Mercurial > repos > galaxyp > peptideshaker
changeset 18:ffed32e397cb draft
Uploaded
| author | galaxyp |
|---|---|
| date | Wed, 11 Jan 2017 13:06:06 -0500 |
| parents | 2f8e9d0351a8 |
| children | ef4ac2d49ff0 |
| files | macros.xml peptide_shaker.xml searchgui.xml tool_dependencies.xml |
| diffstat | 4 files changed, 234 insertions(+), 351 deletions(-) [+] |
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--- a/macros.xml Fri Jun 10 09:57:31 2016 -0400 +++ b/macros.xml Wed Jan 11 13:06:06 2017 -0500 @@ -4,6 +4,7 @@ <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"/> + <regex match="CompomicsError" level="fatal" description="Compomics Error"/> </stdio> </xml> <token name="@GENERAL_PARAMETERS@"> @@ -25,8 +26,8 @@ -fi $forward_ion -ri $reverse_ion </token> - <token name="@SEARCHGUI_MAJOR_VERSION@">2</token> - <token name="@SEARCHGUI_VERSION@">2.9</token> + <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> + <token name="@SEARCHGUI_VERSION@">3.1.4</token> <xml name="general_options"> <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
--- a/peptide_shaker.xml Fri Jun 10 09:57:31 2016 -0400 +++ b/peptide_shaker.xml Wed Jan 11 13:06:06 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> @@ -6,7 +6,7 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="1.11">peptide_shaker</requirement> + <requirement type="package" version="1.13.6">peptide-shaker</requirement> </requirements> <expand macro="stdio" /> <command> @@ -15,36 +15,30 @@ #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" + #set $bin_dir = "bin" mkdir output_reports; cwd=`pwd`; - cp -r "\${PEPTIDESHAKER_JAR_PATH%/*}" bin; - tmp_peptideshaker_jar_path=`echo "\$cwd/bin/\${PEPTIDESHAKER_JAR_PATH\#\#/*/}"`; - ln -s '$searchgui_input' searchgui_input.zip && + jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par && ###################### ## PeptideShakerCLI ## ###################### - (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.PeptideShakerCLI + (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI + --exec_dir="\$cwd/${bin_dir}" -temp_folder \$cwd/PeptideShakerCLI -experiment '$exp_str' -sample '$samp_str' -replicate 1 -identification_files \$cwd/searchgui_input.zip + -id_params \$cwd/SEARCHGUI_IdentificationParameters.par -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}" @@ -85,16 +79,33 @@ #if 'mzidentML' in str($outputs).split(','): echo "Generating mzIdentML"; - (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.MzidCLI + (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI + --exec_dir="\$cwd/${bin_dir}" -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" + #if $contact_options.contact_options_selector == "yes": + -contact_first_name "$contact_options.contact_first_name" + -contact_last_name "$contact_options.contact_last_name" + -contact_email "$contact_options.contact_email" + -contact_address "$contact_options.contact_address" + #if str($contact_options.contact_url).strip() != '': + -contact_url = "$contact_options.contact_url" + #end if + -organization_name "$contact_options.organization_name" + -organization_email "$contact_options.organization_email" + -organization_address "$contact_options.organization_address" + #if str($contact_options.organization_url).strip() != '': + -organization_url = "$contact_options.organization_url" + #end if + #else: + -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 2>> $temp_stderr) && #end if @@ -104,7 +115,8 @@ ## and will not be passed to the command line #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): - (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.ReportCLI + (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI + --exec_dir="\$cwd/${bin_dir}" -temp_folder \$cwd/ReportCLI -in \$cwd/peptideshaker_output.zip -out_reports \$cwd/output_reports @@ -125,6 +137,7 @@ && #end if + ## # ls -l \$cwd/output_reports/* ; #if '0' in str($outputs).split(','): find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; @@ -138,6 +151,10 @@ find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \; ; #end if + #if '8' in str($outputs).split(','): + find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \; + ; + #end if #if '3' in str($outputs).split(','): find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \; ; @@ -172,287 +189,6 @@ <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> @@ -503,15 +239,53 @@ <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> </when> </conditional> + <conditional name="contact_options"> + <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML" + help="Create a Galaxy workflow to save these values"> + <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option> + <option value="yes">Specify Contact Information</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="contact_first_name" type="text" value="" label="Contact first name."> + <validator type="regex" message="">\S+.*</validator> + </param> + <param name="contact_last_name" type="text" value="" label="Contact last name."> + <validator type="regex" message="">\S+.*</validator> + </param> + <param name="contact_email" type="text" value="" label="Contact e-mail."> + <validator type="regex" message="">\S+@\S+</validator> + </param> + <param name="contact_address" type="text" value="" label="Contact address."> + <validator type="regex" message="">\S+.*</validator> + </param> + <param name="contact_url" type="text" value="" optional="true" label="Contact URL."> + </param> + <param name="organization_name" type="text" value="" label="Organization name."> + <validator type="regex" message="">\S+.*</validator> + </param> + <param name="organization_email" type="text" value="" label="Organization e-mail."> + <validator type="regex" message="">\S+@\S+</validator> + </param> + <param name="organization_address" type="text" value="" label="Organization address."> + <validator type="regex" message="">\S+.*</validator> + </param> + <param name="organization_url" type="text" value="" optional="true" label="Organization URL."> + </param> + </when> + </conditional> + + <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" /> <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="3">PSM Report</option> + <option value="8">Extended PSM Report</option> <option value="2">PSM Phosphorylation Report</option> + <option value="5">Peptide Report</option> + <option value="4">Peptide Phosphorylation Report</option> + <option value="7">Protein Report</option> + <option value="6">Protein Phosphorylation Report</option> <option value="0">Certificate of Analysis</option> <option value="1">Hierarchical Report</option> <option value="cps">CPS file</option> @@ -541,6 +315,9 @@ <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> <filter>'3' in outputs</filter> </data> + <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report"> + <filter>'8' in outputs</filter> + </data> <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> <filter>'4' in outputs</filter> </data>
--- a/searchgui.xml Fri Jun 10 09:57:31 2016 -0400 +++ b/searchgui.xml Wed Jan 11 13:06:06 2017 -0500 @@ -7,7 +7,9 @@ </macros> <requirements> <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> + <!-- <environment_variable name="LC_ALL" action="set_to">C</environment_variable> + --> </requirements> <expand macro="stdio" /> <command> @@ -16,21 +18,25 @@ #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 = "searchgui_stderr" + #set $bin_dir = "bin" mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=\$cwd; + ## echo the search engines to run + echo "$engines"; + echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}"; + ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties; - cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin; - tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`; - #for $mgf in $peak_lists: #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" ln -s -f '${mgf}' '${input_name}'; + #set $encoded_id = $__app__.security.encode_id($mgf.id) + echo "Spectrums:${mgf.display_name}(API:${encoded_id}) "; #end for ##ln -s "${input_database}" input_database.fasta; cp "${input_database}" input_database.fasta; @@ -40,7 +46,7 @@ ########################################### #if $create_decoy: echo "Creating decoy database."; - java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && + searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -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; @@ -49,8 +55,8 @@ ##################################################### ## generate IdentificationParameters for SearchGUI ## ##################################################### - - (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI + (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI + --exec_dir="\$cwd/${bin_dir}" -out SEARCHGUI_IdentificationParameters.par @GENERAL_PARAMETERS@ @@ -196,6 +202,7 @@ -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length} -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length} -andromeda_max_psms ${andromeda.andromeda_max_psms} + -andromeda_decoy_mode ${andromeda.andromeda_decoy_mode} #end if *# @@ -245,15 +252,16 @@ #if $comet.comet_spectrum.comet_spectrum_selector == "yes" -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks} -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int} - -comet_remove_prec ${comet.comet_spectrum.comet_remove_prec} + + -comet_remove_prec ${comet.comet_spectrum.comet_prec.comet_remove_prec} - #if $comet.comet_spectrum.comet_remove_prec == "1" - -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol} + #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "1" + -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol} #end if - #if $comet.comet_spectrum.comet_remove_prec == "2" - -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol} + #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "2" + -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol} #end if -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower} @@ -279,13 +287,44 @@ #end if #end if + #if $directtag.directtag_advanced == "yes" + -directag_tic_cutoff ${directtag.directag_tic_cutoff} + -directag_max_peak_count ${directtag.directag_max_peak_count} + -directag_intensity_classes ${directtag.directag_intensity_classes} + -directag_adjust_precursor ${directtag.directag_adjust_precursor} + -directag_min_adjustment ${directtag.directag_min_adjustment} + -directag_max_adjustment ${directtag.directag_max_adjustment} + -directag_adjustment_step ${directtag.directag_adjustment_step} + -directag_charge_states ${directtag.directag_charge_states} + #if str($directtag.directag_output_suffix).strip() != '': + -directag_output_suffix ${directtag.directag_output_suffix} + #end if + -directag_ms_charge_state ${directtag.directag_ms_charge_state} + -directag_duplicate_spectra ${directtag.directag_duplicate_spectra} + -directag_deisotoping ${directtag.directag_deisotoping} + -directag_isotope_tolerance ${directtag.directag_isotope_tolerance} + -directag_complement_tolerance ${directtag.directag_complement_tolerance} + -directag_tag_length ${directtag.directag_tag_length} + -directag_max_var_mods ${directtag.directag_max_var_mods} + -directag_max_tag_count ${directtag.directag_max_tag_count} + -directag_intensity_weight ${directtag.directag_intensity_weight} + -directag_fidelity_weight ${directtag.directag_fidelity_weight} + -directag_complement_weight ${directtag.directag_complement_weight} + #end if + + #if $novor.novor_advanced == "yes" + -novor_fragmentation ${novor.novor_fragmentation} + -novor_mass_analyzer ${novor.novor_mass_analyzer} + #end if + 2> $temp_stderr) && ################ ## Search CLI ## ################ - (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI + (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI + --exec_dir="\$cwd/${bin_dir}" -temp_folder `pwd` -spectrum_files \$cwd -output_folder \$cwd/output @@ -355,6 +394,18 @@ -andromeda 0 #end if + #if 'Novor' in $engines_list: + -novor 1 + #else + -novor 0 + #end if + + #if 'DirecTag' in $engines_list: + -directag 1 + #else + -directag 0 + #end if + ## single zip file -output_option 0 @@ -396,19 +447,26 @@ <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> <option value="X!Tandem" selected="True">X!Tandem</option> - <!-- Not working in tests - <option value="MyriMatch">MyriMatch</option> - <option value="MS_Amanda">MS_Amanda</option> - --> + <option value="MSGF" selected="True">MS-GF+</option> <option value="OMSSA" selected="True">OMSSA</option> <option value="Comet">Comet</option> <!-- Not working in tests + --> <option value="Tide">Tide</option> + <!-- Not working in tests --> + <option value="MyriMatch">MyriMatch</option> + <option value="MS_Amanda">MS_Amanda</option> <!-- Windows only <option value="Andromeda">Andromeda</option> --> + <!-- New with version 3.0 + --> + <!--working in tests + --> + <option value="DirecTag">DirecTag</option> + <option value="Novor">Novor (Select for non-commercial use only)</option> <validator type="no_options" message="Please select at least one output file" /> </param> @@ -439,7 +497,7 @@ <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"/> - </when> + </when> </conditional> @@ -470,7 +528,7 @@ <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models" label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> <param name="xtandem_evalue" help="Highest value for recorded peptides" - label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" /> + label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" /> <param name="xtandem_output_proteins" help="Controls output of protein sequences" label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" /> <param name="xtandem_output_sequences" help="Controls output of sequence information" @@ -867,6 +925,7 @@ <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" /> <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" /> <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" /> + <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" /> </when> </conditional> --> @@ -891,20 +950,22 @@ label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" /> <param name="comet_min_peak_int" type="float" value="0.0" label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" /> - <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal"> - <option value="0" selected="True" >off</option> - <option value="1">on</option> - <option value="2">as expected for ETD/ECD spectra</option> - </param> - <when value="0" /> - <when value="1"> - <param name="comet_remove_prec_tol" type="float" value="1.5" - label="Comet: Remove Precursor Tolerance" /> - </when> - <when value="2"> - <param name="comet_remove_prec_tol" type="float" value="1.5" - label="Comet: Remove Precursor Tolerance" /> - </when> + <conditional name="comet_prec"> + <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal"> + <option value="0" selected="True" >off</option> + <option value="1">on</option> + <option value="2">as expected for ETD/ECD spectra</option> + </param> + <when value="0" /> + <when value="1"> + <param name="comet_remove_prec_tol" type="float" value="1.5" + label="Comet: Remove Precursor Tolerance" /> + </when> + <when value="2"> + <param name="comet_remove_prec_tol" type="float" value="1.5" + label="Comet: Remove Precursor Tolerance" /> + </when> + </conditional> <param name="comet_clear_mz_range_lower" type="float" value="0.0" label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" /> <param name="comet_clear_mz_range_upper" type="float" value="0.0" @@ -964,6 +1025,59 @@ </conditional> </when> </conditional> + <conditional name="directtag"> + <param name="directtag_advanced" type="select" label="DirectTag Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/> + <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/> + <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/> + <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/> + <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/> + <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/> + <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/> + <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/> + <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/> + <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/> + <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/> + <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping"> + <option value="0" selected="true">no deisotoping</option> + <option value="1">precursor only</option> + <option value="2">precursor and candidate</option> + </param> + <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/> + <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/> + <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/> + <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/> + <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/> + <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/> + <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/> + <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/> + </when> + </conditional> + + <conditional name="novor"> + <param name="novor_advanced" type="select" label="Novor Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="novor_fragmentation" type="select" label="Novor fragmentation method"> + <option value="HCD" selected="True">HCD</option> + <option value="CID">CID</option> + </param> + <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra"> + <option value="FT" selected="True">FT</option> + <option value="Trap" >Trap</option> + <option value="TOF" >TOF</option> + </param> + </when> + </conditional> + </inputs> <outputs> <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
--- a/tool_dependencies.xml Fri Jun 10 09:57:31 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="searchgui" version="2.9"> - <repository changeset_revision="ad67fd4127ae" name="package_searchgui_2_9" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="peptide_shaker" version="1.11"> - <repository changeset_revision="7c812d11f172" name="package_peptideshaker_1_11" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>