# HG changeset patch # User iracooke # Date 1427241518 14400 # Node ID b6f4f4689f5fd5271f657ed6309bf1a3810a22af # Parent 8caa7b72a9223641351c9297fdeefa87faecc801 Uploaded diff -r 8caa7b72a922 -r b6f4f4689f5f admin_scripts/build_mods_loc.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/build_mods_loc.py Tue Mar 24 19:58:38 2015 -0400 @@ -0,0 +1,12 @@ +#!/usr/bin/env python + +import xml.etree.ElementTree as ET +from os.path import exists + +with open("searchgui_mods.loc.sample", "w") as output: + for mods_path in ["searchGUI_mods.xml", "searchGUI_usermods.xml"]: + tree = ET.parse(mods_path) + modifications_el = tree.getroot() + for mod in modifications_el.findall("{http://www.ncbi.nlm.nih.gov}MSModSpec"): + name_el = mod.find("{http://www.ncbi.nlm.nih.gov}MSModSpec_name") + output.write("%s\n" % name_el.text.lower()) diff -r 8caa7b72a922 -r b6f4f4689f5f admin_scripts/build_species.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/build_species.py Tue Mar 24 19:58:38 2015 -0400 @@ -0,0 +1,10 @@ +#!/usr/bin/env python + +import sys + +for line in open( sys.argv[1] ): + line = line.strip() + if line and not line.startswith('>'): + name, id = line.split('\t') + line = '' % (name, name) + print line diff -r 8caa7b72a922 -r b6f4f4689f5f admin_scripts/searchGUI_mods.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/searchGUI_mods.xml Tue Mar 24 19:58:38 2015 -0400 @@ -0,0 +1,3021 @@ + + + + + 0 + + + 0 + + methylation of K + 14.015650 + 14.0266 + 0 + + K + + 34 + Methyl + + + + 1 + + + 0 + + oxidation of M + 15.994915 + 15.9994 + 0 + + M + + 35 + Oxidation + + + + 2 + + + 0 + + carboxymethyl C + 58.005479 + 58.0361 + 0 + + C + + 6 + Carboxymethyl + + + + 3 + + + 0 + + carbamidomethyl C + 57.021464 + 57.0513 + 0 + + C + + 4 + Carbamidomethyl + + + + 4 + + + 0 + + deamidation of N and Q + 0.984016 + 0.9848 + 0 + + N + Q + + 7 + Deamidated + + + + 5 + + + 0 + + propionamide C + 71.037114 + 71.0779 + 0 + + C + + 24 + 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236.214016 + 236.3929 + 0 + + C + + 431 + Palmitoleyl + + + + 188 + + + 0 + + palmitoleyl of T + 236.214016 + 236.3929 + 0 + + T + + 431 + Palmitoleyl + + + + 189 + + + 0 + + CHD2-di-methylation of K + 32.056407 + 32.0778 + 0 + + K + + 199 + Dimethyl:2H(4) + + + + 190 + + + 5 + + CHD2-di-methylation of peptide n-term + 32.056407 + 32.0778 + 0 + 199 + Dimethyl:2H(4) + + + + 191 + + + 0 + + Maleimide-PEO2-Biotin of C + 525.225719 + 525.6183 + 0 + + C + + 522 + Maleimide-PEO2-Biotin + + + + 192 + + + 0 + + phosphorylation of H + 79.966331 + 79.9799 + 0 + + H + + 21 + Phospho + + + + 193 + + + 0 + + oxidation of C + 15.994915 + 15.9994 + 0 + + C + + 35 + Oxidation + + + + 194 + + + 0 + + oxidation of Y (duplicate of 64) + 15.994915 + 15.9994 + 0 + + Y + + 35 + Oxidation + + + + 195 + + + 0 + + Uniblue A on K + 484.039891 + 484.5016 + 0 + + K + + + + + 196 + + + 0 + + deamidation of N + 0.984016 + 0.9848 + 0 + + N + + 7 + Deamidated + + + + 197 + + + 0 + + trideuteration of L (SILAC) + 3.018830 + 3.0185 + 0 + + L + + 262 + Label:2H(3) + + + + 198 + + + 0 + + TMT duplex on K + 225.155833 + 225.2921 + 0 + + K + + 738 + + + + 199 + + + 5 + + TMT duplex on n-term peptide + 225.155833 + 225.2921 + 0 + + X + + 738 + + + + 198 + + + 0 + + TMT 6-plex on K + 229.162932 + 229.2634 + 0 + + K + + 738 + + + + 199 + + + 5 + + TMT 6-plex on n-term peptide + 229.162932 + 229.2634 + 0 + + X + + 738 + + + + 200 + + + 5 + + iTRAQ8plex:13C(7)15N(1) on nterm + 304.205360 + 304.3074 + 0 + 730 + + + + 201 + + + 0 + + iTRAQ8plex:13C(7)15N(1) on K + 304.205360 + 304.3074 + 0 + + K + + 730 + + + + 202 + + + 0 + + iTRAQ8plex:13C(7)15N(1) on Y + 304.205360 + 304.3074 + 0 + + Y + + 730 + + + + 203 + + + 5 + + iTRAQ8plex:13C(6)15N(2) on nterm + 304.199040 + 304.3081 + 0 + 731 + + + + 204 + + + 0 + + iTRAQ8plex:13C(6)15N(2) on K + 304.199040 + 304.3081 + 0 + + K + + 731 + + + + 205 + + + 0 + + iTRAQ8plex:13C(6)15N(2) on Y + 304.199040 + 304.3081 + 0 + + Y + + 731 + + + + 206 + + + 0 + + selenocysteine + 47.944449 + 46.8950 + 0 + + C + + 162 + + + + 207 + + + 0 + + carboxymethylated selenocysteine + 105.949928 + 104.9311 + 0 + + C + + + diff -r 8caa7b72a922 -r b6f4f4689f5f admin_scripts/searchGUI_usermods.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/searchGUI_usermods.xml Tue Mar 24 19:58:38 2015 -0400 @@ -0,0 +1,455 @@ + + + + + + 119 + + + 5 + + dimethyl 2d n-terminus + 32.0564 + 0 + 0 + + + + 120 + + + 0 + + dimethyl 2d k + 32.0564 + 0 + 0 + + K + + + + + 121 + + + 0 + + gtp desthiobiotinc12 + 196.121178 + 0 + 0 + + K + + + + + 122 + + + 0 + + gtp desthiobiotinc13 + 202.141307 + 0 + 0 + + K + + + + + 123 + + + 0 + + User modification 5 + 0 + 0 + 0 + + X + + + + + 124 + + + 0 + + User modification 6 + 0 + 0 + 0 + + X + + + + + 125 + + + 0 + + User modification 7 + 0 + 0 + 0 + + X + + + + + 126 + + + 0 + + User modification 8 + 0 + 0 + 0 + + X + + + + + 127 + + + 0 + + User modification 9 + 0 + 0 + 0 + + X + + + + + 128 + + + 0 + + User modification 10 + 0 + 0 + 0 + + X + + + + + 142 + + + 0 + + User modification 11 + 0 + 0 + 0 + + X + + + + + 143 + + + 0 + + User modification 12 + 0 + 0 + 0 + + X + + + + + 144 + + + 0 + + User modification 13 + 0 + 0 + 0 + + X + + + + + 145 + + + 0 + + User modification 14 + 0 + 0 + 0 + + X + + + + + 146 + + + 0 + + User modification 15 + 0 + 0 + 0 + + X + + + + + 147 + + + 0 + + User modification 16 + 0 + 0 + 0 + + X + + + + + 148 + + + 0 + + User modification 17 + 0 + 0 + 0 + + X + + + + + 149 + + + 0 + + User modification 18 + 0 + 0 + 0 + + X + + + + + 150 + + + 0 + + User modification 19 + 0 + 0 + 0 + + X + + + + + 151 + + + 0 + + User modification 20 + 0 + 0 + 0 + + X + + + + + 152 + + + 0 + + User modification 21 + 0 + 0 + 0 + + X + + + + + 153 + + + 0 + + User modification 22 + 0 + 0 + 0 + + X + + + + + 154 + + + 0 + + User modification 23 + 0 + 0 + 0 + + X + + + + + 155 + + + 0 + + User modification 24 + 0 + 0 + 0 + + X + + + + + 156 + + + 0 + + User modification 25 + 0 + 0 + 0 + + X + + + + + 157 + + + 0 + + User modification 26 + 0 + 0 + 0 + + X + + + + + 158 + + + 0 + + User modification 27 + 0 + 0 + 0 + + X + + + + + 159 + + + 0 + + User modification 28 + 0 + 0 + 0 + + X + + + + + 160 + + + 0 + + User modification 29 + 0 + 0 + 0 + + X + + + + + 161 + + + 0 + + User modification 30 + 0 + 0 + 0 + + X + + + diff -r 8caa7b72a922 -r b6f4f4689f5f admin_scripts/species --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admin_scripts/species Tue Mar 24 19:58:38 2015 -0400 @@ -0,0 +1,252 @@ +>Fungi +Ashbya gossypii agossypii_eg_gene +Aspergillus clavatus aclavatus_eg_gene +Aspergillus flavus aflavus_eg_gene +Aspergillus fumigatus afumigatus_eg_gene +Aspergillus fumigatusa1163 afumigatusa1163_eg_gene +Aspergillus nidulans anidulans_eg_gene +Aspergillus niger aniger_eg_gene +Aspergillus oryzae aoryzae_eg_gene +Aspergillus terreus aterreus_eg_gene +Blumeria graminis bgraminis_eg_gene +Botrytis cinerea bcinerea_eg_gene +Colletotrichum gloeosporioides cgloeosporioides_eg_gene +Colletotrichum higginsianum chigginsianum_eg_gene +Colletotrichum orbiculare corbiculare_eg_gene +Cryptococcus neoformans cneoformans_eg_gene +Dothistroma septosporum dseptosporum_eg_gene +Fusarium fujikuroi ffujikuroi_eg_gene +Fusarium graminearum fgraminearum_eg_gene +Fusarium oxysporum foxysporum_eg_gene +Fusarium pseudograminearum fpseudograminearum_eg_gene +Fusarium solani fsolani_eg_gene +Fusarium verticillioides fverticillioides_eg_gene +Gaeumannomyces graminis ggraminis_eg_gene +Colletotrichum graminicola cgraminicola_eg_gene +Komagataella pastoris kpastoris_eg_gene +Leptosphaeria maculans lmaculans_eg_gene +Magnaporthe oryzae moryzae_eg_gene +Magnaporthe poae mpoae_eg_gene +Melampsora larici-populina mlaricipopulina_eg_gene +Neosartorya fischeri nfischeri_eg_gene +Neurospora crassa ncrassa_eg_gene +Phaeosphaeria nodorum pnodorum_eg_gene +Puccinia graminis pgraminis_eg_gene +Puccinia graminis Ug99 pgraminisug99_eg_gene +Puccinia triticina ptriticina_eg_gene +Pyrenophora teres pteres_eg_gene +Pyrenophora tritici-repentis ptriticirepentis_eg_gene +Saccharomyces cerevisiae scerevisiae_eg_gene +Schizosaccharomyces cryophilus scryophilus_eg_gene +Schizosaccharomyces japonicus japonicus_eg_gene +Schizosaccharomyces octosporus octosporus_eg_gene +Schizosaccharomyces pombe spombe_eg_gene +Sclerotinia sclerotiorum ssclerotiorum_eg_gene +Sporisorium reilianum sreilianum_eg_gene +Trichoderma reesei treesei_eg_gene +Trichoderma virens tvirens_eg_gene +Tuber melanosporum tmelanosporum_eg_gene +Ustilago maydis umaydis_eg_gene +Verticillium dahliae JR2 vdahliaejr2_eg_gene +Verticillium dahliae dahliae_eg_gene +Yarrowia lipolytica ylipolytica_eg_gene +Zymoseptoria tritici ztritici_eg_gene + +>Metazoa +Acyrthosiphon pisum apisum_eg_gene +Aedes aegypti (Yellow fever mosquito) aaegypti_eg_gene +Amphimedon queenslandica aqueenslandica_eg_gene +Anopheles darlingi adarlingi_eg_gene +Anopheles gambiae (African malaria mosquito) agambiae_eg_gene +Apis mellifera amellifera_eg_gene +Atta cephalotes acephalotes_eg_gene +Bombyx mori bmori_eg_gene +Brugia malayi bmalayi_eg_gene +Caenorhabditis brenneri cbrenneri_eg_gene +Caenorhabditis briggsae cbriggsae_eg_gene +Caenorhabditis elegans celegans_eg_gene +Caenorhabditis japonica cjaponica_eg_gene +Caenorhabditis remanei cremanei_eg_gene +Culex quinquefasciatus (Southern house mosquito) cquinquefasciatus_eg_gene +Danaus plexippus dplexippus_eg_gene +Daphnia pulex dpulex_eg_gene +Dendroctonus ponderosae ponderosae_eg_gene +Drosophila ananassae dananassae_eg_gene +Drosophila erecta derecta_eg_gene +Drosophila grimshawi dgrimshawi_eg_gene +Drosophila melanogaster (Fruit fly) dmelanogaster_eg_gene +Drosophila mojavensis dmojavensis_eg_gene +Drosophila persimilis dpersimilis_eg_gene +Drosophila pseudoobscura dpseudoobscura_eg_gene +Drosophila sechellia dsechellia_eg_gene +Drosophila simulans dsimulans_eg_gene +Drosophila virilis dvirilis_eg_gene +Drosophila willistoni dwillistoni_eg_gene +Drosophila yakuba dyakuba_eg_gene +Heliconius melpomene hmelpomene_eg_gene +Helobdella robusta robusta_eg_gene +Ixodes scapularis (Black-legged tick) iscapularis_eg_gene +Loa loa lloa_eg_gene +Lottia gigantea lgigantea_eg_gene +Megaselia scalaris mscalaris_eg_gene +Melitaea cinxia mcinxia_eg_gene +Mnemiopsis leidyi mleidyi_eg_gene +Nasonia vitripennis nvitripennis_eg_gene +Nematostella vectensis nvectensis_eg_gene +Onchocerca volvulus ovolvulus_eg_gene +Pediculus humanus (Human louse) phumanus_eg_gene +Pristionchus pacificus ppacificus_eg_gene +Rhodnius prolixus rprolixus_eg_gene +Schistosoma mansoni smansoni_eg_gene +Solenopsis invicta (Red fire ant) sinvicta_eg_gene +Strigamia maritima smaritima_eg_gene +Strongylocentrotus purpuratus spurpuratus_eg_gene +Tetranychus urticae turticae_eg_gene +Tribolium castaneum (red flour beetle) tcastaneum_eg_gene +Trichinella spiralis tspiralis_eg_gene +Trichoplax adhaerens tadhaerens_eg_gene +Zootermopsis nevadensis znevadensis_eg_gene + +>Plants +Amborella (Amborella trichopoda) atrichopoda_eg_gene +Arabidopsis lyrata (Lyrate rockcress) alyrata_eg_gene +Arabidopsis thaliana (Thale-cress) athaliana_eg_gene +Brachypodium distachyon (False brome) bdistachyon_eg_gene +Brassica oleracea boleracea_eg_gene +Brassica rapa genes (Field mustard) brapa_eg_gene +Chlamydomonas reinhardtii (Green algae) creinhardtii_eg_gene +Cyanidioschyzon merolae (Red algae) cmerolae_eg_gene +Glycine max (Soybean) gmax_eg_gene +Hordeum vulgare (Barley) hvulgare_eg_gene +Leersia perrieri (Leersia) lperrieri_eg_gene +Medicago truncatula (Barrel medic) mtruncatula_eg_gene +Musa acuminata (Banana) macuminata_eg_gene +Oryza brachyantha obrachyantha_eg_gene +Oryza glumaepatula oglumaepatula_eg_gene +Oryza meridionalis omeridionalis_eg_gene +Oryza nivara onivara_eg_gene +Oryza punctata opunctata_eg_gene +Oryza rufipogon (Common wild rice) orufipogon_eg_gene +Oryza sativa (Indica rice) osativa_eg_gene +Oryza sativa Indica Group oindica_eg_gene +Oryza sativa Japonica (Japonica rice) osativa_eg_gene +Ostreococcus lucimarinus (Green algae) olucimarinus_eg_gene +Physcomitrella patens ppatens_eg_gene +Physcomitrella patens (Moss) ppatens_eg_gene +Populus trichocarpa ptrichocarpa_eg_gene +Populus trichocarpa (Western balsam poplar) ptrichocarpa_eg_gene +Prunus persica (Peach) ppersica_eg_gene +Selaginella moellendorffii (Spike moss) smoellendorffii_eg_gene +Setaria italica (Foxtail millet) sitalica_eg_gene +Solanum lycopersicum (Tomato) slycopersicum_eg_gene +Solanum tuberosum (Potato) stuberosum_eg_gene +Sorghum bicolor (Sorghum) sbicolor_eg_gene +Theobroma cacao (Cocoa) tcacao_eg_gene +Triticum aestivum (Bread wheat) taestivum_eg_gene +Triticum urartu (Einkorn) turartu_eg_gene +Vitis vinifera (Wine grape) vvinifera_eg_gene +Zea mays (Maize) zmays_eg_gene + +>Protists +Albugo laibachii alaibachii_eg_gene +Bigelowiella natans bnatans_eg_gene +Dictyostelium discoideum ddiscoideum_eg_gene +Emiliania huxleyi ehuxleyi_eg_gene +Entamoeba histolytica ehistolytica_eg_gene +Giardia lamblia glamblia_eg_gene +Guillardia theta CCMP2712 gtheta_eg_gene +Hyaloperonospora arabidopsidis harabidopsidis_eg_gene +Leishmania major lmajor_eg_gene +Paramecium tetraurelia ptetraurelia_eg_gene +Phaeodactylum tricornutum ptricornutum_eg_gene +Phytophthora infestans pinfestans_eg_gene +Phytophthora kernoviae pkernoviae_eg_gene +Phytophthora lateralis plateralis_eg_ge +Phytophthora parasitica pparasitica_eg_gene +Phytophthora ramorum pramorum_eg_gene +Phytophthora sojae psojae_eg_gene +Plasmodium berghei pberghei_eg_gene +Plasmodium chabaudi pchabaudi_eg_gene +Plasmodium falciparum pfalciparum_eg_gene +Plasmodium knowlesi pknowlesi_eg_gene +Plasmodium vivax pvivax_eg_gene +Pythium aphanidermatum paphanidermatum_eg_gene +Pythium arrhenomanes parrhenomanes_eg_gene +Pythium irregulare pirregulare_eg_gene +Pythium iwayamai piwayamai_eg_gene +Pythium ultimum pultimum_eg_gene +Pythium vexans pvexans_eg_gene +Tetrahymena thermophila tthermophila_eg_gene +Thalassiosira pseudonana tpseudonana_eg_gene +Toxoplasma gondii tgondii_eg_gene +Trypanosoma brucei tbrucei_eg_gene + +>Vertebrates +Alpaca (Vicugna pacos) vpacos_gene_ensembl +Amazon molly (Poecilia formosa) pformosa_gene_ensembl +Anole lizard (Anolis carolinensis) acarolinensis_gene_ensembl +Armadillo (Dasypus novemcinctus) dnovemcinctus_gene_ensembl +Bushbaby (Otolemur garnettii) ogarnettii_gene_ensembl +C. elegans (Caenorhabditis elegans) celegans_gene_ensembl +C.intestinalis (Ciona intestinalis) cintestinalis_gene_ensembl +C.savignyi (Ciona savignyi) csavignyi_gene_ensembl +Cat (Felis catus) fcatus_gene_ensembl +Cave fish (Astyanax mexicanus) amexicanus_gene_ensembl +Chicken (Gallus gallus) ggallus_gene_ensembl +Chimpanzee (Pan troglodytes) ptroglodytes_gene_ensembl +Chinese softshell turtle (Pelodiscus sinensis) psinensis_gene_ensembl +Cod (Gadus morhua) gmorhua_gene_ensembl +Coelacanth (Latimeria chalumnae) lchalumnae_gene_ensembl +Cow (Bos taurus) btaurus_gene_ensembl +Dog (Canis lupus familiaris) cfamiliaris_gene_ensembl +Dolphin (Tursiops truncatus) ttruncatus_gene_ensembl +Duck (Anas platyrhynchos) aplatyrhynchos_gene_ensembl +Elephant (Loxodonta africana) lafricana_gene_ensembl +Ferret (Mustela putorius furo) mfuro_gene_ensembl +Flycatcher (Ficedula albicollis) falbicollis_gene_ensembl +Fruitfly (Drosophila melanogaster) dmelanogaster_gene_ensembl +Fugu (Takifugu rubripes) trubripes_gene_ensembl +Gibbon (Nomascus leucogenys) nleucogenys_gene_ensembl +Gorilla (Gorilla gorilla gorilla) ggorilla_gene_ensembl +Guinea Pig (Cavia porcellus) cporcellus_gene_ensembl +Hedgehog (Erinaceus europaeus) eeuropaeus_gene_ensembl +Horse (Equus caballus) ecaballus_gene_ensembl +Human (Homo sapiens) hsapiens_gene_ensembl +Hyrax (Procavia capensis) pcapensis_gene_ensembl +Kangaroo rat (Dipodomys ordii) dordii_gene_ensembl +Lamprey (Petromyzon marinus) pmarinus_gene_ensembl +Lesser hedgehog tenrec (Echinops telfairi) etelfairi_gene_ensembl +Macaque (Macaca mulatta) mmulatta_gene_ensembl +Marmoset (Callithrix jacchus) cjacchus_gene_ensembl +Medaka (Oryzias latipes) olatipes_gene_ensembl +Megabat (Pteropus vampyrus) pvampyrus_gene_ensembl +Microbat (Myotis lucifugus) mlucifugus_gene_ensembl +Mouse (Mus musculus) mmusculus_gene_ensembl +Mouse Lemur (Microcebus murinus) mmurinus_gene_ensembl +Opossum (Monodelphis domestica) mdomestica_gene_ensembl +Orangutan (Pongo abelii) pabelii_gene_ensembl +Panda (Ailuropoda melanoleuca) amelanoleuca_gene_ensembl +Pig (Sus scrofa) sscrofa_gene_ensembl +Pika (Ochotona princeps) oprinceps_gene_ensembl +Platyfish (Xiphophorus maculatus) xmaculatus_gene_ensembl +Platypus (Ornithorhynchus anatinus) oanatinus_gene_ensembl +Rabbit (Oryctolagus cuniculus) ocuniculus_gene_ensembl +Rat (Rattus norvegicus) rnorvegicus_gene_ensembl +S. cerevisiae (Saccharomyces cerevisiae) scerevisiae_gene_ensembl +Sheep (Ovis aries) oaries_gene_ensembl +Shrew (Sorex araneus) saraneus_gene_ensembl +Sloth (Choloepus hoffmanni) choffmanni_gene_ensembl +Spotted gar (Lepisosteus oculatus) loculatus_gene_ensembl +Squirrel (Ictidomys tridecemlineatus) itridecemlineatus_gene_ensembl +Stickleback (Gasterosteus aculeatus) gaculeatus_gene_ensembl +Tarsier (Tarsius syrichta) tsyrichta_gene_ensembl +Tasmanian devil (Sarcophilus harrisii) sharrisii_gene_ensembl +Tetraodon (Tetraodon nigroviridis) tnigroviridis_gene_ensembl +Tilapia (Oreochromis niloticus) oniloticus_gene_ensembl +Tree Shrew (Tupaia belangeri) tbelangeri_gene_ensembl +Turkey (Meleagris gallopavo) mgallopavo_gene_ensembl +Vervet-AGM (Chlorocebus sabaeus) csabaeus_gene_ensembl +Wallaby (Macropus eugenii) meugenii_gene_ensembl +Xenopus (Xenopus tropicalis) xtropicalis_gene_ensembl +Zebra Finch (Taeniopygia guttata) tguttata_gene_ensembl +Zebrafish (Danio rerio) drerio_gene_ensembl \ No newline at end of file diff -r 8caa7b72a922 -r b6f4f4689f5f macros.xml --- a/macros.xml Mon Feb 16 16:28:52 2015 -0500 +++ b/macros.xml Tue Mar 24 19:58:38 2015 -0400 @@ -30,7 +30,7 @@ - + diff -r 8caa7b72a922 -r b6f4f4689f5f peptide_shaker.xml --- a/peptide_shaker.xml Mon Feb 16 16:28:52 2015 -0500 +++ b/peptide_shaker.xml Tue Mar 24 19:58:38 2015 -0400 @@ -24,7 +24,7 @@ ## PeptideShakerCLI ## ###################### (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI - -temp_folder `pwd` + -temp_folder \$cwd/PeptideShakerCLI -experiment '$exp_str' -sample '$samp_str' -replicate 1 @@ -100,7 +100,7 @@ #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI - -temp_folder `pwd` + -temp_folder \$cwd/ReportCLI -in \$cwd/peptideshaker_output.zip -out_reports \$cwd/output_reports #set $cleaned_list = str($outputs).split(',') diff -r 8caa7b72a922 -r b6f4f4689f5f searchgui.xml --- a/searchgui.xml Mon Feb 16 16:28:52 2015 -0500 +++ b/searchgui.xml Tue Mar 24 19:58:38 2015 -0400 @@ -150,6 +150,12 @@ -comet 0 #end if + #if $advanced.tide.tide_selector == "yes" + -tide 1 + #else + -tide 0 + #end if + #else -ms_amanda 0 #end if @@ -315,6 +321,17 @@ + + + + + + + + + + + diff -r 8caa7b72a922 -r b6f4f4689f5f test-data/peptide_shaker_certificate_result2.tabular --- a/test-data/peptide_shaker_certificate_result2.tabular Mon Feb 16 16:28:52 2015 -0500 +++ b/test-data/peptide_shaker_certificate_result2.tabular Tue Mar 24 19:58:38 2015 -0400 @@ -1,7 +1,7 @@ Project Details1: PeptideShaker Version: 0.37.4-beta -2: Date: Sun Feb 15 09:12:50 CET 2015 -3: Experiment: Galaxy_Experiment_2015021509121423987968 -4: Sample: Sample_2015021509121423987968 +2: Date: Sat Feb 14 20:04:49 CET 2015 +3: Experiment: Galaxy_Experiment_2015021420041423940686 +4: Sample: Sample_2015021420041423940686 5: Replicate Number: 1 6: Identification Algorithms: X!Tandem and MS-GF+ Database Search Parameters diff -r 8caa7b72a922 -r b6f4f4689f5f test-data/peptide_shaker_peptides_result3.tabular --- a/test-data/peptide_shaker_peptides_result3.tabular Mon Feb 16 16:28:52 2015 -0500 +++ b/test-data/peptide_shaker_peptides_result3.tabular Tue Mar 24 19:58:38 2015 -0400 @@ -1,17 +0,0 @@ - Protein(s) Sequence Modified Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #Validated PSMs #PSMs Confidence Decoy Validation -1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH LK; LK IN; IN 2 2 100.0 0 Doubtful -2 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH MR; MR YQ; YQ 2 2 100.0 0 Doubtful -3 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH AK; AK IS; IS 4 4 100.0 0 Doubtful -4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH VR; VR LK; LK 2 2 100.0 0 Doubtful -5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH AR; AR LI; LI 2 2 100.0 0 Doubtful -6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH MK; MK SN; SN 2 2 100.0 0 Doubtful -7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH NK; NK LS; LS 3 3 100.0 0 Doubtful -8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH AR; AR QS; QS 2 2 100.0 0 Doubtful -9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH QK; QK SV; SV 4 4 100.0 0 Doubtful -10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful -11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful -12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH RR; RR AS; AS 2 2 100.0 0 Doubtful -13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH NR; NR SE; SE 4 4 100.0 0 Doubtful -14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH RR; RR NL; NL 2 2 100.0 0 Doubtful -15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful -16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH GR; GR DM; DM 2 2 100.0 0 Doubtful diff -r 8caa7b72a922 -r b6f4f4689f5f test-data/peptide_shaker_result1.cps Binary file test-data/peptide_shaker_result1.cps has changed diff -r 8caa7b72a922 -r b6f4f4689f5f test-data/peptide_shaker_result1.zip Binary file test-data/peptide_shaker_result1.zip has changed diff -r 8caa7b72a922 -r b6f4f4689f5f tool_dependencies.xml --- a/tool_dependencies.xml Mon Feb 16 16:28:52 2015 -0500 +++ b/tool_dependencies.xml Tue Mar 24 19:58:38 2015 -0400 @@ -1,9 +1,9 @@ - + - +