# HG changeset patch
# User galaxyp
# Date 1549924212 18000
# Node ID c8bdcf574413e4df4e4d83d9ecd2dfba763a4760
# Parent  8df9fe030d687daf834f1838cca5e95149d494e8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864

diff -r 8df9fe030d68 -r c8bdcf574413 mz_to_sqlite.xml
--- a/mz_to_sqlite.xml	Fri Jun 17 15:03:22 2016 -0400
+++ b/mz_to_sqlite.xml	Mon Feb 11 17:30:12 2019 -0500
@@ -1,36 +1,47 @@
-<tool id="mz_to_sqlite" name="mz to sqlite" version="1.2.0">
+<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="1.2.0">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" />
    </stdio>
     <command>
 <![CDATA[
-java -jar \$MZTOSQLITE_JAR_PATH -s $mzsqlite 
-#if len($scanfiles) > 0:
-$scanfiles.__str__.replace(',',' ') 
-#end if
-#if len($searchdbs) > 0:
-$searchdbs.__str__.replace(',',' ') 
-#end if
-#if len($mzinputs) > 0:
-$mzinputs.__str__.replace(',',' ')
-#end if
+mz_to_sqlite -Xms1g -Xmx6g 
+     -numthreads "\${GALAXY_SLOTS:-4}"
+     -dbname 'sqlite.db'
+     -mzid '$mzinput'
+     #if len($scanfiles) > 0:
+     #set $files = " ".join(["'"+ a.strip() + "'" for a in str($scanfiles).split(',')])
+     -scanfiles $files
+     #set $dfiles = [a for a in $scanfiles]
+     -scanFilesDisplayName 
+          #for $f in $dfiles
+          '$f.display_name'  
+          #end for
+     #end if
+     #if len($searchdbs) > 0:
+     #set $dbFiles =  " ".join(["'"+ a.strip() + "'" for a in str($searchdbs).split(',')])
+     -fasta $dbFiles
+     #end if
 ]]>
     </command>
     <inputs>
-        <param name="mzinputs" type="data" format="mzid" multiple="true" optional="true" label="Proteomics Identification files"/>
+        <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files"/>
         <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/>
         <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta"
                help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/>
     </inputs>
     <outputs>
-        <data format="mz.sqlite" name="mzsqlite" label="${tool.name} on ${on_string}"/>
+        <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db"/>
     </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>
@@ -39,4 +50,5 @@
 
 ]]>
     </help>
+    <citations></citations>
 </tool>
diff -r 8df9fe030d68 -r c8bdcf574413 test-data/sqlite.db
Binary file test-data/sqlite.db has changed
diff -r 8df9fe030d68 -r c8bdcf574413 test-data/test.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.fasta	Mon Feb 11 17:30:12 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
diff -r 8df9fe030d68 -r c8bdcf574413 test-data/test.mgf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.mgf	Mon Feb 11 17:30:12 2019 -0500
@@ -0,0 +1,209 @@
+COM=Conversion to mascot generic
+CHARGE=2+ and 3+
+BEGIN IONS
+PEPMASS=356.204468
+CHARGE=2+
+SCANS=949
+TITLE=Mo_Tai_iTRAQ_f8.00949.00949.2
+110.828506 2491.272705
+112.094696 13699.349609
+113.091728 18020.962891
+114.110344 1125576.500000
+115.107330 1100947.250000
+116.110695 22822.193359
+119.096985 2535.831299
+126.174309 2810.447998
+127.046684 6835.585449
+128.049973 7331.433594
+128.189621 2914.005371
+129.101974 2570.599609
+129.279678 2607.758545
+132.757004 5481.246582
+143.090988 7752.233887
+143.097107 5783.437012
+143.102463 6564.677734
+143.108566 2564.047363
+144.098862 5652.665039
+144.104889 7361.954590
+145.102219 4936.177734
+145.107025 146758.843750
+145.112335 131714.093750
+147.123001 2650.172119
+147.128372 2737.861816
+148.005478 2639.512939
+148.238419 2869.093750
+155.299225 3088.353027
+158.077728 2793.953369
+162.139252 4774.894531
+162.387039 2827.835449
+165.678162 2818.111328
+166.938889 2684.265625
+167.580872 2939.096680
+175.140564 5432.401855
+175.147156 3378.035156
+183.266129 2539.922852
+183.412628 2670.645752
+184.894104 2803.014893
+185.091522 3216.686035
+187.330780 2998.108643
+188.148529 5007.840332
+188.155151 4465.146973
+195.075851 3438.550293
+200.147873 24339.453125
+200.155838 26661.476563
+201.119965 10145.449219
+201.126175 6782.928711
+202.134979 3300.751221
+212.101944 4973.188477
+216.179565 7723.956055
+220.137726 5468.829102
+226.145721 4482.779785
+228.143005 29964.037109
+228.149582 35742.863281
+228.177368 17399.912109
+228.186249 14105.214844
+233.847382 3023.852539
+237.328430 2774.574463
+246.153275 5242.495117
+246.188858 4635.713867
+247.078400 2846.372314
+247.229568 3600.163818
+252.681946 17567.197266
+252.687744 11091.435547
+257.160217 2689.109863
+258.143890 8518.477539
+259.193176 5211.037598
+260.112854 2996.645508
+265.560181 3225.694824
+267.997864 3700.312744
+268.610748 2618.740479
+273.650787 2803.174316
+274.679718 22228.267578
+274.878204 2877.273682
+276.155609 4863.589355
+280.178680 6539.792480
+280.683990 7219.905762
+281.182739 73752.156250
+281.680695 11313.489258
+285.008820 7076.163574
+286.008789 13322.283203
+287.492432 2768.095459
+288.190704 10070.780273
+289.212860 10554.054688
+290.215210 8197.624023
+291.214630 224196.781250
+292.144562 17330.738281
+292.216919 9077.991211
+294.200745 3728.015869
+294.694580 2759.699951
+295.199768 21009.978516
+295.677765 2779.048828
+295.697662 2965.697998
+301.196075 14519.786133
+302.192566 13183.798828
+302.681702 3274.821045
+303.182465 26307.968750
+304.200134 16413.566406
+308.134003 3247.440674
+309.692322 3523.904541
+310.200165 4997.131348
+310.689606 5659.117676
+314.701416 3665.613525
+315.196594 17897.263672
+315.694458 7221.386230
+322.705383 10645.053711
+323.201050 144162.281250
+323.709473 775901.062500
+324.202362 1445754.250000
+329.190155 6962.873535
+331.171021 5107.174316
+342.255768 3228.923828
+345.230133 4261.129883
+346.701050 7799.938965
+347.194824 2865.516113
+347.688904 5667.636719
+348.197693 24573.441406
+348.233978 5957.279785
+348.692688 25993.126953
+355.150269 4949.070313
+355.174652 2909.161377
+355.204315 14366.736328
+355.708588 75645.015625
+356.069336 6637.967773
+356.134460 13835.235352
+356.202423 120693.640625
+357.188660 16815.277344
+359.191010 6374.648438
+359.210419 3294.687256
+369.224609 3175.326660
+371.329681 3001.630615
+374.215424 34076.957031
+374.250427 13415.376953
+375.198608 45562.394531
+380.471497 3438.794189
+384.042755 2828.394043
+384.233093 3161.169678
+386.881042 3011.077881
+388.835114 3405.797363
+388.912476 2871.228760
+390.210266 6639.722168
+392.209045 4713.115723
+393.195221 4687.627441
+401.264465 37685.667969
+402.246643 145106.453125
+403.250397 14226.839844
+404.223999 3190.761475
+406.204926 9580.385742
+417.220215 9699.318359
+417.257477 9506.871094
+418.205566 9361.549805
+418.253967 9258.392578
+419.273285 87147.929688
+420.256622 156809.703125
+421.189087 5501.845215
+429.258087 8062.255859
+430.242737 14485.661133
+431.274200 6112.059082
+432.241486 5955.781250
+433.228119 9966.237305
+435.205902 2964.356445
+438.212616 8717.499023
+439.198639 11913.517578
+441.878082 2893.906494
+442.281189 5167.858887
+445.253510 3384.076172
+445.289856 5610.796387
+446.234955 3694.613525
+457.289215 9395.412109
+467.271301 9033.137695
+468.256622 6531.868164
+474.277374 6496.598145
+475.266510 12334.884766
+476.296448 56116.445313
+477.277374 97097.773438
+483.278931 3317.250244
+484.297638 7861.101074
+485.283264 40491.058594
+500.063904 3317.183105
+501.286499 36715.671875
+502.309967 507225.437500
+503.293182 868823.875000
+504.296600 21048.537109
+504.326172 13437.491211
+505.307159 13403.533203
+535.264282 3424.624268
+539.916931 3302.101318
+548.299927 5319.335449
+548.877441 3060.022705
+549.283264 12761.772461
+551.285889 5062.984863
+552.265686 6901.311035
+562.301086 3297.966309
+564.321716 7031.061035
+565.314087 6086.279297
+566.308350 57366.886719
+567.291321 87307.140625
+568.995239 3542.976563
+682.357788 3350.750488
+688.612488 3475.960205
+END IONS
diff -r 8df9fe030d68 -r c8bdcf574413 test-data/test_id.mzid
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_id.mzid	Mon Feb 11 17:30:12 2019 -0500
@@ -0,0 +1,392 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<MzIdentML id="PeptideShaker v1.16.9" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" version="1.1.0" creationDate="2018-01-19T02:00:07">
+	<cvList>
+		<cv id="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" fullName="PSI-MS"/>
+		<cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>
+		<cv id="UO" uri="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" fullName="UNIT-ONTOLOGY"/>
+		<cv id="PRIDE" uri="https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride_cv.obo" fullName="PRIDE"/>
+	</cvList>
+	<AnalysisSoftwareList>
+		<AnalysisSoftware name="PeptideShaker" version="1.16.9" id="ID_software" uri="http://compomics.github.io/projects/peptide-shaker.html">
+			<ContactRole contact_ref="PS_DEV">
+				<Role>
+					<cvParam cvRef="PSI-MS" accession="MS:1001267" name="software vendor"/>
+				</Role>
+			</ContactRole>
+			<SoftwareName>
+				<cvParam cvRef="PSI-MS" accession="MS:1002458" name="PeptideShaker"/>
+			</SoftwareName>
+			<Customizations>No customisations</Customizations>
+		</AnalysisSoftware>
+	</AnalysisSoftwareList>
+	<Provider id="PROVIDER">
+		<ContactRole contact_ref="PROVIDER">
+			<Role>
+				<cvParam cvRef="PSI-MS" accession="MS:1001271" name="researcher"/>
+			</Role>
+		</ContactRole>
+	</Provider>
+	<AuditCollection>
+		<Person firstName="Proteomics" lastName="Galaxy" id="PROVIDER">
+			<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="galaxyp@umn.edu"/>
+			<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="galaxyp@umn.edu"/>
+			<Affiliation organization_ref="ORG_DOC_OWNER"/>
+		</Person>
+		<Organization name="University of Minnesota" id="ORG_DOC_OWNER">
+			<cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="University of Minnesota"/>
+			<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="Minneapolis, MN 55455, Vereinigte Staaten"/>
+			<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="galaxyp@umn.edu"/>
+		</Organization>
+		<Organization name="PeptideShaker developers" id="PS_DEV">
+			<cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="PeptideShaker developers"/>
+			<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="Proteomics Unit, Building for Basic Biology, University of Bergen, Jonas Liesvei 91, N-5009 Bergen, Norway"/>
+			<cvParam cvRef="PSI-MS" accession="MS:1000588" name="contact URL" value="http://compomics.github.io/projects/peptide-shaker.html"/>
+			<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="peptide-shaker@googlegroups.com"/>
+		</Organization>
+	</AuditCollection>
+	<SequenceCollection></SequenceCollection>
+	<AnalysisCollection>
+		<SpectrumIdentification spectrumIdentificationList_ref="SIL_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">
+			<InputSpectra spectraData_ref="Mascot formatted MGF of data 13.mgf"/>
+			<InputSpectra spectraData_ref="Mascot formatted MGF of data 8.mgf"/>
+			<InputSpectra spectraData_ref="Mascot formatted MGF of data 7.mgf"/>
+			<InputSpectra spectraData_ref="Mascot formatted MGF of data 6.mgf"/>
+			<InputSpectra spectraData_ref="Mascot formatted MGF of data 12.mgf"/>
+			<InputSpectra spectraData_ref="Mascot formatted MGF of data 14.mgf"/>
+			<InputSpectra spectraData_ref="Mascot formatted MGF of data 11.mgf"/>
+			<InputSpectra spectraData_ref="Mascot formatted MGF of data 10.mgf"/>
+			<InputSpectra spectraData_ref="Mascot formatted MGF of data 9.mgf"/>
+			<SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>
+		</SpectrumIdentification>
+		<ProteinDetection proteinDetectionProtocol_ref="PeptideShaker_1" proteinDetectionList_ref="Protein_groups" id="PD_1">
+			<InputSpectrumIdentifications spectrumIdentificationList_ref="SIL_1"/>
+		</ProteinDetection>
+	</AnalysisCollection>
+	<AnalysisProtocolCollection>
+		<SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
+			<SearchType>
+				<cvParam cvRef="PSI-MS" accession="MS:1001083" name="ms-ms search"/>
+			</SearchType>
+			<AdditionalSearchParams>
+				<cvParam cvRef="PSI-MS" accession="MS:1001211" name="parent mass type mono"/>
+				<cvParam cvRef="PSI-MS" accession="MS:1001256" name="fragment mass type mono"/>
+			</AdditionalSearchParams>
+			<ModificationParams>
+				<SearchModification residues="C" massDelta="57.021464" fixedMod= "true" >
+					<cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/>
+				</SearchModification>
+				<SearchModification residues="K" massDelta="144.102062" fixedMod= "true" >
+					<cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/>
+				</SearchModification>
+				<SearchModification residues="." massDelta="144.102062" fixedMod= "true" >
+					<SpecificityRules>
+						<cvParam cvRef="PSI-MS" accession="MS:1001189" name="modification specificity peptide N-term"/>
+					</SpecificityRules>
+					<cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/>
+				</SearchModification>
+				<SearchModification residues="M" massDelta="15.994915" fixedMod= "false" >
+					<cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>
+				</SearchModification>
+				<SearchModification residues="Y" massDelta="144.102062" fixedMod= "false" >
+					<cvParam cvRef="UNIMOD" accession="UNIMOD:214" name="iTRAQ4plex"/>
+				</SearchModification>
+			</ModificationParams>
+			<Enzymes independent="false">
+			<Enzyme missedCleavages="2" semiSpecific="false" id="Enz1" name="Trypsin">
+				<EnzymeName>
+					<cvParam cvRef="PSI-MS" accession="MS:1001251" name="Trypsin"/>
+				</EnzymeName>
+			</Enzyme>
+		</Enzymes>
+		<FragmentTolerance>
+			<cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="0.05" name="search tolerance plus value" />
+			<cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="0.05" name="search tolerance minus value" />
+		</FragmentTolerance>
+		<ParentTolerance>
+			<cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="10.0" name="search tolerance plus value" />
+			<cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="10.0" name="search tolerance minus value" />
+		</ParentTolerance>
+		<Threshold>
+			<cvParam cvRef="PSI-MS" accession="MS:1001364" name="peptide sequence-level global FDR" value="1.0"/>
+			<cvParam cvRef="PSI-MS" accession="MS:1002350" name="PSM-level global FDR" value="1.0"/>
+			<cvParam cvRef="PSI-MS" accession="MS:1002567" name="phosphoRS score threshold" value="95.0"/>
+			<cvParam cvRef="PSI-MS" accession="MS:1002557" name="D-Score threshold" value="95.0"/>
+		</Threshold>
+	</SpectrumIdentificationProtocol>
+	<ProteinDetectionProtocol analysisSoftware_ref="ID_software" id="PeptideShaker_1">
+		<Threshold>
+			<cvParam cvRef="PSI-MS" accession="MS:1002369" name="protein group-level global FDR" value="0.01"/>
+		</Threshold>
+	</ProteinDetectionProtocol>
+</AnalysisProtocolCollection>
+<DataCollection>
+	<Inputs>
+		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%2010.t.xml" id="SourceFile_1">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
+			</FileFormat>
+		</SourceFile>
+		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%2011.t.xml" id="SourceFile_2">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
+			</FileFormat>
+		</SourceFile>
+		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%2012.t.xml" id="SourceFile_3">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
+			</FileFormat>
+		</SourceFile>
+		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%2013.t.xml" id="SourceFile_4">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
+			</FileFormat>
+		</SourceFile>
+		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%2014.t.xml" id="SourceFile_5">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
+			</FileFormat>
+		</SourceFile>
+		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%206.t.xml" id="SourceFile_6">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
+			</FileFormat>
+		</SourceFile>
+		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%207.t.xml" id="SourceFile_7">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
+			</FileFormat>
+		</SourceFile>
+		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%208.t.xml" id="SourceFile_8">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
+			</FileFormat>
+		</SourceFile>
+		<SourceFile location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/Mascot%20formatted%20MGF%20of%20data%209.t.xml" id="SourceFile_9">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
+			</FileFormat>
+		</SourceFile>
+		<SearchDatabase numDatabaseSequences="50348" location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/input_database.fasta" id="SearchDB_1">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001348" name="FASTA format"/>
+			</FileFormat>
+			<DatabaseName>
+				<userParam name="input_database.fasta"/>
+			</DatabaseName>
+			<cvParam cvRef="PSI-MS" accession="MS:1001073" name="database type amino acid"/>
+		</SearchDatabase>
+		<SpectraData location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/Mascot%20formatted%20MGF%20of%20data%2013.mgf" id="Mascot formatted MGF of data 13.mgf" name="Mascot formatted MGF of data 13.mgf">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>
+			</FileFormat>
+			<SpectrumIDFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
+			</SpectrumIDFormat>
+		</SpectraData>
+		<SpectraData location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/Mascot%20formatted%20MGF%20of%20data%208.mgf" id="Mascot formatted MGF of data 8.mgf" name="Mascot formatted MGF of data 8.mgf">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>
+			</FileFormat>
+			<SpectrumIDFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
+			</SpectrumIDFormat>
+		</SpectraData>
+		<SpectraData location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/Mascot%20formatted%20MGF%20of%20data%207.mgf" id="Mascot formatted MGF of data 7.mgf" name="Mascot formatted MGF of data 7.mgf">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>
+			</FileFormat>
+			<SpectrumIDFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
+			</SpectrumIDFormat>
+		</SpectraData>
+		<SpectraData location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/Mascot%20formatted%20MGF%20of%20data%206.mgf" id="Mascot formatted MGF of data 6.mgf" name="Mascot formatted MGF of data 6.mgf">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>
+			</FileFormat>
+			<SpectrumIDFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
+			</SpectrumIDFormat>
+		</SpectraData>
+		<SpectraData location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/Mascot%20formatted%20MGF%20of%20data%2012.mgf" id="Mascot formatted MGF of data 12.mgf" name="Mascot formatted MGF of data 12.mgf">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>
+			</FileFormat>
+			<SpectrumIDFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
+			</SpectrumIDFormat>
+		</SpectraData>
+		<SpectraData location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/Mascot%20formatted%20MGF%20of%20data%2014.mgf" id="Mascot formatted MGF of data 14.mgf" name="Mascot formatted MGF of data 14.mgf">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>
+			</FileFormat>
+			<SpectrumIDFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
+			</SpectrumIDFormat>
+		</SpectraData>
+		<SpectraData location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/Mascot%20formatted%20MGF%20of%20data%2011.mgf" id="Mascot formatted MGF of data 11.mgf" name="Mascot formatted MGF of data 11.mgf">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>
+			</FileFormat>
+			<SpectrumIDFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
+			</SpectrumIDFormat>
+		</SpectraData>
+		<SpectraData location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/Mascot%20formatted%20MGF%20of%20data%2010.mgf" id="Mascot formatted MGF of data 10.mgf" name="Mascot formatted MGF of data 10.mgf">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>
+			</FileFormat>
+			<SpectrumIDFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
+			</SpectrumIDFormat>
+		</SpectraData>
+		<SpectraData location="file:/panfs/roc/website/galaxyp.msi.umn.edu/GALAXYP/database/job_working_directory/000/158/158323/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/peptideshaker_output_PeptideShaker_temp/data/Mascot%20formatted%20MGF%20of%20data%209.mgf" id="Mascot formatted MGF of data 9.mgf" name="Mascot formatted MGF of data 9.mgf">
+			<FileFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>
+			</FileFormat>
+			<SpectrumIDFormat>
+				<cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
+			</SpectrumIDFormat>
+		</SpectraData>
+	</Inputs>
+	<AnalysisData>
+		<SpectrumIdentificationList id="SIL_1">
+			<FragmentationTable>
+				<Measure id="Measure_MZ">
+					<cvParam cvRef="PSI-MS" accession="MS:1001225" name="product ion m/z" unitCvRef="PSI-MS" unitAccession="MS:1000040" unitName="m/z" />
+				</Measure>
+				<Measure id="Measure_Int">
+					<cvParam cvRef="PSI-MS" accession="MS:1001226" name="product ion intensity" unitCvRef="PSI-MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
+				</Measure>
+				<Measure id="Measure_Error">
+					<cvParam cvRef="PSI-MS" accession="MS:1001227" name="product ion m/z error" unitCvRef="PSI-MS" unitAccession="MS:1000040" unitName="m/z"/>
+				</Measure>
+			</FragmentationTable>
+			<SpectrumIdentificationResult spectraData_ref="Mascot formatted MGF of data 13.mgf" spectrumID="index=8003" id="SIR_1">
+				<SpectrumIdentificationItem passThreshold="false" rank="1" peptide_ref="YPDSVCTVPSPPK_144.10206242080005-ATAA-1" calculatedMassToCharge="627.004694306842" experimentalMassToCharge="627.01001" chargeState="3" id="SII_1_1">
+					<PeptideEvidenceRef peptideEvidence_ref="PepEv_30384"/>
+					<Fragmentation>
+						<IonType charge="1" index="1">
+							<FragmentArray measure_ref="Measure_MZ" values="136.075226"/>
+							<FragmentArray measure_ref="Measure_Int" values="766.121643"/>
+							<FragmentArray measure_ref="Measure_Error" values="-4.643798020254053E-4"/>
+							<cvParam cvRef="PSI-MS" accession="MS:1001239" name="frag: immonium ion"/>
+						</IonType>
+						<IonType charge="1" index="0">
+							<FragmentArray measure_ref="Measure_MZ" values="114.110435"/>
+							<FragmentArray measure_ref="Measure_Int" values="26313.552734"/>
+							<FragmentArray measure_ref="Measure_Error" values="-2.4469905203261533E-4"/>
+							<cvParam cvRef="PSI-MS" accession="MS:1002668" name="frag: iTRAQ 4plex reporter ion" value="114"/>
+						</IonType>
+						<IonType charge="1" index="0">
+							<FragmentArray measure_ref="Measure_MZ" values="115.107475"/>
+							<FragmentArray measure_ref="Measure_Int" values="28673.560547"/>
+							<FragmentArray measure_ref="Measure_Error" values="-2.3959245203286628E-4"/>
+							<cvParam cvRef="PSI-MS" accession="MS:1002668" name="frag: iTRAQ 4plex reporter ion" value="115"/>
+						</IonType>
+						<IonType charge="1" index="1">
+							<FragmentArray measure_ref="Measure_MZ" values="452.243103"/>
+							<FragmentArray measure_ref="Measure_Int" values="6402.285156"/>
+							<FragmentArray measure_ref="Measure_Error" values="-0.031626840962132974"/>
+							<cvParam cvRef="PSI-MS" accession="MS:1001224" name="frag: b ion"/>
+						</IonType>
+						<IonType charge="2" index="11">
+							<FragmentArray measure_ref="Measure_MZ" values="746.385559"/>
+							<FragmentArray measure_ref="Measure_Int" values="990.364075"/>
+							<FragmentArray measure_ref="Measure_Error" values="0.012332756817841073"/>
+							<cvParam cvRef="PSI-MS" accession="MS:1001224" name="frag: b ion"/>
+						</IonType>
+						<IonType charge="1" index="0">
+							<FragmentArray measure_ref="Measure_MZ" values="116.11042"/>
+							<FragmentArray measure_ref="Measure_Int" values="1398.408447"/>
+							<FragmentArray measure_ref="Measure_Error" values="-6.494302520252404E-4"/>
+							<cvParam cvRef="PSI-MS" accession="MS:1002668" name="frag: iTRAQ 4plex reporter ion" value="116"/>
+						</IonType>
+						<IonType charge="1" index="1 2 4 5 9">
+							<FragmentArray measure_ref="Measure_MZ" values="291.216156 388.266693 572.326904 669.367859 1128.594971"/>
+							<FragmentArray measure_ref="Measure_Int" values="3281.50415 2398.454346 483.902496 8817.573242 515.554626"/>
+							<FragmentArray measure_ref="Measure_Error" values="0.0012894146879034452 -9.374341621537496E-4 -0.025518687282101382 -0.037327536132124806 -0.02537033580233583"/>
+							<cvParam cvRef="PSI-MS" accession="MS:1001220" name="frag: y ion"/>
+						</IonType>
+						<IonType charge="2" index="2 5 10">
+							<FragmentArray measure_ref="Measure_MZ" values="194.601517 335.187775 608.353699"/>
+							<FragmentArray measure_ref="Measure_Int" values="449.08316 3051.163086 580.203918"/>
+							<FragmentArray measure_ref="Measure_Error" values="-0.03593645048707117 -0.018456501472030595 0.023875896557797205"/>
+							<cvParam cvRef="PSI-MS" accession="MS:1001220" name="frag: y ion"/>
+						</IonType>
+					</Fragmentation>
+					<cvParam cvRef="PSI-MS" accession="MS:1002466" name="PeptideShaker PSM score" value="-5.9106"/>
+					<cvParam cvRef="PSI-MS" accession="MS:1002467" name="PeptideShaker PSM confidence" value="10.1695"/>
+					<cvParam cvRef="PSI-MS" accession="MS:1001330" name="X!Tandem:expect" value="3.9"/>
+					<cvParam cvRef="PSI-MS" accession="MS:1001117" name="theoretical mass" value="1877.99225352009" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>
+					<cvParam cvRef="PSI-MS" accession="MS:1002540" name="PeptideShaker PSM confidence type" value="Not Validated"/>
+				</SpectrumIdentificationItem>
+				<cvParam cvRef="PSI-MS" accession="MS:1000796" name="spectrum title" value="Mo_Tai_iTRAQ_f8.09495.09495.3"/>
+				<cvParam cvRef="PSI-MS" accession="MS:1000894" name="retention time" value="-1.0" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
+			</SpectrumIdentificationResult>
+			
+			
+			
+		</SpectrumIdentificationList>
+		<ProteinDetectionList id="Protein_groups">
+			<ProteinAmbiguityGroup id="PAG_0">
+				<ProteinDetectionHypothesis id="PAG_0_1" dBSequence_ref="P27048" passThreshold="true">
+					<PeptideHypothesis peptideEvidence_ref="PepEv_5247">
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_27936_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_35350_1"/>
+					</PeptideHypothesis>
+					<PeptideHypothesis peptideEvidence_ref="PepEv_11948">
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28486_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_32857_1"/>
+					</PeptideHypothesis>
+					<PeptideHypothesis peptideEvidence_ref="PepEv_38645">
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28823_1"/>
+					</PeptideHypothesis>
+					<PeptideHypothesis peptideEvidence_ref="PepEv_64667">
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_40692_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_46888_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_49545_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_59118_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_62451_1"/>
+					</PeptideHypothesis>
+					<PeptideHypothesis peptideEvidence_ref="PepEv_68343">
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_41960_1"/>
+					</PeptideHypothesis>
+					<cvParam cvRef="PSI-MS" accession="MS:1002403" name="group representative"/>
+					<cvParam cvRef="PSI-MS" accession="MS:1002401" name="leading protein"/>
+					<cvParam cvRef="PSI-MS" accession="MS:1001093" name="sequence coverage" value="0.0649"/>
+				</ProteinDetectionHypothesis>
+				<ProteinDetectionHypothesis id="PAG_0_2" dBSequence_ref="P63163" passThreshold="true">
+					<PeptideHypothesis peptideEvidence_ref="PepEv_5248">
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_27936_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_35350_1"/>
+					</PeptideHypothesis>
+					<PeptideHypothesis peptideEvidence_ref="PepEv_11949">
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28486_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_32857_1"/>
+					</PeptideHypothesis>
+					<PeptideHypothesis peptideEvidence_ref="PepEv_38646">
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_28823_1"/>
+					</PeptideHypothesis>
+					<PeptideHypothesis peptideEvidence_ref="PepEv_64668">
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_40692_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_46888_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_49545_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_59118_1"/>
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_62451_1"/>
+					</PeptideHypothesis>
+					<PeptideHypothesis peptideEvidence_ref="PepEv_68344">
+						<SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_41960_1"/>
+					</PeptideHypothesis>
+					<cvParam cvRef="PSI-MS" accession="MS:1002401" name="leading protein"/>
+				</ProteinDetectionHypothesis>
+				<cvParam cvRef="PSI-MS" accession="MS:1002470" name="PeptideShaker protein group score" value="62.4192"/>
+				<cvParam cvRef="PSI-MS" accession="MS:1002471" name="PeptideShaker protein group confidence" value="99.9665"/>
+				<cvParam cvRef="PSI-MS" accession="MS:1002542" name="PeptideShaker protein confidence type" value="Confident"/>
+				<cvParam cvRef="PSI-MS" accession="MS:1002415" name="protein group passes threshold" value="true"/>
+			</ProteinAmbiguityGroup>
+			
+			<cvParam cvRef="PSI-MS" accession="MS:1002404" name="count of identified proteins" value="3290"/>
+		</ProteinDetectionList>
+	</AnalysisData>
+</DataCollection>
+</MzIdentML>
\ No newline at end of file
diff -r 8df9fe030d68 -r c8bdcf574413 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jun 17 15:03:22 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="mztosqlite" version="1.2.0">
-        <repository changeset_revision="d8db06905567" name="package_mztosqlite_1_2_0" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>