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changeset 6:0a376f581288 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7
author galaxyp
date Thu, 12 Jan 2017 15:24:49 -0500
parents 468e8d70a073
children 51fd56b09e64
files msgfplus.xml test-data/201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.tsv tool_dependencies.xml
diffstat 3 files changed, 97 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/msgfplus.xml	Wed Dec 07 17:26:02 2016 -0500
+++ b/msgfplus.xml	Thu Jan 12 15:24:49 2017 -0500
@@ -4,7 +4,6 @@
     </description>
     <requirements>
         <requirement type="package" version="2016.10.26">msgf_plus</requirement>
-        <environment_variable name="LC_ALL" action="set_to">C</environment_variable>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
@@ -56,6 +55,13 @@
             -maxCharge $advanced.maxCharge
             -n $advanced.n
             -addFeatures $advanced.addFeatures
+	#if $tsvcheck
+	    &&
+	    msgf_plus
+	        edu.ucsd.msjava.ui.MzIDToTsv
+	        -i '$output_name'
+	        -o output.tsv
+	#end if
         &&
         mv '$output_name' output
 ]]>
@@ -75,6 +81,7 @@
 			  label="Collection: Pairs of FASTA database (forward) and spectra (reverse)"/>
           </when>
         </conditional>
+        <param name="tsvcheck" type="boolean" label="Output TSV as well?" />
         <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" />
         <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>
         <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments">
@@ -217,12 +224,15 @@
     </inputs>
     <outputs>
         <data name="output" format="mzid" from_work_dir="output" />
+        <data name="tsvoutput" format="tabular" from_work_dir="output.tsv" >
+          <filter>tsvcheck</filter>
+        </data>
     </outputs>
     <tests>
         <test>
-	    <param name="msgf_input.intype_selector" value="single" />
-            <param name="msgf_input.s" value="input/201208-378803.mzML" />
-            <param name="msgf_input.d" value="input/cow.protein.PRG2012-subset.fasta" />
+            <param name="msgf_input|intype_selector" value="single" />
+            <param name="msgf_input|s" value="input/201208-378803.mzML" ftype="mzml" />
+            <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" ftype="fasta" />
             <param name="tda" value="1" />
             <param name="ntt" value="1" />
             <param name="t" value="50" />
@@ -232,21 +242,39 @@
             <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" />
         </test>
         <test>
-	    <param name="msgf_input.intype_selector" value="fractions" />
-            <param name="msgf_input.db_spectra.forward" value="input/201208-378803.mzML" />
-            <param name="msgf_input.db_spectra.reverse" value="input/cow.protein.PRG2012-subset.fasta" />
+            <param name="msgf_input|intype_selector" value="single" />
+            <param name="msgf_input|s" value="input/201208-378803.mzML" />
+            <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" />
+            <param name="tsvcheck" value="true" />
+            <param name="tda" value="1" />
+            <param name="ntt" value="1" />
+            <param name="t" value="50" />
+            <param name="precursor_ion_tol_units" value="ppm" />
+            <param name="common_fixed_modifications" value="" />
+            <param name="common_variable_modifications" value="" />
+            <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" />
+            <output name="tsvoutput" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.tsv" compare="sim_size" delta="20" />
+        </test>
+        <test>
+            <param name="msgf_input|intype_selector" value="fractions" />
+            <param name="msgf_input|db_spectra">
+                <collection type="paired">
+                    <element name="forward" value="input/201208-378803.mzML" />
+                    <element name="reverse" value="input/cow.protein.PRG2012-subset.fasta" />
+                </collection>
+            </param>
             <param name="tda" value="1" />
             <param name="ntt" value="1" />
             <param name="t" value="50" />
             <param name="precursor_ion_tol_units" value="ppm" />            
             <param name="common_fixed_modifications" value="" />
             <param name="common_variable_modifications" value="" />
-            <output name="output" file="201208-378803-msgf-50ppm-semitryptic-no_mods.mzid" lines_diff="6" />
+            <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" />
         </test>
         <test>
-	    <param name="msgf_input.intype_selector" value="single" />
-            <param name="msgf_input.s" value="input/201208-378803.mzML" />
-            <param name="msgf_input.d" value="input/cow.protein.PRG2012-subset.fasta" />
+            <param name="msgf_input|intype_selector" value="single" />
+            <param name="msgf_input|s" value="input/201208-378803.mzML" />
+            <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" />
             <param name="tda" value="1" />
             <param name="t" value="0.02" />
             <param name="precursor_ion_tol_units" value="Da" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.tsv	Thu Jan 12 15:24:49 2017 -0500
@@ -0,0 +1,58 @@
+#SpecFile	SpecID	ScanNum	FragMethod	Precursor	IsotopeError	PrecursorError(ppm)	Charge	Peptide	Protein	DeNovoScore	MSGFScore	SpecEValue	EValue	QValue	PepQValue
+201208-378803.mzML	sample=1 period=1 cycle=1209 experiment=2	-1	HCD	452.25464	1	-28.719826	3	PKNDPKLKTQGK	gi|528993971|ref|XP_005219929.1|(pre=F,post=C);gi|528993973|ref|XP_005219930.1|(pre=F,post=C);gi|528993975|ref|XP_005219931.1|(pre=F,post=C);gi|27806851|ref|NP_776358.1|(pre=F,post=C)	54	7	8.911494E-7	0.0355328	0.5	0.5
+201208-378803.mzML	sample=1 period=1 cycle=1215 experiment=4	-1	HCD	674.35315	1	-2.036408	2	EPISVSSQQMLK	gi|30466252|ref|NP_848667.1|(pre=K,post=F)	62	-1	1.9064777E-6	0.076016985	0.5	0.5
+201208-378803.mzML	sample=1 period=1 cycle=1219 experiment=4	-1	HCD	482.2116	0	-38.413548	2	PTAEFQDR	gi|32880221|ref|NP_872593.1|(pre=V,post=I)	45	-4	2.6478965E-6	0.10364397	0.5	0.5
+201208-378803.mzML	sample=1 period=1 cycle=1207 experiment=3	-1	HCD	467.23608	0	0.71846676	3	TVMENFVAFVDK	gi|30794280|ref|NP_851335.1|(pre=K,post=C)	57	-6	3.189995E-6	0.12719467	0.5	0.5
+201208-378803.mzML	sample=1 period=1 cycle=1212 experiment=4	-1	HCD	598.30597	0	-30.093014	3	KKYMRWMNHKKSR	gi|528944676|ref|XP_005204734.1|(pre=R,post=V);gi|528944678|ref|XP_005204735.1|(pre=R,post=V);gi|219804516|ref|NP_001137332.1|(pre=R,post=V)	65	-8	8.5034735E-6	0.34040257	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1217 experiment=2	-1	HCD	501.74426	0	-40.019917	2	LAEAEKEGR	gi|528944676|ref|XP_005204734.1|(pre=T,post=L)	81	15	8.546935E-6	0.3362706	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1223 experiment=2	-1	HCD	610.7609	0	-38.472713	2	AEMFEHLSEK	gi|528944676|ref|XP_005204734.1|(pre=Q,post=L);gi|528944678|ref|XP_005204735.1|(pre=Q,post=L);gi|219804516|ref|NP_001137332.1|(pre=Q,post=L)	96	3	8.9886025E-6	0.35534644	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1210 experiment=2	-1	HCD	597.28906	1	-5.9811645	2	PNTEPTHHFI	gi|528928354|ref|XP_005193233.1|(pre=R,post=H)	93	0	1.0661531E-5	0.42148226	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1217 experiment=4	-1	HCD	571.8232	1	-41.180023	2	QLEDILVLAK	gi|528944676|ref|XP_005204734.1|(pre=K,post=Q);gi|528944678|ref|XP_005204735.1|(pre=K,post=Q);gi|219804516|ref|NP_001137332.1|(pre=K,post=Q)	59	-1	1.18926155E-5	0.47015077	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1223 experiment=3	-1	HCD	478.24365	0	-42.496838	2	AAQGALQPSL	gi|528921178|ref|XP_592304.7|(pre=K,post=Y);gi|528921180|ref|XP_005195747.1|(pre=K,post=Y);gi|528995523|ref|XP_002695913.2|(pre=K,post=Y)	56	-16	1.2600591E-5	0.49813917	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1214 experiment=5	-1	HCD	519.65906	0	35.002014	3	VNPVTALTLLEKMK	gi|528968106|ref|XP_005212568.1|(pre=R,post=D)	56	-5	1.9413415E-5	0.780167	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1231 experiment=2	-1	HCD	490.2488	1	4.9017324	3	TIFDTEIESTSPK	gi|528968104|ref|XP_005212567.1|(pre=Y,post=S);gi|528968106|ref|XP_005212568.1|(pre=Y,post=S);gi|528968108|ref|XP_005212569.1|(pre=Y,post=S);gi|115497338|ref|NP_001069884.1|(pre=Y,post=S)	65	-18	2.1515163E-5	0.8612735	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1220 experiment=2	-1	HCD	410.21426	1	-45.215214	3	QLEGRLQDLR	gi|528944676|ref|XP_005204734.1|(pre=E,post=A)	51	-8	2.3277607E-5	0.9202336	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1181 experiment=2	-1	HCD	506.74472	1	-13.802416	2	LECTNLYR	gi|528944676|ref|XP_005204734.1|(pre=R,post=K);gi|528944678|ref|XP_005204735.1|(pre=R,post=K);gi|219804516|ref|NP_001137332.1|(pre=R,post=K)	35	-17	2.9523253E-5	1.1555992	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1202 experiment=2	-1	HCD	489.23615	0	-25.636705	3	LMLLSRDDSGSGSK	gi|528944676|ref|XP_005204734.1|(pre=R,post=T);gi|528944678|ref|XP_005204735.1|(pre=R,post=T);gi|219804516|ref|NP_001137332.1|(pre=R,post=T)	75	-17	3.1620126E-5	1.270718	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1222 experiment=2	-1	HCD	582.2852	0	-48.73894	3	IQNGALNCEEKLTLAK	gi|528944676|ref|XP_005204734.1|(pre=K,post=N);gi|528944678|ref|XP_005204735.1|(pre=K,post=N);gi|219804516|ref|NP_001137332.1|(pre=K,post=N)	94	-17	3.4877667E-5	1.4119875	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1229 experiment=3	-1	HCD	710.8027	0	12.279265	2	CVCDECGRGFGFK	gi|528908802|ref|XP_005199340.1|(pre=P,post=S);gi|528908804|ref|XP_005199341.1|(pre=P,post=S);gi|528908806|ref|XP_005199342.1|(pre=P,post=S);gi|528908808|ref|XP_005199343.1|(pre=P,post=S);gi|528908810|ref|XP_005199344.1|(pre=P,post=S);gi|528908812|ref|XP_609847.5|(pre=P,post=S);gi|528959647|ref|XP_005210511.1|(pre=P,post=S);gi|528959649|ref|XP_005210512.1|(pre=P,post=S);gi|528959651|ref|XP_005210513.1|(pre=P,post=S);gi|528959653|ref|XP_005210514.1|(pre=P,post=S);gi|528959655|ref|XP_005210515.1|(pre=P,post=S);gi|528959657|ref|XP_002689899.2|(pre=P,post=S)	53	-24	3.7364465E-5	1.495737	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1219 experiment=2	-1	HCD	487.24332	0	-15.908564	3	RSDVEQLDQEIK	gi|528944676|ref|XP_005204734.1|(pre=I,post=E);gi|528944678|ref|XP_005204735.1|(pre=I,post=E);gi|219804516|ref|NP_001137332.1|(pre=I,post=E)	80	-10	4.2131483E-5	1.6799086	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1228 experiment=3	-1	HCD	606.27484	1	-8.0082855	2	WQEYQSRVD	gi|528944676|ref|XP_005204734.1|(pre=R,post=S);gi|528944678|ref|XP_005204735.1|(pre=R,post=S);gi|219804516|ref|NP_001137332.1|(pre=R,post=S)	36	-21	4.2569478E-5	1.6748536	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1209 experiment=3	-1	HCD	570.7028	1	20.262213	3	RKFIIHRGKRKAAQ	gi|528921178|ref|XP_592304.7|(pre=K,post=G);gi|528921180|ref|XP_005195747.1|(pre=K,post=G);gi|528995523|ref|XP_002695913.2|(pre=K,post=G)	89	-13	4.495753E-5	1.8067082	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1216 experiment=2	-1	HCD	464.21527	1	-44.885506	3	QLAQQTEQKGCR	gi|528944676|ref|XP_005204734.1|(pre=S,post=A)	61	-17	4.9378592E-5	1.9688725	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1212 experiment=2	-1	HCD	653.3102	1	29.944271	3	VFEEMIEPYCLHESCK	gi|358414198|ref|XP_002700672.2|(pre=K,post=D);gi|528966552|ref|XP_005211956.1|(pre=K,post=D);gi|528966554|ref|XP_005211957.1|(pre=K,post=D);gi|297479727|ref|XP_002690982.1|(pre=K,post=D)	87	-14	5.4227086E-5	2.1953294	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1580 experiment=2	-1	HCD	533.26227	1	-43.25022	3	LIIQLEQGDEPWR	gi|528908802|ref|XP_005199340.1|(pre=K,post=E);gi|528908804|ref|XP_005199341.1|(pre=K,post=E);gi|528908806|ref|XP_005199342.1|(pre=K,post=E);gi|528908808|ref|XP_005199343.1|(pre=K,post=E);gi|528908810|ref|XP_005199344.1|(pre=K,post=E);gi|528908812|ref|XP_609847.5|(pre=K,post=E);gi|528959647|ref|XP_005210511.1|(pre=K,post=E);gi|528959649|ref|XP_005210512.1|(pre=K,post=E);gi|528959651|ref|XP_005210513.1|(pre=K,post=E);gi|528959653|ref|XP_005210514.1|(pre=K,post=E);gi|528959655|ref|XP_005210515.1|(pre=K,post=E);gi|528959657|ref|XP_002689899.2|(pre=K,post=E)	38	-31	5.964108E-5	2.387492	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1191 experiment=3	-1	HCD	400.68393	0	-14.166251	2	EVMEHR	gi|528944676|ref|XP_005204734.1|(pre=K,post=L);gi|528944678|ref|XP_005204735.1|(pre=K,post=L);gi|219804516|ref|NP_001137332.1|(pre=K,post=L)	27	-14	6.842939E-5	2.6465752	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1209 experiment=5	-1	HCD	404.1922	0	-21.819786	3	QLAQKYNCDK	gi|528954392|ref|XP_005208526.1|(pre=R,post=M);gi|115496708|ref|NP_001069831.1|(pre=R,post=M)	51	-14	7.684107E-5	3.037758	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1202 experiment=3	-1	HCD	423.6786	0	-15.198104	2	DLGEEHF	gi|30794280|ref|NP_851335.1|(pre=K,post=K)	36	-12	7.7868164E-5	3.0307846	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1215 experiment=3	-1	HCD	613.78107	1	-47.61758	2	DLPFLSNEYK	gi|528944676|ref|XP_005204734.1|(pre=K,post=E)	53	-26	8.023354E-5	3.1718724	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1198 experiment=3	-1	HCD	613.27563	1	-36.601665	2	QLQEELAEHQ	gi|528944676|ref|XP_005204734.1|(pre=K,post=V);gi|528944678|ref|XP_005204735.1|(pre=K,post=V);gi|219804516|ref|NP_001137332.1|(pre=K,post=V)	47	-29	8.59888E-5	3.3993952	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1219 experiment=3	-1	HCD	509.25696	0	-0.53933096	2	DAENTVRGR	gi|528944676|ref|XP_005204734.1|(pre=R,post=L)	42	-23	8.931347E-5	3.5139492	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1192 experiment=3	-1	HCD	433.18747	0	-46.987206	2	LSETEMR	gi|528928354|ref|XP_005193233.1|(pre=Q,post=P)	34	-20	9.6144715E-5	3.7421446	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1209 experiment=4	-1	HCD	481.199	0	-36.782173	2	HAAEEEIY	gi|528968104|ref|XP_005212567.1|(pre=R,post=T);gi|528968106|ref|XP_005212568.1|(pre=R,post=T);gi|528968108|ref|XP_005212569.1|(pre=R,post=T)	46	-31	1.1874728E-4	4.648006	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1215 experiment=2	-1	HCD	605.81055	1	-36.649742	2	MPPLIPAEVDK	gi|528944676|ref|XP_005204734.1|(pre=R,post=I);gi|528944678|ref|XP_005204735.1|(pre=R,post=I);gi|219804516|ref|NP_001137332.1|(pre=R,post=I)	45	-26	1.2084616E-4	4.7984385	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1215 experiment=2	-1	HCD	605.81055	0	20.855597	2	QLAQKYNCDK	gi|528954392|ref|XP_005208526.1|(pre=R,post=M);gi|115496708|ref|NP_001069831.1|(pre=R,post=M)	45	-26	1.2084616E-4	4.7774115	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1196 experiment=2	-1	HCD	409.18747	1	-15.97708	2	YYKVDE	gi|528968221|ref|XP_005212615.1|(pre=K,post=N);gi|27807503|ref|NP_777203.1|(pre=K,post=N)	43	-16	1.217629E-4	4.709302	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1214 experiment=2	-1	HCD	510.20837	0	28.05353	2	MMSASSYNE	gi|528928354|ref|XP_005193233.1|(pre=R,post=D)	67	-20	1.2431844E-4	4.891185	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1217 experiment=5	-1	HCD	476.69785	1	-36.653725	2	ARGCSEELS	gi|358418103|ref|XP_600387.4|(pre=R,post=K);gi|528923273|ref|XP_005196452.1|(pre=R,post=K);gi|297488451|ref|XP_002696970.1|(pre=R,post=K);gi|529000951|ref|XP_005222651.1|(pre=R,post=K)	35	-25	1.4944564E-4	5.8797894	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1238 experiment=2	-1	HCD	455.65408	1	42.005333	3	LIRRQRLRPR	gi|139948503|ref|NP_001077142.1|(pre=K,post=E)	25	-35	1.6960995E-4	6.70519	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1201 experiment=2	-1	HCD	440.18204	1	-28.454306	2	CDDQNKR	gi|528944676|ref|XP_005204734.1|(pre=E,post=S)	44	-21	1.7229663E-4	6.706129	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1210 experiment=3	-1	HCD	461.71622	0	30.008469	2	EACFAVEGP	gi|30794280|ref|NP_851335.1|(pre=K,post=K)	59	-18	1.7894078E-4	7.040246	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1218 experiment=3	-1	HCD	471.21652	1	-38.450603	3	SKEVSNLEFSDR	gi|528944676|ref|XP_005204734.1|(pre=G,post=K)	57	-27	1.8095516E-4	7.215225	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1221 experiment=3	-1	HCD	684.79614	0	-44.82985	2	EGQMVEEKYQK	gi|528944676|ref|XP_005204734.1|(pre=E,post=A);gi|528944678|ref|XP_005204735.1|(pre=E,post=A);gi|219804516|ref|NP_001137332.1|(pre=E,post=A)	85	-34	2.1989181E-4	8.731244	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1199 experiment=2	-1	HCD	608.2569	0	-33.012207	3	ELNPEEGQMVEEKYQ	gi|528944676|ref|XP_005204734.1|(pre=K,post=K);gi|528944678|ref|XP_005204735.1|(pre=K,post=K);gi|219804516|ref|NP_001137332.1|(pre=K,post=K)	76	-38	3.0840118E-4	12.439979	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1201 experiment=4	-1	HCD	792.833	0	-44.263622	2	NQDALTFFNSNQVS	gi|528944676|ref|XP_005204734.1|(pre=R,post=E)	70	-57	3.212409E-4	12.909707	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1214 experiment=4	-1	HCD	545.8876	1	-14.505296	3	NCNGSAACGLGYDFSR	gi|358414198|ref|XP_002700672.2|(pre=M,post=C);gi|528966552|ref|XP_005211956.1|(pre=M,post=C);gi|528966554|ref|XP_005211957.1|(pre=M,post=C);gi|297479727|ref|XP_002690982.1|(pre=M,post=C)	120	-12	3.4639085E-4	14.023288	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1214 experiment=4	-1	HCD	545.8876	1	-31.845514	3	QSFGLSQEEYGFDGA	gi|28849955|ref|NP_788795.1|(pre=K,post=P);gi|119924469|ref|XP_001252524.1|(pre=K,post=P)	120	-12	3.4639085E-4	13.972368	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1225 experiment=2	-1	HCD	550.7279	0	-4.211383	2	AEDEPEWPQ	gi|358418103|ref|XP_600387.4|(pre=R,post=P);gi|528923273|ref|XP_005196452.1|(pre=R,post=P);gi|297488451|ref|XP_002696970.1|(pre=R,post=P);gi|529000951|ref|XP_005222651.1|(pre=R,post=P)	46	-39	3.8618056E-4	15.193888	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1218 experiment=5	-1	HCD	587.7718	1	-4.5191565	2	KQEESAEAGAPG	gi|528921178|ref|XP_592304.7|(pre=R,post=G);gi|528921180|ref|XP_005195747.1|(pre=R,post=G);gi|528995523|ref|XP_002695913.2|(pre=R,post=G)	52	-31	4.938522E-4	19.69137	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1201 experiment=3	-1	HCD	512.217	0	-47.184654	2	PFVCLECGR	gi|528908802|ref|XP_005199340.1|(pre=R,post=G);gi|528908804|ref|XP_005199341.1|(pre=R,post=G);gi|528908806|ref|XP_005199342.1|(pre=R,post=G);gi|528908808|ref|XP_005199343.1|(pre=R,post=G);gi|528908810|ref|XP_005199344.1|(pre=R,post=G);gi|528908812|ref|XP_609847.5|(pre=R,post=G);gi|528959647|ref|XP_005210511.1|(pre=R,post=G);gi|528959649|ref|XP_005210512.1|(pre=R,post=G);gi|528959651|ref|XP_005210513.1|(pre=R,post=G);gi|528959653|ref|XP_005210514.1|(pre=R,post=G);gi|528959655|ref|XP_005210515.1|(pre=R,post=G);gi|528959657|ref|XP_002689899.2|(pre=R,post=G)	44	-26	5.290015E-4	20.813036	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1208 experiment=3	-1	HCD	490.20404	0	-36.60451	2	ENLEQAFE	gi|528944676|ref|XP_005204734.1|(pre=R,post=V);gi|528944678|ref|XP_005204735.1|(pre=R,post=V);gi|219804516|ref|NP_001137332.1|(pre=R,post=V)	76	-34	5.55107E-4	21.727999	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1204 experiment=4	-1	HCD	464.18753	1	-3.946628	2	HYCGKCCL	gi|528968221|ref|XP_005212615.1|(pre=R,post=T);gi|27807503|ref|NP_777203.1|(pre=R,post=T)	32	-44	6.305883E-4	24.682487	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1200 experiment=2	-1	HCD	563.21234	0	15.388735	2	EEDASSCQEQ	gi|528944676|ref|XP_005204734.1|(pre=R,post=L);gi|528944678|ref|XP_005204735.1|(pre=R,post=L);gi|219804516|ref|NP_001137332.1|(pre=R,post=L)	79	-44	9.1590727E-4	36.20856	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1183 experiment=2	-1	HCD	416.16492	0	8.50641	2	DENYYQ	gi|528944676|ref|XP_005204734.1|(pre=R,post=L);gi|528944678|ref|XP_005204735.1|(pre=R,post=L);gi|219804516|ref|NP_001137332.1|(pre=R,post=L)	52	-39	9.4161194E-4	36.417786	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1228 experiment=2	-1	HCD	500.6953	1	-1.0961035	2	MCNFHYQG	gi|528968104|ref|XP_005212567.1|(pre=K,post=F);gi|528968106|ref|XP_005212568.1|(pre=K,post=F);gi|528968108|ref|XP_005212569.1|(pre=K,post=F);gi|115497338|ref|NP_001069884.1|(pre=K,post=F)	54	-36	0.0011096081	43.43228	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1236 experiment=3	-1	HCD	673.7862	0	-47.91735	2	EDLVPWIEDCK	gi|528944676|ref|XP_005204734.1|(pre=V,post=A);gi|528944678|ref|XP_005204735.1|(pre=V,post=A);gi|219804516|ref|NP_001137332.1|(pre=V,post=A)	56	-52	0.0015187213	60.30387	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1199 experiment=3	-1	HCD	495.18527	0	-25.883345	2	YNCDKMIC	gi|528954392|ref|XP_005208526.1|(pre=K,post=R);gi|115496708|ref|NP_001069831.1|(pre=K,post=R)	40	-41	0.0025026577	97.95903	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1199 experiment=3	-1	HCD	495.18527	1	-8.696244	2	CGDCKFNVC	gi|358418103|ref|XP_600387.4|(pre=R,post=K);gi|528923273|ref|XP_005196452.1|(pre=R,post=K);gi|297488451|ref|XP_002696970.1|(pre=R,post=K);gi|529000951|ref|XP_005222651.1|(pre=R,post=K)	40	-41	0.0025026577	98.46456	1.0	1.0
+201208-378803.mzML	sample=1 period=1 cycle=1188 experiment=2	-1	HCD	489.16623	0	-47.910866	3	CTNFSSCWSDGKM	gi|528944676|ref|XP_005204734.1|(pre=K,post=F);gi|528944678|ref|XP_005204735.1|(pre=K,post=F);gi|219804516|ref|NP_001137332.1|(pre=K,post=F)	64	-61	0.0058590886	234.54517	1.0	1.0
--- a/tool_dependencies.xml	Wed Dec 07 17:26:02 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="msgfplus" version="10089">
-        <repository changeset_revision="3c75e2b6233d" name="package_msgfplus_v10089" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>