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README.md peptide_shaker.xml repository_dependencies.xml searchgui_mods.loc.sample tool_dependencies.xml |
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COPYING test-data/._tinyoutput.cps test-data/tinydb.fasta test-data/tinyoutput.cps test-data/tinyspectra.mgf |
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| diff -r 6cdbfdffb38e -r a5f9b959d5d1 COPYING --- a/COPYING Wed Jun 25 11:49:19 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,121 +0,0 @@ -Creative Commons Legal Code - -CC0 1.0 Universal - - CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE - LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN - ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS - INFORMATION ON AN "AS-IS" BASIS. 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| diff -r 6cdbfdffb38e -r a5f9b959d5d1 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Jun 25 11:49:45 2014 -0400 |
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| @@ -0,0 +1,74 @@ +GalaxyP - PeptideShaker +======================= + +* Home: <https://bitbucket.org/galaxyp/peptideshaker> +* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> +* Tool ID: `peptideshaker` +* Tool Type: `default` + + +Description +----------- + +Perform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. + +Tool wrapper for SearchGUI and PeptideShaker. This tool takes any number of mgf files and performs X! Tandem and OMSSA searches on these via SearchGUI and merges the results using PeptideShaker. + +Configuration +------------- + +This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell; + +export _JAVA_OPTIONS='-Xmx1500M' + +It is also possible to set this on a per tool basis using advanced features of the galaxy job config system + +Note: + +- SearchGUI requires a version greater than 1.12.2 which contained several bugs preventing this from working on the command-line and via Linux. + +- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. + +See: + +* <https://code.google.com/p/peptide-shaker/> +* <https://code.google.com/p/searchgui/> + + +GalaxyP Community +----------------- + +Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: + +<https://bitbucket.org/galaxyp/galaxyp> + + +License +------- + +Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. + +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. + +You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. + + +Contributing +------------ + +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out. + + +Authors +------- + +Authors and contributors: + +* Bjoern Gruening <bjoern.gruening@gmail.com> +* Ira Cooke +* Cody Wang +* Fred Sadler +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota |
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| diff -r 6cdbfdffb38e -r a5f9b959d5d1 peptide_shaker.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptide_shaker.xml Wed Jun 25 11:49:45 2014 -0400 |
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| b'@@ -0,0 +1,958 @@\n+<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.5.0">\n+ <description>\n+ Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="0.31.4">peptide_shaker</requirement>\n+ <requirement type="package" version="1.19.5">searchgui</requirement>\n+ <!--<requirement type="package" version="2.2.29">blast+</requirement>-->\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Job Failed" />\n+ <regex match="java.*Exception" level="fatal" description="Java Exception"/> \n+ <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>\n+ </stdio>\n+ <command>\n+\n+ #from datetime import datetime\n+ #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n+ #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n+ #set $temp_stderr = \'macs2_stderr\'\n+\n+ mkdir output;\n+ mkdir output_reports;\n+ cwd=`pwd`;\n+ #for $mgf in $peak_lists:\n+ #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"\n+ ln -s \'${mgf}\' \'${input_name}\';\n+ #end for\n+ ##ln -s "${input_database}" input_database.fasta;\n+ cp "${input_database}" input_database.fasta;\n+\n+ ###########################################\n+ #### Creating decoy database ####\n+ ###########################################\n+ #if $create_decoy:\n+ echo "Creating decoy database.";\n+ java -cp \\$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy;\n+ rm input_database.fasta;\n+ cp input_database_concatenated_target_decoy.fasta input_database.fasta;\n+ ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;\n+ #end if\n+\n+ #####################################################\n+ ## generate IdentificationParameters for SearchGUI ##\n+ #####################################################\n+\n+ (java -cp \\$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI\n+ -out SEARCHGUI_IdentificationParameters.parameters\n+ -prec_ppm "${precursor_ion_tol_units}"\n+ -prec_tol "${precursor_ion_tol}"\n+ -frag_tol "${fragment_tol}"\n+ -enzyme "${enzyme}"\n+ #set $fixed_mods_str = $fixed_modifications or \'\'\n+ #set $variable_mods_str = $variable_modifications or \'\'\n+ #if $fixed_mods_str\n+ -fixed_mods "${fixed_mods_str}" \n+ #end if\n+ #if $variable_mods_str\n+ -variable_mods "${variable_mods_str}"\n+ #end if\n+ -min_charge "${min_charge}"\n+ -max_charge "${max_charge}"\n+ -mc "${missed_cleavages}"\n+ -fi "${forward_ion}"\n+ -ri "${reverse_ion}"\n+ -db input_database.fasta\n+\n+ #if $advanced.advanced_type_selector == "advanced":\n+\n+ #if $advanced.xtandem.xtandem_selector == "yes"\n+\n+ -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}\n+ -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}\n+ -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}\n+ -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}\n+ -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}\n+\n+ #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"\n+ -xtandem_refine 1\n+ -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}\n+ -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_'..b' peptide is a decoy (1: yes, 0: no).\n+* Validation:\tIndicates the validation level of the protein group.\n+\n+\n+Hierachical Report\n+------------------\n+\n+* Main Accession:\tMain accession of the protein group.\n+* Description:\tDescription of the protein designed by the main accession.\n+* PI:\tProtein Inference status of the protein group.\n+* Secondary Accessions:\tOther accessions in the protein group (alphabetical order).\n+* Protein Group:\tThe complete protein group (alphabetical order).\n+* #Peptides:\tTotal number of peptides.\n+* #Validated Peptides:\tNumber of validated peptides.\n+* #Unique:\tTotal number of peptides unique to this protein group.\n+* #PSMs:\tNumber of PSMs\n+* #Validated PSMs:\tNumber of validated PSMs\n+* Coverage (%):\tSequence coverage in percent of the protein designed by the main accession.\n+* Possible Coverage (%):\tPossible sequence coverage in percent of the protein designed by the main accession according to the search settings.\n+* MW (kDa):\tMolecular Weight.\n+* Spectrum Counting NSAF: \tNormalized Spectrum Abundance Factor (NSAF)\n+* Spectrum Counting emPAI:\texponentially modified Protein Abundance Index (emPAI)\n+* Confident Modification Sites: # Confident Modification Sites\tList of the sites where a variable modification was confidently localized.\n+* Other Modification Sites: # Other Modification Sites\tList of the non-confident sites where a variable modification was localized.\n+* Score:\tScore of the protein group.\n+* Confidence:\tConfidence in percent associated to the protein group.\n+* Decoy:\tIndicates whether the protein group is a decoy (1: yes, 0: no).\n+* Validation:\tIndicates the validation level of the protein group.\n+* Protein(s):\tProtein(s) to which this peptide can be attached.\n+* AAs Before:\tThe amino-acids before the sequence.\n+* Sequence:\tSequence of the peptide.\n+* AAs After:\tThe amino-acids after the sequence.\n+* Variable Modifications:\tThe variable modifications.\n+* Localization Confidence:\tThe confidence in PTMs localization.\n+* Fixed Modifications:\tThe fixed modifications.\n+* #Validated PSMs:\tNumber of validated PSMs.\n+* #PSMs:\tNumber of PSMs.\n+* Score:\tScore of the peptide.\n+* Confidence:\tConfidence in percent associated to the peptide.\n+* Decoy:\tIndicates whether the peptide is a decoy (1: yes, 0: no).\n+* Validation:\tIndicates the validation level of the protein group.\n+* Protein(s):\tProtein(s) to which the peptide can be attached.\n+* Sequence:\tSequence of the peptide.\n+* Modified Sequence:\tThe peptide sequence annotated with variable modifications.\n+* Variable Modifications:\tThe variable modifications.\n+* D-score:\tD-score for variable PTM localization.\n+* probabilistic PTM score:\tThe probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.\n+* Localization Confidence:\tThe confidence in variable PTM localization.\n+* Fixed Modifications:\tThe fixed modifications.\n+* Spectrum File:\tThe spectrum file.\n+* Spectrum Title:\tThe title of the spectrum.\n+* Spectrum Scan Number:\tThe spectrum scan number.\n+* RT:\tRetention time\n+* m/z:\tMeasured m/z\n+* Measured Charge:\tThe charge as given in the spectrum file.\n+* Identification Charge:\tThe charge as inferred by the search engine.\n+* Theoretical Mass:\tThe theoretical mass of the peptide.\n+* Isotope Number:\tThe isotope number targetted by the instrument.\n+* Precursor m/z Error:\tThe precursor m/z matching error.\n+* Score:\tScore of the retained peptide as a combination of the algorithm scores (used to rank PSMs).\n+* Confidence:\tConfidence in percent associated to the retained PSM.\n+* Decoy:\tIndicates whether the peptide is a decoy (1: yes, 0: no).\n+* Validation:\tIndicates the validation level of the protein group.\n+\n+\n+\n+\n+------\n+\n+**Citation**\n+\n+To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com \n+\n+If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker\n+ </help>\n+</tool>\n' |
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| diff -r 6cdbfdffb38e -r a5f9b959d5d1 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Jun 25 11:49:45 2014 -0400 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Required proteomics dependencies."> + <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 6cdbfdffb38e -r a5f9b959d5d1 searchgui_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui_mods.loc.sample Wed Jun 25 11:49:45 2014 -0400 |
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| @@ -0,0 +1,210 @@ +methylation of k +oxidation of m +carboxymethyl c +carbamidomethyl c +deamidation of n and q +propionamide c +phosphorylation of s +phosphorylation of t +phosphorylation of y +m cleavage from protein n-term +acetylation of protein n-term +methylation of protein n-term +tri-methylation of protein n-term +beta methythiolation of d +methylation of q +tri-methylation of k +methylation of d +methylation of e +methylation of peptide c-term +tri-deuteromethylation of d +tri-deuteromethylation of e +tri-deuteromethylation of peptide c-term +n-formyl met addition +2-amino-3-oxo-butanoic acid t +acetylation of k +amidation of peptide c-term +beta-methylthiolation of d (duplicate of 13) +carboxyamidomethylation of k +carboxyamidomethylation of h +carboxyamidomethylation of d +carboxyamidomethylation of e +carbamylation of k +carbamylation of n-term peptide +citrullination of r +oxidation of c to cysteic acid +di-iodination of y +di-methylation of k +di-methylation of r +di-methylation of peptide n-term +oxidation of f to dihydroxyphenylalanine +gammathiopropionylation of k +gammathiopropionylation of peptide n-term +farnesylation of c +formylation of k +formylation of peptide n-term +oxidation of w to formylkynurenin +fluorophenylalanine +beta-carboxylation of d +gamma-carboxylation of e +geranyl-geranyl +glucuronylation of protein n-term +glutathione disulfide +ubiquitinylation residue +guanidination of k +oxidation of h to n +oxidation of h to d +homoserine +homoserine lactone +oxidation of w to hydroxykynurenin +hydroxylation of d +hydroxylation of k +hydroxylation of n +hydroxylation of p +hydroxylation of f +hydroxylation of y +iodination of y +oxidation of w to kynurenin +lipoyl k +methyl ester of peptide c-term (duplicate of 18) +methyl ester of d +methyl ester of e (duplicate of 17) +methyl ester of s +methyl ester of y +methyl c +methyl h +methyl n +methylation of peptide n-term +methyl r +myristoleylation of g +myristoyl-4h of g +myristoylation of peptide n-term g +myristoylation of k +formylation of protein n-term +nem c +nipcam +oxidation of w to nitro +oxidation of y to nitro +o18 on peptide n-term +di-o18 on peptide n-term +oxidation of h +oxidation of w +phosphopantetheine s +palmitoylation of c +palmitoylation of k +palmitoylation of s +palmitoylation of t +phosphorylation of s with prompt loss +phosphorylation of t with prompt loss +phosphorylation with prompt loss on y +phosphorylation with neutral loss on c +phosphorylation with neutral loss on d +phosphorylation with neutral loss on h +propionyl light k +propionyl light on peptide n-term +propionyl heavy k +propionyl heavy peptide n-term +pyridyl k +pyridyl peptide n-term +pyro-cmc +pyro-glu from n-term e +pyro-glu from n-term q +oxidation of p to pyroglutamic acid +s-pyridylethylation of c +semet +sulfation of y +sulphone of m +tri-iodination of y +tri-methylation of r +n-acyl diglyceride cysteine +icat light +icat heavy +camthiopropanoyl k +phosphorylation with neutral loss on s +phosphorylation with neutral loss on t +phosphorylation of s with etd loss +phosphorylation of t with etd loss +heavy arginine-13c6 +heavy arginine-13c6-15n4 +heavy lysine-13c6 +pngasf in o18 water +beta elimination of s +beta elimination of t +oxidation of c to sulfinic acid +arginine to ornithine +dehydro of s and t +carboxykynurenin of w +sumoylation of k +itraq114 on nterm +itraq114 on k +itraq114 on y +itraq115 on nterm +itraq115 on k +itraq115 on y +itraq116 on nterm +itraq116 on k +itraq116 on y +itraq117 on nterm +itraq117 on k +itraq117 on y +mmts on c +heavy lysine - 2h4 +heavy lysine - 13c6 15n2 +asparagine hexnac +asparagine dhexhexnac +serine hexnac +threonine hexnac +palmitoleyl of s +palmitoleyl of c +palmitoleyl of t +chd2-di-methylation of k +chd2-di-methylation of peptide n-term +maleimide-peo2-biotin of c +phosphorylation of h +oxidation of c +oxidation of y (duplicate of 64) +uniblue a on k +deamidation of n +trideuteration of l (silac) +tmt duplex on k +tmt duplex on n-term peptide +tmt 6-plex on k +tmt 6-plex on n-term peptide +itraq8plex:13c(7)15n(1) on nterm +itraq8plex:13c(7)15n(1) on k +itraq8plex:13c(7)15n(1) on y +itraq8plex:13c(6)15n(2) on nterm +itraq8plex:13c(6)15n(2) on k +itraq8plex:13c(6)15n(2) on y +selenocysteine +carboxymethylated selenocysteine +dimethyl 2d n-terminus +dimethyl 2d k +gtp desthiobiotinc12 +gtp desthiobiotinc13 +user modification 5 +user modification 6 +user modification 7 +user modification 8 +user modification 9 +user modification 10 +user modification 11 +user modification 12 +user modification 13 +user modification 14 +user modification 15 +user modification 16 +user modification 17 +user modification 18 +user modification 19 +user modification 20 +user modification 21 +user modification 22 +user modification 23 +user modification 24 +user modification 25 +user modification 26 +user modification 27 +user modification 28 +user modification 29 +user modification 30 |
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| diff -r 6cdbfdffb38e -r a5f9b959d5d1 test-data/._tinyoutput.cps |
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| Binary file test-data/._tinyoutput.cps has changed |
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| diff -r 6cdbfdffb38e -r a5f9b959d5d1 test-data/tinydb.fasta --- a/test-data/tinydb.fasta Wed Jun 25 11:49:19 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,24 +0,0 @@ ->cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68 -LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV ->cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14 -DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ ->cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32 -KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR ->cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 -METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 -METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 -SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 -YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL ->cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 -MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF ->cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 -MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF ->cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0 -MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ ->cds.comp55448_c0_seq1|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87 -MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN ->cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 -FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP |
| b |
| diff -r 6cdbfdffb38e -r a5f9b959d5d1 test-data/tinyoutput.cps |
| b |
| Binary file test-data/tinyoutput.cps has changed |
| b |
| diff -r 6cdbfdffb38e -r a5f9b959d5d1 test-data/tinyspectra.mgf --- a/test-data/tinyspectra.mgf Wed Jun 25 11:49:19 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,6153 +0,0 @@\n-BEGIN IONS\r\n-TITLE= Cmpd 636, +MSn(730.3981), 66.9 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IONS\r\n-\r\n' |
| b |
| diff -r 6cdbfdffb38e -r a5f9b959d5d1 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jun 25 11:49:45 2014 -0400 |
| b |
| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="searchgui" version="1.19.5"> + <repository changeset_revision="e544ffa7ea6f" name="package_searchgui_1_19" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="peptide_shaker" version="0.31.4"> + <repository changeset_revision="45ee9e65471f" name="package_peptideshaker_0_31" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <!--<package name="blast+" version="2.2.29"> + <repository name="package_blast_plus_2_2_29" owner="iuc" /> + </package>--> +</tool_dependency> |