor (Sorghum)</option> <option value="Theobroma cacao (Cocoa)">Theobroma cacao (Cocoa)</option> <option value="Triticum aestivum (Bread wheat)">Triticum aestivum (Bread wheat)</option> <option value="Triticum urartu (Einkorn)">Triticum urartu (Einkorn)</option> <option value="Vitis vinifera (Wine grape)">Vitis vinifera (Wine grape)</option> <option value="Zea mays (Maize)">Zea mays (Maize)</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 (Yellow fever mosquito)">Aedes aegypti (Yellow fever mosquito)</option> <option value="Amphimedon queenslandica">Amphimedon queenslandica</option> <option value="Anopheles darlingi">Anopheles darlingi</option> <option value="Anopheles gambiae (African malaria mosquito) ">Anopheles gambiae (African malaria mosquito) </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 (Southern house mosquito) ">Culex quinquefasciatus (Southern house mosquito) </option> <option value="Danaus plexippus ">Danaus plexippus </option> <option value="Daphnia pulex ">Daphnia pulex </option> <option value="Dendroctonus ponderosae">Dendroctonus ponderosae</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 (Fruit fly) ">Drosophila melanogaster (Fruit fly) </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="Helobdella robusta">Helobdella robusta</option> <option value="Ixodes scapularis (Black-legged tick) ">Ixodes scapularis (Black-legged tick) </option> <option value="Loa loa ">Loa loa </option> <option value="Lottia gigantea">Lottia gigantea</option> <option value="Megaselia scalaris ">Megaselia scalaris </option> <option value="Melitaea cinxia">Melitaea cinxia</option> <option value="Mnemiopsis leidyi">Mnemiopsis leidyi</option> <option value="Nasonia vitripennis ">Nasonia vitripennis </option> <option value="Nematostella vectensis ">Nematostella vectensis </option> <option value="Onchocerca volvulus">Onchocerca volvulus</option> <option value="Pediculus humanus (Human louse) ">Pediculus humanus (Human louse) </option> <option value="Pristionchus pacificus ">Pristionchus pacificus </option> <option value="Rhodnius prolixus">Rhodnius prolixus</option> <option value="Schistosoma mansoni ">Schistosoma mansoni </option> <option value="Solenopsis invicta (Red fire ant)">Solenopsis invicta (Red fire ant)</option> <option value="Strigamia maritima ">Strigamia maritima </option> <option value="Strongylocentrotus purpuratus ">Strongylocentrotus purpuratus </option> <option value="Tetranychus urticae">Tetranychus urticae</option> <option value="Tribolium castaneum (red flour beetle) ">Tribolium castaneum (red flour beetle) </option> <option value="Trichinella spiralis ">Trichinella spiralis </option> <option value="Trichoplax adhaerens ">Trichoplax adhaerens </option> <option value="Zootermopsis nevadensis">Zootermopsis nevadensis</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="Blumeria graminis">Blumeria graminis</option> <option value="Botrytis cinerea">Botrytis cinerea</option> <option value="Colletotrichum gloeosporioides">Colletotrichum gloeosporioides</option> <option value="Colletotrichum higginsianum">Colletotrichum higginsianum</option> <option value="Colletotrichum orbiculare">Colletotrichum orbiculare</option> <option value="Cryptococcus neoformans">Cryptococcus neoformans</option> <option value="Dothistroma septosporum">Dothistroma septosporum</option> <option value="Fusarium fujikuroi">Fusarium fujikuroi</option> <option value="Fusarium graminearum">Fusarium graminearum</option> <option value="Fusarium oxysporum">Fusarium oxysporum</option> <option value="Fusarium pseudograminearum">Fusarium pseudograminearum</option> <option value="Fusarium solani">Fusarium solani</option> <option value="Fusarium verticillioides">Fusarium verticillioides</option> <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option> <option value="Colletotrichum graminicola">Colletotrichum 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="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 graminis Ug99">Puccinia graminis Ug99</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 cryophilus">Schizosaccharomyces cryophilus</option> <option value="Schizosaccharomyces japonicus">Schizosaccharomyces japonicus</option> <option value="Schizosaccharomyces octosporus">Schizosaccharomyces octosporus</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="Verticillium dahliae JR2">Verticillium dahliae JR2</option> <option value="Verticillium dahliae">Verticillium dahliae</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="Alpaca (Vicugna pacos)">Alpaca (Vicugna pacos)</option> <option value="Amazon molly (Poecilia formosa)">Amazon molly (Poecilia formosa)</option> <option value="Anole lizard (Anolis carolinensis)">Anole lizard (Anolis carolinensis)</option> <option value="Armadillo (Dasypus novemcinctus)">Armadillo (Dasypus novemcinctus)</option> <option value="Bushbaby (Otolemur garnettii)">Bushbaby (Otolemur garnettii)</option> <option value="C. elegans (Caenorhabditis elegans)">C. elegans (Caenorhabditis elegans)</option> <option value="C.intestinalis (Ciona intestinalis)">C.intestinalis (Ciona intestinalis)</option> <option value="C.savignyi (Ciona savignyi)">C.savignyi (Ciona savignyi)</option> <option value="Cat (Felis catus)">Cat (Felis catus)</option> <option value="Cave fish (Astyanax mexicanus)">Cave fish (Astyanax mexicanus)</option> <option value="Chicken (Gallus gallus)">Chicken (Gallus gallus)</option> <option value="Chimpanzee (Pan troglodytes)">Chimpanzee (Pan troglodytes)</option> <option value="Chinese softshell turtle (Pelodiscus sinensis)">Chinese softshell turtle (Pelodiscus sinensis)</option> <option value="Cod (Gadus morhua)">Cod (Gadus morhua)</option> <option value="Coelacanth (Latimeria chalumnae)">Coelacanth (Latimeria chalumnae)</option> <option value="Cow (Bos taurus)">Cow (Bos taurus)</option> <option value="Dog (Canis lupus familiaris)">Dog (Canis lupus familiaris)</option> <option value="Dolphin (Tursiops truncatus)">Dolphin (Tursiops truncatus)</option> <option value="Duck (Anas platyrhynchos)">Duck (Anas platyrhynchos)</option> <option value="Elephant (Loxodonta africana)">Elephant (Loxodonta africana)</option> <option value="Ferret (Mustela putorius furo)">Ferret (Mustela putorius furo)</option> <option value="Flycatcher (Ficedula albicollis)">Flycatcher (Ficedula albicollis)</option> <option value="Fruitfly (Drosophila melanogaster)">Fruitfly (Drosophila melanogaster)</option> <option value="Fugu (Takifugu rubripes)">Fugu (Takifugu rubripes)</option> <option value="Gibbon (Nomascus leucogenys)">Gibbon (Nomascus leucogenys)</option> <option value="Gorilla (Gorilla gorilla gorilla)">Gorilla (Gorilla gorilla gorilla)</option> <option value="Guinea Pig (Cavia porcellus)">Guinea Pig (Cavia porcellus)</option> <option value="Hedgehog (Erinaceus europaeus)">Hedgehog (Erinaceus europaeus)</option> <option value="Horse (Equus caballus)">Horse (Equus caballus)</option> <option value="Human (Homo sapiens)">Human (Homo sapiens)</option> <option value="Hyrax (Procavia capensis)">Hyrax (Procavia capensis)</option> <option value="Kangaroo rat (Dipodomys ordii)">Kangaroo rat (Dipodomys ordii)</option> <option value="Lamprey (Petromyzon marinus)">Lamprey (Petromyzon marinus)</option> <option value="Lesser hedgehog tenrec (Echinops telfairi)">Lesser hedgehog tenrec (Echinops telfairi)</option> <option value="Macaque (Macaca mulatta)">Macaque (Macaca mulatta)</option> <option value="Marmoset (Callithrix jacchus)">Marmoset (Callithrix jacchus)</option> <option value="Medaka (Oryzias latipes)">Medaka (Oryzias latipes)</option> <option value="Megabat (Pteropus vampyrus)">Megabat (Pteropus vampyrus)</option> <option value="Microbat (Myotis lucifugus)">Microbat (Myotis lucifugus)</option> <option value="Mouse (Mus musculus)">Mouse (Mus musculus)</option> <option value="Mouse Lemur (Microcebus murinus)">Mouse Lemur (Microcebus murinus)</option> <option value="Opossum (Monodelphis domestica)">Opossum (Monodelphis domestica)</option> <option value="Orangutan (Pongo abelii)">Orangutan (Pongo abelii)</option> <option value="Panda (Ailuropoda melanoleuca)">Panda (Ailuropoda melanoleuca)</option> <option value="Pig (Sus scrofa)">Pig (Sus scrofa)</option> <option value="Pika (Ochotona princeps)">Pika (Ochotona princeps)</option> <option value="Platyfish (Xiphophorus maculatus)">Platyfish (Xiphophorus maculatus)</option> <option value="Platypus (Ornithorhynchus anatinus)">Platypus (Ornithorhynchus anatinus)</option> <option value="Rabbit (Oryctolagus cuniculus)">Rabbit (Oryctolagus cuniculus)</option> <option value="Rat (Rattus norvegicus)">Rat (Rattus norvegicus)</option> <option value="S. cerevisiae (Saccharomyces cerevisiae)">S. cerevisiae (Saccharomyces cerevisiae)</option> <option value="Sheep (Ovis aries)">Sheep (Ovis aries)</option> <option value="Shrew (Sorex araneus)">Shrew (Sorex araneus)</option> <option value="Sloth (Choloepus hoffmanni)">Sloth (Choloepus hoffmanni)</option> <option value="Spotted gar (Lepisosteus oculatus)">Spotted gar (Lepisosteus oculatus)</option> <option value="Squirrel (Ictidomys tridecemlineatus)">Squirrel (Ictidomys tridecemlineatus)</option> <option value="Stickleback (Gasterosteus aculeatus)">Stickleback (Gasterosteus aculeatus)</option> <option value="Tarsier (Tarsius syrichta)">Tarsier (Tarsius syrichta)</option> <option value="Tasmanian devil (Sarcophilus harrisii)">Tasmanian devil (Sarcophilus harrisii)</option> <option value="Tetraodon (Tetraodon nigroviridis)">Tetraodon (Tetraodon nigroviridis)</option> <option value="Tilapia (Oreochromis niloticus)">Tilapia (Oreochromis niloticus)</option> <option value="Tree Shrew (Tupaia belangeri)">Tree Shrew (Tupaia belangeri)</option> <option value="Turkey (Meleagris gallopavo)">Turkey (Meleagris gallopavo)</option> <option value="Vervet-AGM (Chlorocebus sabaeus)">Vervet-AGM (Chlorocebus sabaeus)</option> <option value="Wallaby (Macropus eugenii)">Wallaby (Macropus eugenii)</option> <option value="Xenopus (Xenopus tropicalis)">Xenopus (Xenopus tropicalis)</option> <option value="Zebra Finch (Taeniopygia guttata)">Zebra Finch (Taeniopygia guttata)</option> <option value="Zebrafish (Danio rerio)">Zebrafish (Danio rerio)</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" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot" 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" optional="true" value="" type="float" help="Automatic mode will be used if not set" /> </when> </conditional> <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/> <!-- 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 Filtering Options</option> </param> <when value="no" /> <when value="yes"> <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" /> <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" /> <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10" help="Next option specifies units (Da or ppm)" /> <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> <option value="1">ppm</option> <option value="0">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="zip">Zip File for import to Desktop App</option> <option value="mzidentML" selected="True">mzidentML File</option> <option value="3" >PSM Report</option> <option value="4" >Peptide Phosphorylation Report</option> <option value="5" >Peptide Report</option> <option value="6" >Protein Phosphorylation Report</option> <option value="7" >Protein Report</option> <option value="2">PSM Phosphorylation 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 ${on_string}: mzidentML file"> <filter>'mzidentML' in outputs</filter> </data> <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file"> <filter>'cps' in outputs</filter> </data> <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> <filter>'zip' in outputs</filter> </data> <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> <filter>'0' in outputs</filter> </data> <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> <filter>'1' in outputs</filter> </data> <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report"> <filter>'2' in outputs</filter> </data> <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> <filter>'3' in outputs</filter> </data> <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> <filter>'4' in outputs</filter> </data> <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> <filter>'5' in outputs</filter> </data> <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report"> <filter>'6' in outputs</filter> </data> <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> <filter>'7' in outputs</filter> </data> </outputs> <tests> <test> <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> <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="outputs" value="zip,cps,3"/> <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" /> <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" /> <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> </test> <test> <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> <param name="species_type_selector" value="no_species_type"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="yes"/> <param name="min_peptide_length" value="1"/> <param name="outputs" value="0,1,2,3,4,5,6,7"/> <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/> <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" /> <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" /> <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" /> <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" /> <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" /> <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" /> <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> </test> <test> <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> <param name="species_type_selector" value="Vertebrates"/> <param name="species" value="Human (Homo sapiens)"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="yes"/> <param name="min_peptide_length" value="1"/> <param name="outputs" value="5"/> <output name="output_peptides" file="peptide_shaker_peptides_result3.tabular" ftype="tabular" /> </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>