Mercurial > repos > galaxyp > mz_to_sqlite
changeset 2:1320693cbf1e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
| author | galaxyp |
|---|---|
| date | Mon, 11 Feb 2019 17:30:46 -0500 |
| parents | e34bdac5b157 |
| children | 728d459bafe8 |
| files | mz_to_sqlite.xml test-data/sqlite.db test-data/test.fasta test-data/test.mgf test-data/test_id.mzid |
| diffstat | 5 files changed, 634 insertions(+), 2 deletions(-) [+] |
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--- a/mz_to_sqlite.xml Wed Mar 28 09:33:18 2018 -0400 +++ b/mz_to_sqlite.xml Mon Feb 11 17:30:46 2019 -0500 @@ -1,7 +1,7 @@ -<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.0"> +<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.2"> <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description> <requirements> - <requirement type="package" version="2.0.0">mztosqlite</requirement> + <requirement type="package" version="2.0.2">mztosqlite</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" /> @@ -38,6 +38,10 @@ </outputs> <tests> <test> + <param name="mzinput" value="test_id.mzid" ftype="mzid"></param> + <param name="scanfiles" value="test.mgf" ftype="mgf"></param> + <param name="searchdbs" value="test.fasta" ftype="fasta"></param> + <output name="sqlite_db" file="sqlite.db" /> </test> </tests> <help> @@ -46,4 +50,5 @@ ]]> </help> + <citations></citations> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fasta Mon Feb 11 17:30:46 2019 -0500 @@ -0,0 +1,26 @@ +>sp|Q8C4J7|TBL3_MOUSE Transducin beta-like protein 3 OS=Mus musculus GN=Tbl3 PE=2 SV=1 +MAETAAGLCRFKANYAVERKIEPFYKGGKAQLDQTGHYLFCVCGTKVNILDVASGALLRSLEQEDQEDITSFDLSPDDEVLVTASRALLLAQWAWREGTVTRLWKAIHTAPVASMAFDATSTLLATGGCDGAVRVWDIVQHYGTHHFRGSPGVVHLVAFHPDPTRLLLFSSAVDTSIRVWSLQDRSCLAVLTAHYSAVTSLSFSEGGHTMLSSGRDKICIVWDLQSYQTTRTVPVFESVEASVLLPEQPAPALGVKSSGLHFLTAGDQGILRVWEAASGQCVYTQPQMPGLRQELTHCTLARAADLLLTVTADHNLLLYEAHSLQLQKQFAGYSEEVLDVRFLGPSDSHIVVASNSPCLKVFELQTLACQILHGHTDIVLALDVFRKGWLFASCAKDQSIRIWKMNKAGQVACVAQGSGHTHSVGTICCSRLKESFLVTGSQDCTVKLWPLPEALLAKSTAADSGPVLLQAQTTRRCHDKDINSLAVSPNDKLLATGSQDRTAKLWALPQCQLLGVFTGHRRGLWNVQFSPTDQVLATASADGTIKLWALQDFSCLKTFEGHDASVLKVAFVSRGSQLLSSGSDGLLKLWTIKSNECVRTLDAHEDKVWGLHCSQLDDHAITGGSDSRIILWKDVTEAEQAEEQAKREEQVIKQQELDNLLHEKRYLRALGLAISLDRPHTVLTVIQAIRRDPEACEKLEATVLRLRRDQKEALLRFCVTWNTNSRHCHEAQAVLGVLLRHEAPEELLAYDGVRGSLEALLPYTERHFQRLSRTLQAATFLDFLWHNMKLSPCPAAAPPAL +>tr|Q80ZP8|Q80ZP8_MOUSE Armet protein OS=Mus musculus GN=Manf PE=1 SV=1 +METNNYLPSPPSFPVCISYLGRFYQDLKDRDVTFSPATIEEELIKFCREARGKENRLCYYIGATDDAATKIINEVSKPLAHHIPVEKICEKLKKKDSQICELKYDKQIDLSTVDLKKLRVKELKKILDDWGEMCKGCAEKSDYIRKINELMPKYAPKAASARTDL +>sp|Q60847|COCA1_MOUSE Collagen alpha-1(XII) chain OS=Mus musculus GN=Col12a1 PE=2 SV=3 +MQTRLPRALAALGVALLLSSIEAEVDPPSDLNFKIIDENTVHMSWERPVDPIVGYRITVDPTTDGPTKEFTLAASTTETLLSDLIPETQYVVTITSYNEVEESVPVIGQLTIQTGGPTKPGEKKPGKTEIQKCSVSAWTDLVFLVDGSWSVGRNNFKYILDFIVALVSAFDIGEEKTRVGVVQYSSDTRTEFNLNQYYRREDLLAAVKKIPYKGGNTMTGDAIDYLVKNTFTESAGSRAGFPKVAIIITDGKSQDEVEIPARELRNIGVEVFSLGIKAADAKELKQIASTPSLNHVFNVANFDAIVDIQNEIISQVCSGVDEQLGELVSGEEVIEPPSNLVVTELSSKYIRLSWDPSPSAVTGYKILLTPMAAGSRHHALSVGPQTTTLNVRDLTADTEYQISVFAMKGLTSSEPTSVMEKTQPMKVQVECSRGVDIKADIVFLVDGSYSIGIANFVKVRAFLEVLAKSFEISPNRVQISLVQYSRDPHTEFTLKEFNRVEDIIKAINTFPYRGGSTNTGKAMTYVREKIFVPNKGSRSNVPKVMILITDGKSSDAFRDPAIKLRNSDVEIFAVGVKDAVRSELEAIASPPAETHVFTVEDFDAFQRISFELTQSICLRIEQELAAIKKKAYVPPKDLRFTQVTANSFKAEWSPPGDNVFSYHVTYKDANGDDEVTVVEPASSTSVVLNNLRPETLYLVNVTAEYEDGFSVPITGEETTAEVKGVPRNLKVTDETTDSFKLTWSQAPGRVLRYRIRYRPVSGGESKEVSTPANQRRKTLENLTPDTKYEISVIAEYSSGPGSPLTGNAATEEVRGNPRDLRVSDATTSTLKLSWSRAPGKVKQYLVTYTPAAGGETQEVTVRGDTTTTMLRKLKEGTQYDLSVTALYASGAGEALSGKGSTLEERGSPQNLVTKDITDTSIGAYWTSAPGMVRGYRVSWKSLYDDIEAGETTLPGDAIHTMIENLQPETKYKISVFATYSSGEGEPVTGDATTELSQDSKILRVDEETEHTMRVTWKAAPGKVVNYRVVYRPQGGGRQMVAKVPPTVTSTVLKRLQPQTTYDITVLPMYKTGEGKLRQGSGTTASRFKSPRNLKTSDPTMSSFRVTWEPAPGEVKGYKVTFHPTGDDRRLGELVLGPYDNTVVLEELRAGTTYRVNVFGMFDGGESLPLVGQEMTTLSDTTVTPFLSSGMDCLTRAEADIVLLVDGSWSIGRANFRTVRSFISRIVEVFEIGPKRVQIALAQYSGDPRTEWQLNAHRDKKSLLQAVANLPYKGGNTLTGMALNFIRQQSFKTQAGMRPRARKIGVLITDGKSQDDVEAPSKKLKDEGVELFAIGIKNADEVELKMIATDPDDTHAYNVADFESLSKIVDDLTINLCNSVKGPGDLEAPTNLVISERTHRSFRVSWTPPSDSVDRYKVEYYPVSGGKRQEFYVSRLDTSTVLKDLKPETDYVVNVYSVVEDEYSEPLKGTEKTLPVPVVSLNIYDVGPTTMHVQWQPVGGATGYTVSYQPTRSPEGTKPKEMRVGPTVNDVQLTGLLPNTEYEVTVQAVLYDLTSEPAKAREVTLPLPRPQDVKLRDVTHSTMNVVWEPVLGKVRKYIVRYKTPDEEFKEVEVDRSRASTILKDLSSQTQYTVSVSAVYDEGTSPPATAYDTTRRVPAPTNLQFTEVTPESFRGTWDHGASDVSLYRITWAPVGNPDKMETILNGDENTLVFENLNPNTPYEVSITAIYPDESESEDLSGTERTLRLIPLTTQAPKSGPRNLQVYNATSNSLTVKWDPASGRVQKYRITYQPSTGEGNEQTITVGGRQNSVLLQKLKPDTPYTITVYSQYPDGEGGRMTGRGKTKPLNTVRNLRVYDPSTSSLSVRWDHAEGNPRQYKLFYAPTSGGPEELVPIPGNTNYAILRNLQPDTPYTITVVPVYTEGDGGRTSDTGRTLVRGLARNIQVYNPTPNSLDVRWDPAPGPVQQYRIVYSPVAGTRPSESIVVPGNTRTVHLERLIPDTPYSVNIVALYSDGEGNPSPSQGRTLPRSGPRNIRVFGETTNSLSVAWDHADGPVQQYRIIYSPTVGDPIDEYTTVPGRRNNVILQPLQPDTPYKITVIAIYEDGDGGHLTGNGRTVGLLPPQNIHIFDEWYTRFRVSWDPSPSPVLGYKIVYKPVGSNEPMEAFVGEVTSYTLHNLNPSTTYDVSVYAQYDSGLSVPLTDQGTTLYLNVTDLKTYQVGWDTFCVKWSPHRAATSYRLKLSPADGTRGQEITVRGSETSHCFTGLSPEAEYGVTVFVQTPNLEGPGVPIKEQTTVKPTEAPTEPPTPSPPPTIPPARDVCKGAKADIVFLTDASWSIGDDNFNKVVKFIFNTVGAFDEVNPAGIQVSFVQYSDEVKSEFKLNTYNDKALALGALQNIRYRGGNTRTGKALTFIKEKVLTWESGMRKNVPKVLVVVTDGRSQDEVKKAAFVIQQSGFSVFVVGVADVDYNELANIASKPSERHVFIVDDFESFEKIEDNLITFVCETATSSCPLIYLDGYTSPGFKMLEAYNLTEKNFASVQGVSLESGSFPSYSAYRLQKNAFINQPTAELHPNGLPPSYTIILLFRLLPETPSDPFAIWQITDRDYRPQVGVIADPSSKTLSFFNKDTRGEVQTVTFDTDEVKTLFYGSFHKVHIVVTSKSVKIYIDCYEIIEKDIKEAGNITTDGYEILGKLLKGERKSATFQIQSFDIVCSPVWTSRDRCCDIPSRRDEAKCPALPNACTCTQDSVGPPGPPGPAGGPGAKGPRGERGINGAVGPPGPRGDTGPPGPQGPPGPQGPNGLSIPGEQGRQGMKGDAGEPGLPGRTGTPGLPGPPGPMGPPGDRGFTGKDGAMGPRGPPGPPGSPGSPGVTGPSGKPGKPGDHGRPGQSGLKGEKGDRGDIASQNMMRAVARQVCEQLISGQMSRFNQMLNQIPNDYHSSRNQPGPPGPPGPPGSAGARGEPGPGGRPGFPGTPGMQGPPGERGLPGEKGERGTGSQGPRGPPGPPGPQGESRTGPPGSTGSRGPPGPPGRPGNSGIRGPPGPPGYCDSSQCASIPYNGQGYPEPYVPEGGAYLPEREPFIVPVEPERTAEYEDDYGADEPDQQHPDHMRWRRALRPGPAE +>tr|D6RFR8|D6RFR8_MOUSE Choline/ethanolaminephosphotransferase 1 OS=Mus musculus GN=Cept1 PE=4 SV=1 +MSGHRSTRKRCGDSHPESPVGFGHMSTTGHLCGLILPVLVAFSFTSLWMP +>tr|Q91VK2|Q91VK2_MOUSE Eef1d protein OS=Mus musculus GN=Eef1d PE=1 SV=1 +MATNFLAHEKIWFDKFKYDDAERRFYEQMNGPVTSGSRQLKVMLPNSPEALGQATPGTSSGPGASSGPGGDHSELIVRITSLEVENQNLRGVVQDLQQAISKLEARLSSLEKSSPTPRATAPQTQHVSPMRQVEPPTKKGATPAEDDEDKDIDLFGSDEEEEDKEAARLREERLRQYAEKKAKKPTLVAKSSILLDVKPWDDETDMAQLETCVRSIQLDGLVWGASKLVPVGYGIRKLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNKI +>tr|F6WN43|F6WN43_MOUSE Iron-sulfur cluster co-chaperone protein HscB, mitochondrial (Fragment) OS=Mus musculus GN=Hscb PE=1 SV=1 +XQKSQTEKHFSDKHSTLVNDAYKTLQAPLTRGLYLVS +>sp|Q6NXK2|ZN532_MOUSE Zinc finger protein 532 OS=Mus musculus GN=Znf532 PE=1 SV=1 +MTMGDMKTPDFDDLLAAFDIPDMVDPKAAIESGHDDHESHIKQNAHVDDDSHTPSSSDVGVSVIVKNVRNIDSSEGVEKDGHNPTGNGLHNGFLTASSLDSYGKDGAKSLKGDTPASEVTLKDPAFSQFSPISSAEEFEDDEKIEVDDPPDKEEARAGFRSNVLTGSAPQQDFDKLKALGGENSSKTGVSTSGHTDKNKVKREAESNSITLSVYEPFKVRKAEDKLKENSEKMLESRVLDGKPSSEKSDSGIAAAASSKTKPSSKLSSCIAAIAALSAKKAASDSCKEPVANSREASPLPKEVNDSPKAADKSPESQNLIDGTKKASLKPSDSPRSVSSENSSKGSPSSPVGSTPAIPKVRIKTIKTSSGEIKRTVTRVLPEVDLDSGKKPSEQAASVMASVTSLLSSSASATVLSSPPRAPLQTAMVTSAVSSAELTPKQVTIKPVATAFLPVSAVKTAGSQVINLKLANNTTVKATVISAASVQSASSAIIKAANAIQQQTVVVPASSLANAKLVPKTVHLANLNLLPQGAQATSELRQVLTKPQQQIKQAIINAAASQPPKKVSRVQVVSSLQSSVVEAFNKVLSSVNPVPVYTPNLSPPANAGITLPMRGYKCLECGDAFALEKSLSQHYDRRSVRIEVTCNHCTKNLVFYNKCSLLSHARGHKEKGVVMQCSHLILKPVPADQMIVPPSSNTAASTLQSSVGAATHTVPKVQPGIAGAVISAPASTPMSPAMPLDEDPSKLCRHSLKCLECNEVFQDEPSLATHFQHAADTSGQQMKKHPCRQCDKSFSSSHSLCRHNRIKHKGIRKVYACSHCPDSRRTFTKRLMLERHIQLMHGIKDPDVKELSDDAGDVTNDEEEEAEIKEDAKVPSPKRKLEEPVLEFRPPRGAITQPLKKLKINVFKVHKCAVCGFTTENLLQFHEHIPQHRSDGSSHQCRECGLCYTSHGSLARHLFIVHKLKEPQPVSKQNGAGEDSQQENKPSPEDEAAEGAASDRKCKVCAKTFETEAALNTHMRTHGMAFIKSKRMSSAEK +>sp|P58006|SESN1_MOUSE Sestrin-1 OS=Mus musculus GN=Sesn1 PE=1 SV=3 +MRLAAASNEAYAASLAVSELLSCHQCGGDRGQDEELGIRIPRPLGHGPSRFIPEKEMLQVGSEDAQMHALFADSFAALGRLDNITLVMVFHPQYLESFLKTQHYLLQMDGPLPLHYRHYIGIMAAARHQCSYLVNLHVSDFLHVGGDPKWLNGLENAPQKLQNLGELNKVLAHRPWLITKEHIEGLLKAEEHSWSLAELVHAVVLLTHYHSLASFTFGCGISPEIHCDGGHTFRPPSVSNYCICDITNGNHSVDEMQVNSAGNASVSDSFFEVEALMEKMRQLQECREEEEASQEEMASRFEMEKRESMFVFSSDDDEVTPARDVSRHFEDTSYGYKDFSRHGMHVPTFRVQDYCWEDHGYSLVNRLYPDVGQLIDEKFHIAYNLTYNTMAMHKDVDTSMLRRAIWNYIHCMFGIRYDDYDYGEINQLLDRSFKVYIKTVVCTPEKVTKRMYDSFWRQFKHSEKVHVNLLLIEARMQAELLYALRAITRYMT +>tr|A0A1B0GSE5|A0A1B0GSE5_MOUSE Ubiquitin carboxyl-terminal hydrolase CYLD OS=Mus musculus GN=Cyld PE=1 SV=1 +MSSGLWSQEKVTSPYWEERIFYLLLQECSVTDKQTQKLLKVPKGSIGQYIQDRSVGHSRVPSTKGKKNQIGLKILEQPHAVLFVDEKDVVEINEKFTELLLAITNCEERLSLFRNRLRLSKGLQVDVGSPVKVQLRSGEEKFPGVVRFRGPLLAERTVSGIFFGVELLEEGRGQGFTDGVYQGKQLFQCDEDCGVFVALDKLELIEDDDNGLESDFAGPGDTMQVEPPPLEINSRVSLKVGESTESGTVIFCDVLPGKESLGYFVGVDMDNPIGNWDGRFDGVQLCSFASVESTILLHINDIIPDSVTQERRPPKLAFMSRGVGDKGSSSHNKPKVTGSTSDPGSRNRSELFYTLNGSSVDSQQSKSKNPWYIDEAFGGYLSEVVEENTPPKMEKEGLEIMIGKKKGIQGHYNSCYLDSTLFCLFAFSSALDTVLLRPKEKNDIEYYSETQELLRTEIVNPLRIYGYVCATKIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHDILRVEPLLKIRSAGQKVQDCNFYQIFMEKNEKVGVPTIQQLLEWSFINSNLKFAEAPSCLIIQMPRFGKDFKLFKKIFPSLELNITDLLEDTPRQCRICGGLAMYECRECYDDPDISAGKIKQFCKTCSTQVHLHPRRLNHSYHPVSLPKDLPDWDWRHGCIPCQKMELFAVLCIETSHYVAFVKYGKDDSAWLFFDSMADRDGGQNGFNIPQVTPCPEVGEYLKMSLEDLHSLDSRRIQGCARRLLCDAYMCMYQSPTMSLYK +>sp|Q60880|OL141_MOUSE Olfactory receptor 141 OS=Mus musculus GN=Olfr141 PE=3 SV=2 +MRNITEATFFVLKGLTDNNELQIILFLLFLAIYIFTLIGNVGLIILVVGDSQLHNPMYCFLSVLSSVDACYSTDITPNMLVGFMSKSKIISFYGCATQMFLAVTFGTTECFLLAAMAYDRYVAIHDPLLYAVSMSPRVYIPLIIASYAGGIVHAIIHTVATFSLSFCRSNEVKHIFCDIPPLLAISCSETYVNELLLFFFVSFIELVTILIVLVSYAFILLSILKMNSSEGRRKVFSTCGAHLTAVSIYYGTILFMYVRPSSNYSLEHDMIVSTFYTIGIPMLNPIIYSLRNKDVKEAMKRVLRKKINIKHRIKKLNDFSVFLMP +>tr|L7N477|L7N477_MOUSE Killer cell lectin-like receptor subfamily C, member 3 OS=Mus musculus GN=Klrc3 PE=4 SV=1 +MSHLLGTEQASEPRKATKKTQAQLRFSNAAGDRLLEFSLQHASQKHLKASRHGYCKNFASPPEKLIAGILGTIWFTLLIALVISTRIVSPSQTYALCPKEWILYSHNCYYIGMERKSWNDSLVSCISKNCSLLYIDSEEEQDFLQSLSLVSWTGILRKGRGQPWVWKKDSTFKPKIAEILHDECNCAMMSASGLTADSCTTLHPYLCKCKFPI +>tr|J3QMI4|J3QMI4_MOUSE Calcium homeostasis modulator 3 OS=Mus musculus GN=Calhm3 PE=4 SV=1 +MDRFRMLFQHLQSSSESVMNGICLLLAAVTVKIYSSLDFNCPCLERYNALYGLGLLLTPPLALFLCGLLVNRQSVLMVEEWRRPAGHRRKDLGIIRYMCSSVLQRALAAPLVWILLALLDGKCFVCAFSNSVDPEKFLDFANMTPRQVQLFLAKVPCKEDELVKNSPARKAVSRYLRCLSQAIGWSITLLVIVVAFLARCLRPCFDQTVFLQRRYWSNYMDLEQKLFDETCCEHARDFAHRCVLHFFANMQSELRALGLRRDPAGGIPESQESSEPPELREDRDSGNGKAHLRAISSREQVDQLLSTWYSSKPPLDLAASPRRWGPGLNHRAPIAAPGTKLCHQLNV +>sp|B1AZ99|OTUD3_MOUSE OTU domain-containing protein 3 OS=Mus musculus GN=Otud3 PE=1 SV=1 +MSRKQAAKSRPGSGGRRAEAERKRDERAARRALAKERRNRPDPGGSGCEEEFVSFANQLQALGLKLREVPGDGNCLFRALGDQLEGHSRNHLKHRQETVDYMIRQREDFEPFVEDDIPFEKHVASLSKPGTFAGNDAIVAFARNHQLNVVIHQLNAPLWQIRGTDKGSTRELHIAYRYGEHYDSVRRINDNSEAPAHLLTDFQMLHQDGANKKEKMKTKGVDVKDGLRDDVEDAVHKVGSATGCTDFNLIVQNLEAENYNIKSAITALLQVNQGTGNDAEENHEPGDRVKQRGPSREEAGSGRRLSGNQGRNEGRMETSEARASPAEESKAHKSQLPKVTNKQRREQQRLEKKKRQEERHRLKALENRNGSRDTGRSEADMNTQVTLVKTFAALNI
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