| Next changeset 1:ecb9ec15083d (2016-12-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty |
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added:
morpheus.xml test-data/test_input.mzML test-data/uniprot-proteome_UP000002311-first100entries.fasta test-data/uniprot-proteome_UP000002311Condensed-first100entries.xml tool_dependencies.xml |
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| diff -r 000000000000 -r 553f0336e43e morpheus.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/morpheus.xml Mon May 23 09:51:47 2016 -0400 |
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| b'@@ -0,0 +1,335 @@\n+<tool id="morpheus" name="Morpheus" version="2.255.0">\n+ <description>database search algorithm for high-resolution tandem mass spectra</description>\n+ <macros>\n+ <xml name="modification_options">\n+ <option value="acetylation of protein N-terminus">acetylation of protein N-terminus</option>\n+ <option value="acetylation of lysine">acetylation of lysine</option>\n+ <option value="phosphorylation of S">phosphorylation of S</option>\n+ <option value="phosphorylation of T">phosphorylation of T</option>\n+ <option value="phosphorylation of Y">phosphorylation of Y</option>\n+ <option value="deamidation of N">deamidation of N</option>\n+ <option value="deamidation of Q">deamidation of Q</option>\n+ <option value="pyro-cmC">pyro-cmC</option>\n+ <option value="pyro-E">pyro-E</option>\n+ <option value="pyro-Q">pyro-Q</option>\n+ <option value="TMT zero on peptide N-terminus">TMT zero on peptide N-terminus</option>\n+ <option value="TMT zero on K">TMT zero on K</option>\n+ <option value="TMT zero on Y">TMT zero on Y</option>\n+ <option value="TMT duplex on peptide N-terminus">TMT duplex on peptide N-terminus</option>\n+ <option value="TMT duplex on K">TMT duplex on K</option>\n+ <option value="TMT duplex on Y">TMT duplex on Y</option>\n+ <option value="TMT sixplex/tenplex on peptide N-terminus">TMT sixplex/tenplex on peptide N-terminus</option>\n+ <option value="TMT sixplex/tenplex on K">TMT sixplex/tenplex on K</option>\n+ <option value="TMT sixplex/tenplex on Y">TMT sixplex/tenplex on Y</option>\n+ <option value="iTRAQ 4-plex on peptide N-terminus">iTRAQ 4-plex on peptide N-terminus</option>\n+ <option value="iTRAQ 4-plex on K">iTRAQ 4-plex on K</option>\n+ <option value="iTRAQ 4-plex on Y">iTRAQ 4-plex on Y</option>\n+ <option value="iTRAQ 8-plex on peptide N-terminus">iTRAQ 8-plex on peptide N-terminus</option>\n+ <option value="iTRAQ 8-plex on K">iTRAQ 8-plex on K</option>\n+ <option value="iTRAQ 8-plex on Y ">iTRAQ 8-plex on Y </option>\n+ </xml>\n+ <xml name="variable_modification_options">\n+ <option value="oxidation of M" selected="true">oxidation of M</option>\n+ <option value="carbamidomethylation of C">carbamidomethylation of C</option>\n+ <expand macro="modification_options"/>\n+ </xml>\n+ <xml name="fixed_modification_options">\n+ <option value="carbamidomethylation of C" selected="true">carbamidomethylation of C</option>\n+ <option value="oxidation of M">oxidation of M</option>\n+ <expand macro="modification_options"/>\n+ </xml>\n+ </macros>\n+\n+ <requirements>\n+ <requirement version="4.0">mono</requirement>\n+ <requirement version="255">morpheus</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <exit_code range="1:" />\n+ <regex match="System..*Exception"\n+ source="both"\n+ level="fatal"\n+ description="Error encountered" />\n+ </stdio>\n+\n+ <command><![CDATA[\n+ mkdir -p output_reports &&\n+ cwd=`pwd`&&\n+ #import re\n+ #set $searchdb_name = $searchdb\n+ #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension(\'uniprotxml\').__class__): \n+ #set $searchdb_name = \'searchdb.xml\'\n+ #else\n+ #set $searchdb_name = \'searchdb.fasta\'\n+ #end if\n+ ln -s $searchdb $searchdb_name\n+ ## Need to link each input to a name in cwd, names must be unique\n+ #set $input_list = []\n+ #for i,input in enumerate($inputs):\n+ #set $input_name = $re.sub(\'(?i)([.]?mzML)*$\',\'.mzML\',$re.sub(\'\\W\',\'_\',$input.name))\n+ #if $input_name in $input_list:\n+ #set $input_name = str($'..b'e="precmt" value="Monoisotopic"/>\n+ <param name="precmtu" value="Da"/>\n+ <param name="precmtv" value="2.5"/>\n+ <output name="output_psms">\n+ <assert_contents>\n+ <has_text text="K.TTGSSSSSSSK.K" />\n+ <not_has_text text="carbamidomethylation of C" />\n+ <not_has_text text="(oxidation of M)" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="test_input.mzML" ftype="mzml"/>\n+ <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>\n+ <param name="fdr" value="1"/>\n+ <param name="mvmi" value="1024"/>\n+ <param name="precmt" value="Monoisotopic"/>\n+ <param name="precmtu" value="Da"/>\n+ <param name="precmtv" value="2.5"/>\n+ <param name="fm" value="carbamidomethylation of C"/>\n+ <param name="vm" value="oxidation of M"/>\n+ <output name="output_psms">\n+ <assert_contents>\n+ <has_text text="K.VETYM(oxidation of M)ETK.I" />\n+ <not_has_text text="K.TTGSSSSSSSK.K" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="test_input.mzML" ftype="mzml"/>\n+ <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>\n+ <param name="fdr" value="1"/>\n+ <param name="mvmi" value="1024"/>\n+ <param name="precmt" value="Monoisotopic"/>\n+ <param name="precmtu" value="Da"/>\n+ <param name="precmtv" value="2.5"/>\n+ <param name="fm" value="carbamidomethylation of C"/>\n+ <param name="vm" value="oxidation of M"/>\n+ <output name="output_psms">\n+ <assert_contents>\n+ <has_text text="R.KRSLFDS(UniProt: Phosphoserine)AFSSR.A" />\n+ <not_has_text text="K.KYFLENKIGTDR.R" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="test_input.mzML" ftype="mzml"/>\n+ <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>\n+ <param name="fdr" value="1"/>\n+ <param name="mvmi" value="1024"/>\n+ <param name="precmt" value="Monoisotopic"/>\n+ <param name="precmtu" value="Da"/>\n+ <param name="precmtv" value="2.5"/>\n+ <param name="fm" value="carbamidomethylation of C"/>\n+ <param name="vm" value="oxidation of M"/>\n+ <param name="adv_options_selector" value="set"/>\n+ <param name="prodmtv" value=".01"/>\n+ <output name="output_psms">\n+ <assert_contents>\n+ <has_text text="K.KTLKSDGVAGLYR.G" />\n+ <not_has_text text="K.RSPSGNISTNSMR.P" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ </tests>\n+ <help><![CDATA[\n+Morpheus_ is a database search algorithm for high-resolution tandem mass spectra. \n+\n+When a Uniprot Proteome XML file is used for the search database, Morpheus will include all known modifications from the proteome in searching for peptide spectral matches. To fetch Uniprot Proteome XML files see: http://www.uniprot.org/help/retrieve_sets\n+\n+**INPUTS**\n+\n+ - spectral data file in mzML format \n+ - protein search database, either a fasta file or a uniprot proteome xml file\n+\n+**OUTPUTS**\n+\n+ - summary.tsv\n+ - input.log.txt\n+ - input.PSMs.tsv\n+ - input.unique_peptides.tsv\n+ - input.protein_groups.tsv\n+ - input.pep.xml\n+\n+.. _Morpheus: http://morpheus-ms.sourceforge.net/\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1021/pr301024c</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 553f0336e43e test-data/test_input.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_input.mzML Mon May 23 09:51:47 2016 -0400 |
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| b'@@ -0,0 +1,1224 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">\n+ <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="11-05-13_YL_1-400th_10-30_rep1" version="1.1.0">\n+ <cvList count="2">\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.65.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n+ </fileContent>\n+ <sourceFileList count="1">\n+ <sourceFile id="RAW1" name="11-05-13_YL_1-400th_10-30_rep1.raw" location="file:///">\n+ <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d2cd84c171e019c364c8a39a1a7b57e2828ef7e9"/>\n+ </sourceFile>\n+ </sourceFileList>\n+ </fileDescription>\n+ <referenceableParamGroupList count="1">\n+ <referenceableParamGroup id="CommonInstrumentParams">\n+ <cvParam cvRef="MS" accession="MS:1001742" name="LTQ Orbitrap Velos" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN03001B"/>\n+ </referenceableParamGroup>\n+ </referenceableParamGroupList>\n+ <softwareList count="2">\n+ <software id="Xcalibur" version="2.6.0">\n+ <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n+ </software>\n+ <software id="pwiz" version="3.0.6618">\n+ <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n+ </software>\n+ </softwareList>\n+ <instrumentConfigurationList count="2">\n+ <instrumentConfiguration id="IC1">\n+ <referenceableParamGroupRef ref="CommonInstrumentParams"/>\n+ <componentList count="3">\n+ <source order="1">\n+ <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>\n+ </source>\n+ <analyzer order="2">\n+ <cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" value=""/>\n+ </analyzer>\n+ <detector order="3">\n+ <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>\n+ </detector>\n+ </componentList>\n+ <softwareRef ref="Xcalibur"/>\n+ </instrumentConfiguration>\n+ <instrumentConfiguration id="IC2">\n+ <referenceableParamGroupRef ref="CommonInstrumentParams"/>\n+ <componentList count="3">\n+ <source order="1">\n+ <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>\n+ </source>\n+ <analyzer order="2">\n+ <cvParam cvRef="MS" accession="MS:1000083" name="radial ejection linear ion trap" value=""/>\n+ </analyzer>\n+ <detector order="3">\n+ <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>\n+ </detector>\n+ </componentList>\n+ <softwareRef ref="Xcalibur"/>\n+ </instrumentConfiguration>\n+ </instrumentConfigu'..b'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</binary>\n+ </binaryDataArray>\n+ </binaryDataArrayList>\n+ </chromatogram>\n+ </chromatogramList>\n+ </run>\n+ </mzML>\n+ <indexList count="2">\n+ <index name="spectrum">\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1970">4496</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1971">45505</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1972">52392</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1973">59702</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1974">66466</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1975">72509</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1976">79609</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1977">85720</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1978">92603</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1979">98677</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1980">105107</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1981">146748</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1982">153078</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1983">159740</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1984">166825</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1985">172633</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1986">179547</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1987">222607</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=1988">228533</offset>\n+ </index>\n+ <index name="chromatogram">\n+ <offset idRef="TIC">234671</offset>\n+ </index>\n+ </indexList>\n+ <indexListOffset>496045</indexListOffset>\n+ <fileChecksum>a6884acf9007eaf671b404780356f0bc15a0e33b</fileChecksum>\n+</indexedmzML>\n' |
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| diff -r 000000000000 -r 553f0336e43e test-data/uniprot-proteome_UP000002311-first100entries.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/uniprot-proteome_UP000002311-first100entries.fasta Mon May 23 09:51:47 2016 -0400 |
| b |
| b'@@ -0,0 +1,947 @@\n+>sp|P38903|2A5D_YEAST Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RTS1 PE=1 SV=2\n+MMRGFKQRLIKKTTGSSSSSSSKKKDKEKEKEKSSTTSSTSKKPASASSSSHGTTHSSAS\n+STGSKSTTEKGKQSGSVPSQGKHHSSSTSKTKTATTPSSSSSSSRSSSVSRSGSSSTKKT\n+SSRKGQEQSKQSQQPSQSQKQGSSSSSAAIMNPTPVLTVTKDDKSTSGEDHAHPTLLGAV\n+SAVPSSPISNASGTAVSSDVENGNSNNNNMNINTSNTQDANHASSQSIDIPRSSHSFERL\n+PTPTKLNPDTDLELIKTPQRHSSSRFEPSRYTPLTKLPNFNEVSPEERIPLFIAKVDQCN\n+TMFDFNDPSFDIQGKEIKRSTLDELIEFLVTNRFTYTNEMYAHVVNMFKINLFRPIPPPV\n+NPVGDIYDPDEDEPVNELAWPHMQAVYEFFLRFVESPDFNHQIAKQYIDQDFILKLLELF\n+DSEDIRERDCLKTTLHRIYGKFLSLRSFIRRSMNNIFLQFIYETEKFNGVAELLEILGSI\n+INGFALPLKEEHKVFLVRILIPLHKVRCLSLYHPQLAYCIVQFLEKDPLLTEEVVMGLLR\n+YWPKINSTKEIMFLNEIEDIFEVIEPLEFIKVEVPLFVQLAKCISSPHFQVAEKVLSYWN\n+NEYFLNLCIENAEVILPIIFPALYELTSQLELDTANGEDSISDPYMLVEQAINSGSWNRA\n+IHAMAFKALKIFLETNPVLYENCNALYLSSVKETQQRKVQREENWSKLEEYVKNLRINND\n+KDQYTIKNPELRNSFNTASENNTLNEENENDCDSEIQ\n+>sp|P31383|2AAA_YEAST Protein phosphatase PP2A regulatory subunit A OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TPD3 PE=1 SV=3\n+MSGARSTTAGAVPSAATTSTTSTTSNSKDSDSNESLYPLALLMDELKHDDIANRVEAMKK\n+LDTIALALGPERTRNELIPFLTEVAQDDEDEVFAVLAEQLGKFVPYIGGPQYATILLPVL\n+EILASAEETLVREKAVDSLNNVAQELSQEQLFSDFVPLIEHLATADWFSSKVSACGLFKS\n+VIVRIKDDSLRKNILALYLQLAQDDTPMVKRAVGKNLPILIDLLTQNLGLSTDEDWDYIS\n+NIFQKIINDNQDSVKFLAVDCLISILKFFNAKGDESHTQDLLNSAVKLIGDEAWRVRYMA\n+ADRFSDLASQFSSNQAYIDELVQPFLNLCEDNEGDVREAVAKQVSGFAKFLNDPSIILNK\n+ILPAVQNLSMDESETVRSALASKITNIVLLLNKDQVINNFLPILLNMLRDEFPDVRLNII\n+ASLKVVNDVIGIELLSDSLLPAITELAKDVNWRVRMAIIEYIPILAEQLGMQFFDQQLSD\n+LCLSWLWDTVYSIREAAVNNLKRLTEIFGSDWCRDEIISRLLKFDLQLLENFVSRFTILS\n+ALTTLVPVVSLDVVTEQLLPFISHLADDGVPNIRFNVAKSYAVIVKVLIKDEAKYDALIK\n+NTILPSLQTLCQDEDVDVKYFAKKSLAECQELLKN\n+>sp|Q00362|2ABA_YEAST Protein phosphatase PP2A regulatory subunit B OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CDC55 PE=1 SV=2\n+MAQNNFDFKFSQCFGDKADIVVTEADLITAVEFDYTGNYLATGDKGGRVVLFERSNSRHC\n+EYKFLTEFQSHDAEFDYLKSLEIEEKINEIKWLRPTQRSHFLLSTNDKTIKLWKVYEKNI\n+KLVSQNNLTEGVTFAKKGKPDNHNSRGGSVRAVLSLQSLKLPQLSQHDKIIAATPKRIYS\n+NAHTYHINSISLNSDQETFLSADDLRINLWNLDIPDQSFNIVDIKPTNMEELTEVITSAE\n+FHPQECNLFMYSSSKGTIKLCDMRQNSLCDNKTKTFEEYLDPINHNFFTEITSSISDIKF\n+SPNGRYIASRDYLTVKIWDVNMDNKPLKTINIHEQLKERLSDTYENDAIFDKFEVNFSGD\n+SSSVMTGSYNNNFMIYPNVVTSGDNDNGIVKTFDEHNAPNSNSNKNIHNSIQNKDSSSSG\n+NSHKRRSNGRNTGMVGSSNSSRSSIAGGEGANSEDSGTEMNEIVLQADKTAFRNKRYGSL\n+AQRSARNKDWGDDIDFKKNILHFSWHPRENSIAVAATNNLFIFSAL\n+>sp|P47177|2NDP_YEAST Putative nitronate monooxygenase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=YJR149W PE=1 SV=2\n+MYFLNQLIFQDVSVMSVDKREDMSRSFQKCLNLRYPIIQAPMAGVTTIEMAAKACIAGAI\n+ASLPLSHLDFRKVNDIEKLKLMVSQFRDQVADESLEGNLNLNFFCHDIVDKPTDLQTANW\n+AKLYRKSMNVPIDMNEIKFDNGNVSFKAFEKENALQDFFQYLSDGFRPKIISFHFGHPSK\n+STIEYLQKIGILIFVTATSVREVRLLARLGINGIVCQGYEAGGHRGNFLVNDPKDDENLS\n+TVQLVKRTVDELAEMKNKGLIHATPFVIAAGGIMDSKDISYMLSQQADAVQVGTAFLGCS\n+ESNASKNFSSPFTRETTTKMVNIISGKPARTISTPFIEKVIANFQGEELPPYGYMYSAFK\n+QVRKKYPELANFILAGQGFQNVQSGITTDKKIETMGARLKIDGK\n+>sp|P47096|3HAO_YEAST 3-hydroxyanthranilate 3,4-dioxygenase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=BNA1 PE=1 SV=1\n+MFNTTPINIDKWLKENEGLLKPPVNNYCLHKGGFTVMIVGGPNERTGYHINPTPEWFYQK\n+KGSMLLKVVDETDAEPKFIDIIINEGDSYLLPGNVPHSPVRFADTVGIVVEQDRPGGEND\n+KIRWYCSHCRQVVHESELQMLDLGTQVKEAILDFENDVEKRTCFHCKTLNYARPQSN\n+>sp|P40433|6P21_YEAST 6-phosphofructo-2-kinase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PFK26 PE=1 SV=1\n+MFKPVDFSETSPVPPDIDLAPTQSPHHVAPSQDSSYDLLSRSSDDKIDAEKGPHDELSKH\n+LPLFQKRPLSDTPISSNWNSPGITEENTPSDSPENSATNLKSLHRLHINDETQLKNAKIP\n+TNDTTDYMPPSDGANEVTRIDLKDIKSPTRHHKRRPTTIDVPGLTKSKTSPDGLISKEDS\n+GSKLVIVMVGLPATGKSFITNKLSRFLNYSLYYCKVFNVGNTRRKFAKEHGLKDQDSKFF\n+EPKNADSTRLRDKWAMDTLDELLDYLLEGSGSVGIFDATNTSRERRKNVLARIRKRSPHL\n+KVLFLESVCSDHALVQKNIRLKLFGPDYKGKDPESSLKDFKSRLANYLKAYEPIEDDENL\n+QYIKMIDVGKKVIAYNIQGFLASQTVYYLLNFNLADRQIWITRSGESEDNVSGRIGGNSH\n+LTPRGLRFAKSLPKFIARQREIFYQNLMQQKKNNENTDGNIYNDFFVWTSMRARTIGTAQ\n+YFNEDDYPIKQMKMLDELSAGDYDGMTYPEIKNNFP'..b'VFKSAAASKSQ\n+PFVLAGSGTLGWDIFASNFILSKAPNKNVLVVSTGTFSDRFADCLRSYGAQVDVVRPLKI\n+GESVPLELITEKLSQNSYGAVTVTHVDTSTAVLSDLKAISQAIKQTSPETFFVVDAVCSI\n+GCEEFEFDEWGVDFALTASQKAIGAPAGLSISLCSSRFMDYALNDSKNGHVHGYFSSLRR\n+WTPIMENYEAGKGAYFATPPVQLINSLDVALKEILEEGLHKRWDLHREMSDWFKDSLVNG\n+LQLTSVSRYPSNMSAHGLTAVYVADPPDVIAFLKSHGVVIAGGIHKDIGPKYIRIGHMGV\n+TACNKNLPYMKNCFDLIKLALQRKK\n+>sp|Q12449|AHA1_YEAST Hsp90 co-chaperone AHA1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=AHA1 PE=1 SV=1\n+MVVNNPNNWHWVDKNCIGWAKEYFKQKLVGVEAGSVKDKKYAKIKSVSSIEGDCEVNQRK\n+GKVISLFDLKITVLIEGHVDSKDGSALPFEGSINVPEVAFDSEASSYQFDISIFKETSEL\n+SEAKPLIRSELLPKLRQIFQQFGKDLLATHGNDIQVPESQVKSNYTRGNQKSSFTEIKDS\n+ASKPKKNALPSSTSTSAPVSSTNKVPQNGSGNSTSIYLEPTFNVPSSELYETFLDKQRIL\n+AWTRSAQFFNSGPKLETKEKFELFGGNVISELVSCEKDKKLVFHWKLKDWSAPFNSTIEM\n+TFHESQEFHETKLQVKWTGIPVGEEDRVRANFEEYYVRSIKLTFGFGAVL\n+>sp|Q12433|AHC1_YEAST Protein AHC1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=AHC1 PE=1 SV=1\n+MMSPAQDKLQHQHHNPNSSSSSSSKMTNVYQVTTPKSPQDLENNMDEPFKMDTATSNPDK\n+DSENTQRLKYECAKGEIQNVLNLHIMLNHKHVRHLRRNVQKVNAKLALLETLHKDTGLLN\n+KIERTYQLKIKQHQQHSVLGGHFHDSTATENTNASNYNLSYPVLSDYNINCQPLSSSSNR\n+NLSTTRIPHHHYHTRSKSNGLLLEPSALRPANSNIIDYRLTGSKSLSEAITKPTPVSLPH\n+SNSDGISSPRSSSISPLDEQPGFQILPFKPSQMHLNHRRNYSSTCLTSNSGIIGKTENNE\n+PIFRRYDGILVIITCSKCDRSGFTSAQGIVNHTRLKHSKLYSSQPLAVLNNQKLLPNDKQ\n+DPEILSKFKKLNLDPNKDYLPSDIAIPKPQSPINHSENHTRAPKTVKNTPHLEKLYQNKE\n+DFKKLIDMVNETPDDLNEYLKQREIQLRYQKEQEEESSKSDDEASYVPSPSLSATATTTT\n+TTDPPSPPVLSSSLQRKLLRKRKLSLNSSTPMEDLPLRERLRANPTDKKPRKAALLTNEL\n+EGPDPAAKSSSYYNLRSKSRLRGSHT\n+>sp|P25649|AHC2_YEAST ADA histone acetyltransferase complex component 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=AHC2 PE=1 SV=1\n+MITPKGTHDAVAKFQKTDLHQDLDYIVLQQRRTQLETLINERESFVKNLCSLFHKIQNTK\n+NYQEFVDVLAENRDLLREIFTVENGFQKQKWISNDDIPQIDWDKFALDINAYIAENDQLL\n+ALYEDGLL\n+>sp|P38013|AHP1_YEAST Peroxiredoxin type-2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=AHP1 PE=1 SV=4\n+MSDLVNKKFPAGDYKFQYIAISQSDADSESCKMPQTVEWSKLISENKKVIITGAPAAFSP\n+TCTVSHIPGYINYLDELVKEKEVDQVIVVTVDNPFANQAWAKSLGVKDTTHIKFASDPGC\n+AFTKSIGFELAVGDGVYWSGRWAMVVENGIVTYAAKETNPGTDVTVSSVESVLAHL\n+>sp|P29589|AHT1_YEAST Putative hexose transport activator protein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=AHT1 PE=5 SV=1\n+MDCKIKAAGKNSGIFHEGGTKSSKSFLTVFIRSVFPLSPSFPAGGGIWGPMEKKPGGVGK\n+KKGSEKKTAQGNIFFSTERDAGQEKCGILYKHCFSILYGFFWKKADKPKEKTGNGSGLGI\n+VFPIGQKKIPEPADSDIFLPCFRYAAASDFTKAKRFLVEITAVYWVSLEAQPSSASCLFI\n+LI\n+>sp|P03876|AI2M_YEAST Putative COX1/OXI3 intron 2 protein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=AI2 PE=3 SV=2\n+MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVV\n+GHAVLMIFCAPFRLIYHCIEVLIDKHISVYSINENFTVSFWFWLLVVTYMVFRYVNHMAY\n+PVGANSTGTMACHKSAGVKQPAQGKNCPMARLTNSCKECLGFSLTPSHLGIVIHAYVLEE\n+EVHELTKNESLALSKSWHLEGCTSSNGKLRNTGLSERGNPGDNGVFMVPKFNLNKVRYFS\n+TLSKLNARKEDSLAYLTKINTTDFSELNKLMENNHNKTETINTRILKLMSDIRMLLIAYN\n+KIKSKKGNMSKGSNNITLDGINISYLNKLSKDINTNMFKFSPVRRVEIPKTSGGFRPLSV\n+GNPREKIVQESMRMMLEIIYNNSFSYYSHGFRPNLSCLTAIIQCKNYMQYCNWFIKVDLN\n+KCFDTIPHNMLINVLNERIKDKGFMDLLYKLLRAGYVDKNNNYHNTTLGIPQGSVVSPIL\n+CNIFLDKLDKYLENKFENEFNTGNMSNRGRNPIYNSLSSKIYRCKLLSEKLKLIRLRDHY\n+QRNMGSDKSFKRAYFVRYADDIIIGVMGSHNDCKNILNDINNFLKENLGMSINMDKSVIK\n+HSKEGVSFLGYDVKVTPWEKRPYRMIKKGDNFIRVRHHTSLVVNAPIRSIVMKLNKHGYC\n+SHGILGKPRGVGRLIHEEMKTILMHYLAVGRGIMNYYRLATNFTTLRGRITYILFYSCCL\n+TLARKFKLNTVKKVILKFGKVLVDPHSKVSFSIDDFKIRHKMNMTDSNYTPDEILDRYKY\n+MLPRSLSLFSGICQICGSKHDLEVHHVRTLNNAANKIKDDYLLGRMIKMNRKQITICKTC\n+HFKVHQGKYNGPGL\n+>sp|Q9ZZX0|AI5B_YEAST Intron-encoded DNA endonuclease aI5 beta OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=AI5_BETA PE=3 SV=1\n+MLMLLMMILTNNKVFMETLYYYLMFNFQLMSPFGVPVPGPAPETKDIKNLYESIMNNYIN\n+ILNKYTININKDNINKLKFLDNYTEEEKGYYLSGLFEGDGNIYTRCFSITFSLEDVLLAN\n+YLCTYFKIGHITAKYNFNKELTAVKWNIMKKKEQEVFMNYINGKLLTYKRYDQYFKYNFN\n+NRLNIKLLKPKEFDLTLNPWLTGFNDADGYFYTGFQKHKNSQWLKFHLELSQKDSYILDI\n+IKKYFKTGGILKRDYKSGATAYIYKAQSSKAMKPFIEYFNNYQPLSTRRYKQYLLLNIAY\n+LLKLNKLHMLTNSLLMLKELMLLQSVKNMSLEMKNELNNRVKIIINKTHYNNIE\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 553f0336e43e test-data/uniprot-proteome_UP000002311Condensed-first100entries.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/uniprot-proteome_UP000002311Condensed-first100entries.xml Mon May 23 09:51:47 2016 -0400 |
| b |
| b'@@ -0,0 +1,3817 @@\n+<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/support/docs/uniprot.xsd">\n+<entry dataset="Swiss-Prot" created="1995-02-01" modified="2015-10-14" version="136">\n+<accession>P38903</accession>\n+<accession>D6W281</accession>\n+<name>2A5D_YEAST</name>\n+<protein>\n+<recommendedName>\n+<fullName>Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform</fullName>\n+</recommendedName>\n+</protein>\n+<gene>\n+<name type="primary">RTS1</name>\n+<name type="synonym">SCS1</name>\n+<name type="ordered locus">YOR014W</name>\n+<name type="ORF">OR26.04</name>\n+</gene>\n+<organism>\n+<name type="scientific">Saccharomyces cerevisiae (strain ATCC 204508 / S288c)</name>\n+<name type="common">Baker\'s yeast</name>\n+</organism>\n+<proteinExistence type="evidence at protein level"/>\n+<feature type="modified residue" description="Phosphothreonine" evidence="1">\n+<location>\n+<position position="242"/>\n+</location>\n+</feature>\n+<feature type="modified residue" description="Phosphothreonine" evidence="2">\n+<location>\n+<position position="257"/>\n+</location>\n+</feature>\n+<sequence length="757" mass="85335" checksum="5A7476C30140331C" modified="1996-10-01" version="2">\n+MMRGFKQRLIKKTTGSSSSSSSKKKDKEKEKEKSSTTSSTSKKPASASSSSHGTTHSSAS\n+STGSKSTTEKGKQSGSVPSQGKHHSSSTSKTKTATTPSSSSSSSRSSSVSRSGSSSTKKT\n+SSRKGQEQSKQSQQPSQSQKQGSSSSSAAIMNPTPVLTVTKDDKSTSGEDHAHPTLLGAV\n+SAVPSSPISNASGTAVSSDVENGNSNNNNMNINTSNTQDANHASSQSIDIPRSSHSFERL\n+PTPTKLNPDTDLELIKTPQRHSSSRFEPSRYTPLTKLPNFNEVSPEERIPLFIAKVDQCN\n+TMFDFNDPSFDIQGKEIKRSTLDELIEFLVTNRFTYTNEMYAHVVNMFKINLFRPIPPPV\n+NPVGDIYDPDEDEPVNELAWPHMQAVYEFFLRFVESPDFNHQIAKQYIDQDFILKLLELF\n+DSEDIRERDCLKTTLHRIYGKFLSLRSFIRRSMNNIFLQFIYETEKFNGVAELLEILGSI\n+INGFALPLKEEHKVFLVRILIPLHKVRCLSLYHPQLAYCIVQFLEKDPLLTEEVVMGLLR\n+YWPKINSTKEIMFLNEIEDIFEVIEPLEFIKVEVPLFVQLAKCISSPHFQVAEKVLSYWN\n+NEYFLNLCIENAEVILPIIFPALYELTSQLELDTANGEDSISDPYMLVEQAINSGSWNRA\n+IHAMAFKALKIFLETNPVLYENCNALYLSSVKETQQRKVQREENWSKLEEYVKNLRINND\n+KDQYTIKNPELRNSFNTASENNTLNEENENDCDSEIQ\n+</sequence>\n+</entry>\n+<entry dataset="Swiss-Prot" created="1993-07-01" modified="2015-10-14" version="133">\n+<accession>P31383</accession>\n+<accession>D6VPK2</accession>\n+<name>2AAA_YEAST</name>\n+<protein>\n+<recommendedName>\n+<fullName>Protein phosphatase PP2A regulatory subunit A</fullName>\n+</recommendedName>\n+</protein>\n+<gene>\n+<name type="primary">TPD3</name>\n+<name type="ordered locus">YAL016W</name>\n+<name type="ORF">FUN32</name>\n+</gene>\n+<organism>\n+<name type="scientific">Saccharomyces cerevisiae (strain ATCC 204508 / S288c)</name>\n+<name type="common">Baker\'s yeast</name>\n+</organism>\n+<proteinExistence type="evidence at protein level"/>\n+<sequence length="635" mass="70907" checksum="7ED350FB20633DC8" modified="2010-10-05" version="3">\n+MSGARSTTAGAVPSAATTSTTSTTSNSKDSDSNESLYPLALLMDELKHDDIANRVEAMKK\n+LDTIALALGPERTRNELIPFLTEVAQDDEDEVFAVLAEQLGKFVPYIGGPQYATILLPVL\n+EILASAEETLVREKAVDSLNNVAQELSQEQLFSDFVPLIEHLATADWFSSKVSACGLFKS\n+VIVRIKDDSLRKNILALYLQLAQDDTPMVKRAVGKNLPILIDLLTQNLGLSTDEDWDYIS\n+NIFQKIINDNQDSVKFLAVDCLISILKFFNAKGDESHTQDLLNSAVKLIGDEAWRVRYMA\n+ADRFSDLASQFSSNQAYIDELVQPFLNLCEDNEGDVREAVAKQVSGFAKFLNDPSIILNK\n+ILPAVQNLSMDESETVRSALASKITNIVLLLNKDQVINNFLPILLNMLRDEFPDVRLNII\n+ASLKVVNDVIGIELLSDSLLPAITELAKDVNWRVRMAIIEYIPILAEQLGMQFFDQQLSD\n+LCLSWLWDTVYSIREAAVNNLKRLTEIFGSDWCRDEIISRLLKFDLQLLENFVSRFTILS\n+ALTTLVPVVSLDVVTEQLLPFISHLADDGVPNIRFNVAKSYAVIVKVLIKDEAKYDALIK\n+NTILPSLQTLCQDEDVDVKYFAKKSLAECQELLKN\n+</sequence>\n+</entry>\n+<entry dataset="Swiss-Prot" created="1993-04-01" modified="2015-10-14" version="147">\n+<accession>Q00362</accession>\n+<accession>D6VTW4</accession>\n+<name>2ABA_YEAST</name>\n+<protein>\n+<recommendedName>\n+<fullName>Protein phosphatase PP2A regulatory subunit B</fullName>\n+</recommendedName>\n+</protein>\n+<gene>\n+<name type="primary">CDC55</name>\n+<name type="ordered locus">YGL190C</name>\n+<name type="ORF">G1345</name>\n+</gene>\n+<organism>\n+<name type="scientific">S'..b'5</name>\n+</gene>\n+<organism>\n+<name type="scientific">Saccharomyces cerevisiae (strain ATCC 204508 / S288c)</name>\n+<name type="common">Baker\'s yeast</name>\n+</organism>\n+<proteinExistence type="inferred from homology"/>\n+<sequence length="854" mass="98008" checksum="6E22D9B5ABCD43F2" modified="2005-12-20" version="2">\n+MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVV\n+GHAVLMIFCAPFRLIYHCIEVLIDKHISVYSINENFTVSFWFWLLVVTYMVFRYVNHMAY\n+PVGANSTGTMACHKSAGVKQPAQGKNCPMARLTNSCKECLGFSLTPSHLGIVIHAYVLEE\n+EVHELTKNESLALSKSWHLEGCTSSNGKLRNTGLSERGNPGDNGVFMVPKFNLNKVRYFS\n+TLSKLNARKEDSLAYLTKINTTDFSELNKLMENNHNKTETINTRILKLMSDIRMLLIAYN\n+KIKSKKGNMSKGSNNITLDGINISYLNKLSKDINTNMFKFSPVRRVEIPKTSGGFRPLSV\n+GNPREKIVQESMRMMLEIIYNNSFSYYSHGFRPNLSCLTAIIQCKNYMQYCNWFIKVDLN\n+KCFDTIPHNMLINVLNERIKDKGFMDLLYKLLRAGYVDKNNNYHNTTLGIPQGSVVSPIL\n+CNIFLDKLDKYLENKFENEFNTGNMSNRGRNPIYNSLSSKIYRCKLLSEKLKLIRLRDHY\n+QRNMGSDKSFKRAYFVRYADDIIIGVMGSHNDCKNILNDINNFLKENLGMSINMDKSVIK\n+HSKEGVSFLGYDVKVTPWEKRPYRMIKKGDNFIRVRHHTSLVVNAPIRSIVMKLNKHGYC\n+SHGILGKPRGVGRLIHEEMKTILMHYLAVGRGIMNYYRLATNFTTLRGRITYILFYSCCL\n+TLARKFKLNTVKKVILKFGKVLVDPHSKVSFSIDDFKIRHKMNMTDSNYTPDEILDRYKY\n+MLPRSLSLFSGICQICGSKHDLEVHHVRTLNNAANKIKDDYLLGRMIKMNRKQITICKTC\n+HFKVHQGKYNGPGL\n+</sequence>\n+</entry>\n+<entry dataset="Swiss-Prot" created="2007-01-09" modified="2015-10-14" version="81">\n+<accession>Q9ZZX0</accession>\n+<accession>A0A0A7NYD5</accession>\n+<name>AI5B_YEAST</name>\n+<protein>\n+<recommendedName>\n+<fullName>Intron-encoded DNA endonuclease aI5 beta</fullName>\n+<ecNumber>3.1.-.-</ecNumber>\n+</recommendedName>\n+</protein>\n+<gene>\n+<name type="primary">AI5_BETA</name>\n+<name type="ordered locus">Q0075</name>\n+</gene>\n+<organism>\n+<name type="scientific">Saccharomyces cerevisiae (strain ATCC 204508 / S288c)</name>\n+<name type="common">Baker\'s yeast</name>\n+</organism>\n+<proteinExistence type="inferred from homology"/>\n+<sequence length="354" mass="42279" checksum="FA9175E5748AD798" modified="1999-05-01" version="1">\n+MLMLLMMILTNNKVFMETLYYYLMFNFQLMSPFGVPVPGPAPETKDIKNLYESIMNNYIN\n+ILNKYTININKDNINKLKFLDNYTEEEKGYYLSGLFEGDGNIYTRCFSITFSLEDVLLAN\n+YLCTYFKIGHITAKYNFNKELTAVKWNIMKKKEQEVFMNYINGKLLTYKRYDQYFKYNFN\n+NRLNIKLLKPKEFDLTLNPWLTGFNDADGYFYTGFQKHKNSQWLKFHLELSQKDSYILDI\n+IKKYFKTGGILKRDYKSGATAYIYKAQSSKAMKPFIEYFNNYQPLSTRRYKQYLLLNIAY\n+LLKLNKLHMLTNSLLMLKELMLLQSVKNMSLEMKNELNNRVKIIINKTHYNNIE\n+</sequence>\n+</entry>\n+<entry dataset="Swiss-Prot" created="1986-07-21" modified="2015-10-14" version="122">\n+<accession>P03875</accession>\n+<accession>A0A0A7NYG1</accession>\n+<accession>Q9ZZX5</accession>\n+<name>AI1M_YEAST</name>\n+<protein>\n+<recommendedName>\n+<fullName>Putative COX1/OXI3 intron 1 protein</fullName>\n+</recommendedName>\n+</protein>\n+<gene>\n+<name type="primary">AI1</name>\n+<name type="ordered locus">Q0050</name>\n+</gene>\n+<organism>\n+<name type="scientific">Saccharomyces cerevisiae (strain ATCC 204508 / S288c)</name>\n+<name type="common">Baker\'s yeast</name>\n+</organism>\n+<proteinExistence type="inferred from homology"/>\n+<sequence length="834" mass="96079" checksum="BFB64B6F36416A5A" modified="2005-12-20" version="2">\n+MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNGAPT\n+SAYISLMRTALVLWIINRYLKHMTNSVGANFTGTMACHKTPMISVGGVKCYMVRLTNFLQ\n+VFIRITISSYHLDMVKQVWLFYVEVIRLWFIVLDSTGSVKKMKDTNNTKGNTKSEGSTER\n+GNSGVDRGMVVPNTQMKMRFLNQVRYYSVNNNLKMGKDTNIELSKDTSTSDLLEFEKLVM\n+DNMNEENMNNNLLSIMKNVDMLMLAYNRIKSKPGNMTPGTTLETLDGMNMMYLNKLSNEL\n+GTGKFKFKPMRMVNIPKPKGGMRPLSVGNPRDKIVQEVMRMILDTIFDKKMSTHSHGFRK\n+NMSCQTAIWEVRNMFGGSNWFIEVDLKKCFDTISHDLIIKELKRYISDKGFIDLVYKLLR\n+AGYIDEKGTYHKPMLGLPQGSLISPILCNIVMTLVDNWLEDYINLYNKGKVKKQHPTYKK\n+LSRMIAKAKMFSTRLKLHKERAKGPTFIYNDPNFKRMKYVRYADDILIGVLGSKNDCKMI\n+KRDLNNFLNSLGLTMNEEKTLITCATETPARFLGYNISITPLKRMPTVTKTIRGKTIRSR\n+NTTRPIINAPIRDIINKLATNGYCKHNKNGRMGVPTRVGRWTYEEPRTIINNYKALGRGI\n+LNYYKLATNYKRLRERIYYVLYYSCVLTLASKYRLKTMSKTIKKFGYNLNIIENDKLIAN\n+FPRNTFDNIKKIENHGMFMYMSEAKVTDPFEYIDSIKYMLPTAKANFNKPCSICNSTIDV\n+EMHHVKQLHRGMLKATKDYITGRMITMNRKQIPLCKQCHIKTHKNKFKNMGPGM\n+</sequence>\n+</entry>\n+</uniprot>\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 553f0336e43e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 23 09:51:47 2016 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mono" version="4.0"> + <repository changeset_revision="4912e4d532cd" name="package_mono_4_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="morpheus" version="255"> + <repository changeset_revision="1beee9ed43fd" name="package_morpheus_255" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |