| Previous changeset 6:8736a28dd1d3 (2018-03-20) Next changeset 8:315dca04e06f (2020-09-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty |
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modified:
PrecursorMassCorrector.xml macros.xml |
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removed:
test-data/DecoyDatabase_input.fasta test-data/DecoyDatabase_output.fasta test-data/FileFilter_1_input.mzML test-data/MetaProSIP_1_input.fasta test-data/MetaProSIP_1_input.featureXML test-data/MetaProSIP_1_input.mzML test-data/MetaProSIP_1_output_1.csv test-data/MetaProSIP_1_output_2.csv test-data/MzMLSplitter_output_part1.mzML test-data/MzMLSplitter_output_part2.mzML |
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| diff -r 8736a28dd1d3 -r 79760732d9e3 PrecursorMassCorrector.xml --- a/PrecursorMassCorrector.xml Tue Mar 20 15:27:13 2018 -0400 +++ b/PrecursorMassCorrector.xml Fri May 17 10:25:32 2019 -0400 |
| [ |
| @@ -10,7 +10,7 @@ <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> - <command>PrecursorMassCorrector + <command detect_errors="aggressive"><![CDATA[PrecursorMassCorrector #if $param_in: -in $param_in @@ -35,7 +35,7 @@ -force #end if #end if -</command> +]]></command> <inputs> <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the spectra" help="(-in) "/> <param name="param_feature_in" type="data" format="featurexml" optional="True" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries <br>will be matched to the feature m/z values if possible" help="(-feature_in) "/> @@ -52,5 +52,5 @@ <help>Corrects the precursor entries of MS/MS spectra, by using MS1 information. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorMassCorrector.html</help> +For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PrecursorMassCorrector.html</help> </tool> |
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| diff -r 8736a28dd1d3 -r 79760732d9e3 macros.xml --- a/macros.xml Tue Mar 20 15:27:13 2018 -0400 +++ b/macros.xml Fri May 17 10:25:32 2019 -0400 |
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| @@ -11,9 +11,9 @@ </xml> <xml name="stdio"> <stdio> - <exit_code range="1:"/> - <exit_code range=":-1"/> - <regex match="Exception:"/> + <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> + <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> + <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> </stdio> </xml> <xml name="references"> |
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| diff -r 8736a28dd1d3 -r 79760732d9e3 test-data/DecoyDatabase_input.fasta --- a/test-data/DecoyDatabase_input.fasta Tue Mar 20 15:27:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,146 +0,0 @@\n->12 \n-MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI\n-STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL\n-YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM\n-VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR\n-DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL\n-MIIVPTDTQNIFFMSKVTNPKQA\n->18\n-MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMK\n-QLNIIQNAEAVHFFCNYEESRGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQ\n-NASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLITMACGSCSNENALKTIFMWYR\n-SKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS\n-FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGG\n-DNHASDDFFRKLRDIARKHGCAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMM\n-TGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIKREDLLNNAAHAGKALLTGLL\n-DLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF\n-RDHHAHLFLNIFSDILADFK\n->88\n-MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIE\n-NIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAE\n-EIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNIQNFHTSW\n-KDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP\n-DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRT\n-IPWLENRTPEKTMQAMQKKLEDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAF\n-MPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLEHLAEKFRQKASTHETWAYGK\n-EQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN\n-DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQ\n-DMFIVHSIEEIQSLITAHEQFKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYS\n-TVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRRQFAAQANAIGPWIQNKMEEI\n-ARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI\n-RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRA\n-CLISMGYDLGEAEFARIMTLVDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILAS\n-DKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALDYAAFSSALYGESDL\n->112\n-MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGP\n-PRCPWQDDAFIRRGGPGKGKELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWR\n-RLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLVLLTAVLLAFHAAPARPQPAY\n-VALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW\n-CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTN\n-VIGICTHYPAEVSQRQAFQETRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINT\n-KKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHC\n-LRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV\n-HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNA\n-YLKEQHIETFLILGASQKRKEEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFR\n-QMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQLRKDHVRRFLLTFQREDLEKK\n-YSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC\n-GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLT\n-PADITACHLQQLNYSLGLDAPLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLA\n-MIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNETFDGLDCPAAGRVALKYMTPV\n-ILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF\n-LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIIS\n-EERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNN\n-FQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVLAAKG\n-YQLECRGVVKVKGKGEMTTYFLNGGPSS\n->114\n-MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGS\n-GSGGSGKASDPAGGGPNHHAPQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASG\n-SGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNSFKSRDLERLYQRYFLGQRRK\n-SEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT\n-YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTS\n-LLQVILQVVIPRLAVISINQVVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEAR\n-LRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQHQFHRIYIHRYENVSILFADV\n-KGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH\n-CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKL\n-ESGGIPGRIHISKATLDCLNGDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPED\n-IVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLAALTRNSINLLPNHLAQALHV\n-QSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF\n-IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINE\n-TYLARNVIIFASILINFLGAILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTG\n'..b'VPEETYLIL\n-KDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV\n-QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP\n->143\n-MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQ\n-LNSIQKNHVHIANPDFIWKSIREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCP\n-DSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKVGMEGGQEAVVVELQCSRDSR\n-DCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL\n-ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGI\n-LLLVKAALKNGETAEQLQKMMTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVC\n-ETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVLQNHHSKSPVDVLQIFRVGRV\n-NETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD\n-SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVT\n-TDFEDDEFVVYKTNQVKMKYIIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQL\n-PDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVIVFQTYTNKSHVPIEAKYIFP\n-LDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN\n-LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTK\n-QSFSLTMSIEMPYVIEFIFSDTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYL\n-PRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIICLDCSSSMEGVTFLQAKQIAL\n-HALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL\n-SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCG\n-AGVFEYFNAKSKHSWRKQIEDQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFL\n-NDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTTGTMIHKLAARALIRDYEDGI\n-LHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK\n-EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSED\n-FEEDGLGVLPAFTSNLERGGVEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILA\n-PAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFDASQFSQGPVPGTCADWIPQS\n-ASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS\n-LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCL\n-LEESVGSLEGSRCPVFAFQSSDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDE\n-IVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNTNGLHSFLKQKGIQSLGVKGR\n-ECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE\n-GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG\n->213\n-MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF\n-EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP\n-ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF\n-FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV\n-ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK\n-ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR\n-RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE\n-QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV\n-LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL\n-SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV\n-AASQAALGL\n->230\n-MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYR\n-QVLFSADDRVKKCIGGVIFFHETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTD\n-GETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPSALAILENANVLARYASICQQ\n-NGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC\n-PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTF\n-SYGRALQASALNAWRGQRDNAGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIA\n-NHAY\n->231\n-MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQ\n-EKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGK\n-EFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKP\n-AVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK\n-HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCA\n-LLSCTSHKDYPFHEEF\n->242\n-MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQD\n-LGELIIIRLHKERYAFFPKDPWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKT\n-TADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIPSYRPPVRRHRNPNRPEWNGY\n-IPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR\n-KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGE\n-GTCLQAELEKGNIYLADYRIMEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQ\n-TPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLLETHLIAEAFCLALLRNLPMC\n-HPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY\n-LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEI\n-FKECLLGRESSGFPRCLRTVPELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMR\n-NPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPDDRRPLGHFPDIHFVEEAPRR\n-SIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI\n' 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| b |
| diff -r 8736a28dd1d3 -r 79760732d9e3 test-data/DecoyDatabase_output.fasta --- a/test-data/DecoyDatabase_output.fasta Tue Mar 20 15:27:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,228 +0,0 @@\n->12 \n-MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI\n-STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL\n-YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM\n-VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR\n-DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL\n-MIIVPTDTQNIFFMSKVTNPKQA\n->18 \n-MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMKQLNIIQNAEAVHFFCNYEES\n-RGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQNASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLIT\n-MACGSCSNENALKTIFMWYRSKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS\n-FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGGDNHASDDFFRKLRDIARKHG\n-CAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMMTGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIK\n-REDLLNNAAHAGKALLTGLLDLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF\n-RDHHAHLFLNIFSDILADFK\n->88 \n-MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVIS\n-GERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLW\n-CQRKTAPYRNVNIQNFHTSWKDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP\n-DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRTIPWLENRTPEKTMQAMQKKL\n-EDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAFMPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLE\n-HLAEKFRQKASTHETWAYGKEQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN\n-DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQDMFIVHSIEEIQSLITAHEQ\n-FKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYSTVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRR\n-QFAAQANAIGPWIQNKMEEIARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI\n-RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRACLISMGYDLGEAEFARIMTL\n-VDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILASDKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALD\n-YAAFSSALYGESDL\n->112 \n-MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGPPRCPWQDDAFIRRGGPGKGK\n-ELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWRRLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLV\n-LLTAVLLAFHAAPARPQPAYVALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW\n-CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTNVIGICTHYPAEVSQRQAFQE\n-TRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINTKKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQEL\n-VMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV\n-HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNAYLKEQHIETFLILGASQKRK\n-EEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFRQMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQL\n-RKDHVRRFLLTFQREDLEKKYSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC\n-GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLTPADITACHLQQLNYSLGLDA\n-PLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLAMIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNET\n-FDGLDCPAAGRVALKYMTPVILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF\n-LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAA\n-SGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDST\n-GVPDRIQVTTDLYQVLAAKGYQLECRGVVKVKGKGEMTTYFLNGGPSS\n->114 \n-MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGSGSGGSGKASDPAGGGPNHHA\n-PQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASGSGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNS\n-FKSRDLERLYQRYFLGQRRKSEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT\n-YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTSLLQVILQVVIPRLAVISINQ\n-VVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEARLRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQH\n-QFHRIYIHRYENVSILFADVKGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH\n-CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKLESGGIPGRIHISKATLDCLN\n-GDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPEDIVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLA\n-ALTRNSINLLPNHLAQALHVQSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF\n-IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINETYLARNVIIFASILINFLGA\n-ILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTGVLAMVTCAVFLRLNSVLKLAVLL'..b'SGSASGSGSREPFVKTGCTSHAREGPGLSYLPLASDGSLQPAHHNPGGGAPDSAKGSGGSGSGSGGRHGH\n-IFRQETIHRVATQWLLRQPRSASRGDGAPPTPHITYLEESGTLCRVDSLEM\n->DECOY_143 \n-GQSYHLVRHLPSVTSIPQLGLLQKTASDWDNGLELRPCISPYQGETRRVWESAQKIAEFAWPINRSISADDMKMLSKFVI\n-GEKELRTRIFQLVLMTAILDLLCERGKVGLSQIGKQKLFSHLGNTNLNLILGLEPTLKWFGDETQLSLLETWPVADQWHQ\n-ICVIEDEEKVELFCLISDDKTDCKIQLFCSDQLVESLEDSETDSSQFAFVPCRSGELSGVSEELLCLDVPTTRSQSCLAE\n-PLASAMPLRLNATLSAASPQFHFPSSASPHYSGFGRIPDPDTPLSFHLQPSDLEPFTGASPRTTFGGPHQLPASQASSLS\n-SGSFVIGCYPSSPPNQPPGTPCSASQPIWDACTGPVPGQSFQSADFQRPPAASGFSAVQRYSAFSLSAPSHARATPPLYS\n-GVAPALIPFFSSTSTEWPSVKKFLPETATPKCSETWSLDLLKEVGGRELNSTFAPLVGLGDEEFDESVEPQSLEMKRKSF\n-PIKRHKRKSLRLEPWESSALLSQNRVAEQPEGQWSMYPLFDVDEKAILESVKPIDPFPSENEDRKEVAVFSTFQTILSNE\n-KSLKIILSKLTQKKMEHSTENEHLIGDEYDRILARAALKHIMTGTTKQLETTSVMTRFEKEQILACLTAQTCHPIFGYVL\n-LRDNLFLSPVQAPAQLAEPVDPNLQQWKVSVSHCSPSCLRTMQDEIQKRWSHKSKANFYEFVGAGCQSLIRLVHRNATSG\n-IGCAFLRTHPRSRKVLQLTLSEDQLHGDSVLLINRSGRAPYLLSLYRLTKWFDTNGMTPTASMIFEAAMTNSTIHKPYSF\n-LEKYGTGFQIINVKQKEGVLSLAHLAIQKAQLFTVGEMSSSCDLCIIVESESALDPLDVDLDPQFVLMCAESEKEPHKEV\n-WMRPLYAASLGIHLSFGSSDLSSGEMTSIVAKCDTRKQKLEHTDSFIFEIVYPMEISMTLSFSQKTGIEKICIKEVTDQL\n-NENLAKDQQWPAVTAPMFFVGVTGLISLETIYTIKILVKAKPPLNGVSVTFVDPADQSMLYAGHGQTVAELYEQQAEEKE\n-KIEGVIHKGNIFAEFGCVAAKDDLPFIYKAEIPVHSKNTYTQFVIVQAVTDIIRGKIHVDELPVLNGSADQLGAKTSSST\n-KADPLQYDEVKSFNSFEPRYEELETHDSPHFDKIQDGPMSFKIIYKMKVQNTKYVVFEDDEFDTTVSATQSVGHVSDYGP\n-PAETLSFDKEHLDMCKGLAVDCILLLRTGDTEGPHSYKISTSLSDSFYIGSGLNGVDTRQVGRDEVVKPLLLGRCLIGVI\n-NQVPSGHLLPRVNGLKSLFETTENVRGVRFIQLVDVPSKSHHNQLVEKRVRLFEETNQEVHEIKCRLARYKALSPPNPKS\n-LNTECVNVMDRILQCLDAKKALLGLNVEKPMTGKHPILRYFETMMKQLQEATEGNKLAAKVLLLIGEAKSVDNLSIRNVP\n-KLLMHELHGLAEAWIMEVLDSVEQSLTSSNMVEELLLAQLQESALQTAEPTFHERLLFGQKKLEEIYNEFYESADESTKK\n-IAFQRRTEMGDDLLFHSSILFPCDRSDRSCQLEVVVAEQGGEMGVKELTNYKAVEFDQPLHPIEVNQMGFETLEVTDEEE\n-TASDPCLGETKVESSSAKQDPPPTIDLPKYPDYNKVDLLRKERISKWIFDPNAIHVHNKQISNLQYQSLVDANDLIIHTC\n-QPNLSFSFKGGNEKIDTQLKKKQQQPLYKVKLCFICNAFIGMVM\n->DECOY_213 \n-LGLAAQSAAVLKKGEEAFCTEKDDAKCCKEVFAAFDDMVAKLQEKTAKPKHKVLEVLATQKKIQREKESLTCIDAHFTFT\n-EANFEKPVYTEDVELASFCPRRNVLSETCCKTVRDSVPTKEHLVCLQNLVVSLYDEACPMRKAEPHKCCKSGVKGLNRSV\n-EVLTPTSVQPVKKTYRVLLANQFKYEGLQEFLECNQKILNQPEEVLPKFEDFVKAYCEHPDAAACCKELTTEYTKALRLL\n-LVVSYDPHRRAYEYLFMGLFVDKAEAYNKCVDKSEVFDAALSPLDAPMEDNEVEAICHSKELLPKECCEKLKSSISDQNE\n-CIYKALDARDDACELLDGHCCETHVKTLDTVLKSVEAFEAKPFRQSLRAVAWAKFAREGFKQLSACKLRQKASSAKGEDR\n-LEDLKPLLCAAKDAAQCCETFAAKYRKAFFLLEPAYFYPHRRAIEYLYKKLFTEENDHFATCMVDVEPRVLRPLNPNDDK\n-HQLFCENREPEQKACCDAMEGYTERLTAVTCLKDGFLTHLSKDCNEASEDAVCTKAFETVENVLKVHDEFPCQQLYQAFA\n-ILVLAKFNEEGLDKFRHAVESKHADRRFVGRSYASSFLFLLSIFTVWKM\n->DECOY_230 \n-YAHNAIYLSQAAAGGDEGSGEYKGQAALGNVEARKIFEETAAGANDRQGRWANLASAQLARGYSFTLAWPRPLPCRNIAN\n-LNFSAEEESQGGSLFTVGPVAPPVTRRLATVTAMAIEEPTYKIPCAHGPTVMNPKLLTGELYVHHDSLAKYVAALVKETV\n-YQCRKLDHDGDPLIEPEVIPVIGNQQCISAYRALVNANELIALASPTRESIKLVCRWKAFDAGDKKYQACRESLGDLGQT\n-TTEGDTGALPVVGKDVKIGVVIGKDQITRVFPVGNDDKQYLTEHFFIVGGICKKVRDDASFLVQRYLRRNEETNEVGIQS\n-LRKAMSGVSEDAALIGKGPAVIRLAIDSLEKKQEASLAPYSHPM\n->DECOY_231 \n-FEEHFPYDKHSTCSLLACVRWNRNYSLLTTMDQSSLEFDFVKFNEAIREPTVSKPIVVLNRQMPFRILVQATTKNHKAAI\n-AKIRPDELLSPDEPKAWPRDPSGLPSYATVVIGKSQCYQILKEQTLYPHCEIQNVAPKYKLGPKNLIMEVQLHNFNSIGI\n-AKVLGEDVLEEMAAWTDLINTDSPVVNGSEDLPFFEKGPKFGTPWHILYLDLYDLKLDSLTKQCAGKVLGKEHYTCWLKS\n-VIFLEERKVVQERLKEQIAVGVENENQYVHACDIHRYGVDIAVKVAETVQGPPSKWTGLGLIPMKAGNNLLLRSAM\n->DECOY_242 \n-ISISNEILVPDLYYYPIPLCKNRQRIDHSIQNLRQRFAEISRRPAEEVFHIDPFHGLPRRDDPERSLTWLVLLTICTTKV\n-DPLTDMFTELTTLGKTQIPPNRMSAPFNPMWATFEMQGTNVAAHKASCTYIVITVYRILEPVTRLCRPFGSSERGLLCEK\n-FIEQVWSQLEPDGEVAADSPYYYTIIETVYKELANWVALSDDRYYYGPLDQVGREVFDNPLYLSDYTLESLARVMVGAFG\n-EVGLSMGKASLGGENLLVARGISNIQVTYRTHPILLKYLPHCMPLNRLLALCFAEAILHTELLHAIAEHSYFEAYRVWTK\n-ALLWDWESDSPLFIPCDPGPTQSLQIAIPMMKGEPGFHLLCLPACHHQKRGSLEVTPIGEMIRYDALYINGKELEAQLCT\n-GEGLFPAVMDDTVPFKDPIRTCRRILGPNVGNLYQYGFFTDEAWHEAVYESVVSKKGPFIKRIDKLRKWSHKCDLLGRVK\n-FALAMPGLRVFFSATKLFSYRLNLNLFKTAKFNILIPFGPIYGNWEPRNPNRHRRVPPRYSPIHVYSPLGPLFVRWHYFD\n-QKARIEEKRHELLVPLSDDATTKGTAERLALTEYGDMWQYAPFHYIRGNPACIQVYNCYWPDKPFFAYREKHLRIIILEG\n-LDQPCQVTYQGVAGTAFDRGFHNLLQKHSEGQTGVITLSISDRTGSLLDTGTAVRVKYTAM\n' |
| b |
| diff -r 8736a28dd1d3 -r 79760732d9e3 test-data/FileFilter_1_input.mzML --- a/test-data/FileFilter_1_input.mzML Tue Mar 20 15:27:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,336 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\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" accession="" version="1.1.0">\n-\t<cvList count="2">\n-\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n-\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n-\t</cvList>\n-\t<fileDescription>\n-\t\t<fileContent>\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n-\t\t</fileContent>\n-\t\t<contact>\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />\n-\t\t</contact>\n-\t</fileDescription>\n-\t<sampleList count="1">\n-\t\t<sample id="sa_0" name="">\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n-\t\t</sample>\n-\t</sampleList>\n-\t<softwareList count="12">\n-\t\t<software id="so_in_0" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_default" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_dp_sp_0_pm_0" version="" 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|
| b |
| diff -r 8736a28dd1d3 -r 79760732d9e3 test-data/MetaProSIP_1_input.fasta --- a/test-data/MetaProSIP_1_input.fasta Tue Mar 20 15:27:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ ->contig23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 -GGIPNEENWNFGSSDGSGLPVRGSGQRRDVLGRLCRRNFTSSIGQSVNVRDVEASGFAGG -MSRYHFKYGGAVDPTVLGGVKLGTWFVKEGFAGWSGYPDWCKYFGFYTDFSYHRFYTRDN -RISGTDFFAAYGGGSAALGDVGFMKTEGMVATWAFMLAARYGFFQDSEVPFGRLQPYVAV -GPAIMFSSMKPKIWTQFNEPNVGFPNPDLVYSPGNQSSTDLGLAVDTGIRYMCLKNVSLD -ISFKYRYAQPHYNFSGQDGSVMVPAHMSLSPALNLYSFQAGVAYHF |
| b |
| diff -r 8736a28dd1d3 -r 79760732d9e3 test-data/MetaProSIP_1_input.featureXML --- a/test-data/MetaProSIP_1_input.featureXML Tue Mar 20 15:27:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,129 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\n-<featureMap version="1.9" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/FeatureXML_1_9.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\n-\t<dataProcessing completion_time="2017-12-08T12:44:40">\n-\t\t<software name="FileFilter" version="2.3.0" />\n-\t\t<processingAction name="Data filtering" />\n-\t\t<UserParam type="string" name="parameter: in" value="MetaProSIP_1_input.featureXML"/>\n-\t\t<UserParam type="string" name="parameter: in_type" value=""/>\n-\t\t<UserParam type="string" name="parameter: out" value="MetaProSIP_1_input.featureXML"/>\n-\t\t<UserParam type="string" name="parameter: out_type" value=""/>\n-\t\t<UserParam type="string" name="parameter: rt" value=":"/>\n-\t\t<UserParam type="string" name="parameter: mz" value=":"/>\n-\t\t<UserParam type="string" name="parameter: int" value=":"/>\n-\t\t<UserParam type="string" name="parameter: sort" value="false"/>\n-\t\t<UserParam type="string" name="parameter: log" value=""/>\n-\t\t<UserParam type="int" name="parameter: debug" value="0"/>\n-\t\t<UserParam type="int" name="parameter: threads" value="1"/>\n-\t\t<UserParam type="string" name="parameter: no_progress" value="false"/>\n-\t\t<UserParam type="string" name="parameter: force" value="false"/>\n-\t\t<UserParam type="string" name="parameter: test" value="false"/>\n-\t\t<UserParam type="float" name="parameter: peak_options:sn" value="0"/>\n-\t\t<UserParam type="intList" name="parameter: peak_options:rm_pc_charge" value="[]"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:pc_mz_range" value=":"/>\n-\t\t<UserParam type="floatList" name="parameter: peak_options:pc_mz_list" value="[]"/>\n-\t\t<UserParam type="intList" name="parameter: peak_options:level" value="[1, 2, 3]"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:sort_peaks" value="false"/>\n-\t\t<UserParam type="string" name="parameter: 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value="false"/>\n-\t\t<UserParam type="string" name="parameter: spectra:remove_mode" value=""/>\n-\t\t<UserParam type="string" name="parameter: spectra:remove_activation" value=""/>\n-\t\t<UserParam type="string" name="parameter: spectra:remove_collision_energy" value=":"/>\n-\t\t<UserParam type="string" name="parameter: spectra:remove_isolation_window_width" value=":"/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_zoom" value="false"/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_mode" value=""/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_activation" value=""/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_collision_energy" value=":"/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_isolation_window_width" value=":"/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_polarity" value=""/>\n-\t\t<UserParam type="string" name="parameter: feature:q" value=":"/>\n-\t\t<UserParam type="intList" name="parameter: consensus:map" value="[]"/>\n-\t\t<UserParam type="string" name="parameter: consensus:map_and" value="false"/>\n-\t\t<UserParam type="string" name="parameter: consensus:blackorwhitelist:bl'..b'id:remove_unannotated_features" value="true"/>\n-\t\t<UserParam type="string" name="parameter: id:remove_unassigned_ids" value="false"/>\n-\t\t<UserParam type="string" name="parameter: id:blacklist" value=""/>\n-\t\t<UserParam type="float" name="parameter: id:rt" value="0.1"/>\n-\t\t<UserParam type="float" name="parameter: id:mz" value="0.001"/>\n-\t\t<UserParam type="string" name="parameter: id:blacklist_imperfect" value="false"/>\n-\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:max_intensity" value="-1"/>\n-\t\t<UserParam type="float" name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" value="3"/>\n-\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_max_percentile" value="95"/>\n-\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_mode" value="0"/>\n-\t\t<UserParam type="float" name="parameter: algorithm:SignalToNoise:win_len" value="200"/>\n-\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:bin_count" value="30"/>\n-\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:min_required_elements" value="10"/>\n-\t\t<UserParam type="float" name="parameter: algorithm:SignalToNoise:noise_for_empty_window" value="1e+20"/>\n-\t\t<UserParam type="string" name="parameter: algorithm:SignalToNoise:write_log_messages" value="true"/>\n-\t</dataProcessing>\n-\t<IdentificationRun id="PI_0" date="2011-03-11T14:53:29" search_engine="OMSSA" search_engine_version="2.1.8">\n-\t\t<SearchParameters db="/raid/sachsenb/Jana/fasta/Zeitz_1and2_454AllContigs_HEX.fasta.psq" db_version="" taxonomy="0" mass_type="monoisotopic" charges="+2-+3" enzyme="trypsin" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="false" peak_mass_tolerance="0.5" peak_mass_tolerance_ppm="false" >\n-\t\t\t<FixedModification name="Carbamidomethyl (C)" />\n-\t\t\t<VariableModification name="Oxidation (M)" />\n-\t\t</SearchParameters>\n-\t\t<ProteinIdentification score_type="OMSSA" higher_score_better="false" significance_threshold="0">\n-\t\t\t<ProteinHit id="PH_0" accession="contig23640_802236" score="0" sequence="">\n-\t\t\t</ProteinHit>\n-\t\t</ProteinIdentification>\n-\t</IdentificationRun>\n-\t<featureList count="1">\n-\t\t<feature id="f_988449706551050085">\n-\t\t\t<position dim="0">4831.43346884947</position>\n-\t\t\t<position dim="1">666.862287171363</position>\n-\t\t\t<intensity>3.25608e+06</intensity>\n-\t\t\t<quality dim="0">0</quality>\n-\t\t\t<quality dim="1">0</quality>\n-\t\t\t<overallquality>0.882314</overallquality>\n-\t\t\t<charge>2</charge>\n-\t\t\t<convexhull nr="0">\n-\t\t\t\t<pt x="4803.8473" y="666.862043575291" />\n-\t\t\t\t<pt x="4805.8211" y="666.862135109963" />\n-\t\t\t</convexhull>\n-\t\t\t<convexhull nr="1">\n-\t\t\t\t<pt x="4803.8473" y="667.364150217852" />\n-\t\t\t\t<pt x="4805.8211" y="667.363529666672" />\n-\t\t\t</convexhull>\n-\t\t\t<convexhull nr="2">\n-\t\t\t\t<pt x="4805.8211" y="667.865608520739" />\n-\t\t\t\t<pt x="4807.3928" y="667.864992849711" />\n-\t\t\t</convexhull>\n-\t\t\t<convexhull nr="3">\n-\t\t\t\t<pt x="4810.5312" y="668.364801015548" />\n-\t\t\t\t<pt x="4812.1021" y="668.365292284748" />\n-\t\t\t</convexhull>\n-\t\t\t<PeptideIdentification identification_run_ref="PI_0" score_type="OMSSA" higher_score_better="false" significance_threshold="0" MZ="666.861999511719" RT="4808.4946" >\n-\t\t\t\t<PeptideHit score="0.174659044235501" sequence="YGGAVDPTVLGGVK" charge="2" aa_before="K" aa_after="L" protein_refs="PH_0">\n-\t\t\t\t\t<UserParam type="string" name="target_decoy" value="target"/>\n-\t\t\t\t\t<UserParam type="string" name="protein_references" value="unique"/>\n-\t\t\t\t</PeptideHit>\n-\t\t\t</PeptideIdentification>\n-\t\t\t<UserParam type="int" name="label" value="453"/>\n-\t\t\t<UserParam type="float" name="score_fit" value="0.783165906030983"/>\n-\t\t\t<UserParam type="float" name="score_correlation" value="0.994014816652796"/>\n-\t\t\t<UserParam type="float" name="FWHM" value="23.5379981994629"/>\n-\t\t\t<UserParam type="int" name="spectrum_index" value="1569"/>\n-\t\t\t<UserParam type="string" name="spectrum_native_id" value="controllerType=0 controllerNumber=1 scan=6112"/>\n-\t\t</feature>\n-\t</featureList>\n-</featureMap>\n' |
| b |
| diff -r 8736a28dd1d3 -r 79760732d9e3 test-data/MetaProSIP_1_input.mzML --- a/test-data/MetaProSIP_1_input.mzML Tue Mar 20 15:27:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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| @@ -1,7 +0,0 @@ -Group 1 # Distinct Peptides # Unambigous Proteins Median Global LR median RIA 1 median RIA 2 - 1 1 0.269627132474428 0.603333333333335 36.4733333333347 - Protein Accession Description # Unique Peptides Median Global LR median RIA 1 median RIA 2 - CONTIG23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 1 0.269627132474428 0.603333333333335 36.4733333333347 - Peptide Sequence RT Exp. m/z Theo. m/z Charge Score TIC fraction #non-natural weights RIA 1 INT 1 Cor. 1 RIA 2 INT 2 Cor. 2 Peak intensities Global LR - YGGAVDPTVLGGVK 80.52 666.8623 666.861538013921 2 0.174659044235501 0.831887919884233 7 0.6 1432379 1.00 36.5 146376 0.87 659720 461384 165174 49177 14782 11728 6541 7410 10868 8404 9437 9556 10203 12619 12159 15831 16288 19847 19258 22222 21275 21576 21294 22006 24019 19046 17493 19060 17884 15631 15769 13964 14131 10090 9445 9216 7297 6670 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.269627132474428 -Non-Unique Peptides Accessions Peptide Sequence Descriptions Score RT Exp. m/z Theo. m/z Charge #non-natural weights Peak intensities Global LR |
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| @@ -1,3 +0,0 @@ -Peptide Sequence Feature Quality Report Spectrum Quality report scores Sample Name Protein Accessions Description Unique #Ambiguity members Score RT Exp. m/z Theo. m/z Charge TIC fraction #non-natural weights Peak intensities Group Global Peptide LR RIA 1 LR of RIA 1 INT 1 Cor. 1 RIA 2 LR of RIA 2 INT 2 Cor. 2 RIA 3 LR of RIA 3 INT 3 Cor. 3 RIA 4 LR of RIA 4 INT 4 Cor. 4 RIA 5 LR of RIA 5 INT 5 Cor. 5 RIA 6 LR of RIA 6 INT 6 Cor. 6 RIA 7 LR of RIA 7 INT 7 Cor. 7 RIA 8 LR of RIA 8 INT 8 Cor. 8 RIA 9 LR of RIA 9 INT 9 Cor. 9 RIA 10 LR of RIA 10 INT 10 Cor. 10 -YGGAVDPTVLGGVK feature test_mode_enabled.mzML CONTIG23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 1 1 0.174659044235501 80.52 666.8623 666.8615 2 0.831887919884232 7 659720 461384 165174 49177 14782 11728 6541 7410 10868 8404 9437 9556 10203 12619 12159 15831 16288 19847 19258 22222 21275 21576 21294 22006 24019 19046 17493 19060 17884 15631 15769 13964 14131 10090 9445 9216 7297 6670 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.269627132474428 0.6 1.0 1432378.6 1.0 36.5 0.0 146375.7 0.9 - |
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| diff -r 8736a28dd1d3 -r 79760732d9e3 test-data/MzMLSplitter_output_part2.mzML --- a/test-data/MzMLSplitter_output_part2.mzML Tue Mar 20 15:27:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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