| Previous changeset 2:058a2ab1d462 (2016-12-07) Next changeset 4:58f9cf0de6d4 (2017-08-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7 |
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modified:
msgfplus.xml |
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added:
test-data/201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.tsv |
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removed:
tool_dependencies.xml |
| b |
| diff -r 058a2ab1d462 -r b4ccaf21855d msgfplus.xml --- a/msgfplus.xml Wed Dec 07 16:43:17 2016 -0500 +++ b/msgfplus.xml Thu Jan 12 15:25:02 2017 -0500 |
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| @@ -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" /> |
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| diff -r 058a2ab1d462 -r b4ccaf21855d test-data/201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.tsv --- /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 15:25:02 2017 -0500 |
| b |
| b'@@ -0,0 +1,58 @@\n+#SpecFile\tSpecID\tScanNum\tFragMethod\tPrecursor\tIsotopeError\tPrecursorError(ppm)\tCharge\tPeptide\tProtein\tDeNovoScore\tMSGFScore\tSpecEValue\tEValue\tQValue\tPepQValue\n+201208-378803.mzML\tsample=1 period=1 cycle=1209 experiment=2\t-1\tHCD\t452.25464\t1\t-28.719826\t3\tPKNDPKLKTQGK\tgi|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)\t54\t7\t8.911494E-7\t0.0355328\t0.5\t0.5\n+201208-378803.mzML\tsample=1 period=1 cycle=1215 experiment=4\t-1\tHCD\t674.35315\t1\t-2.036408\t2\tEPISVSSQQMLK\tgi|30466252|ref|NP_848667.1|(pre=K,post=F)\t62\t-1\t1.9064777E-6\t0.076016985\t0.5\t0.5\n+201208-378803.mzML\tsample=1 period=1 cycle=1219 experiment=4\t-1\tHCD\t482.2116\t0\t-38.413548\t2\tPTAEFQDR\tgi|32880221|ref|NP_872593.1|(pre=V,post=I)\t45\t-4\t2.6478965E-6\t0.10364397\t0.5\t0.5\n+201208-378803.mzML\tsample=1 period=1 cycle=1207 experiment=3\t-1\tHCD\t467.23608\t0\t0.71846676\t3\tTVMENFVAFVDK\tgi|30794280|ref|NP_851335.1|(pre=K,post=C)\t57\t-6\t3.189995E-6\t0.12719467\t0.5\t0.5\n+201208-378803.mzML\tsample=1 period=1 cycle=1212 experiment=4\t-1\tHCD\t598.30597\t0\t-30.093014\t3\tKKYMRWMNHKKSR\tgi|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)\t65\t-8\t8.5034735E-6\t0.34040257\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1217 experiment=2\t-1\tHCD\t501.74426\t0\t-40.019917\t2\tLAEAEKEGR\tgi|528944676|ref|XP_005204734.1|(pre=T,post=L)\t81\t15\t8.546935E-6\t0.3362706\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1223 experiment=2\t-1\tHCD\t610.7609\t0\t-38.472713\t2\tAEMFEHLSEK\tgi|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)\t96\t3\t8.9886025E-6\t0.35534644\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1210 experiment=2\t-1\tHCD\t597.28906\t1\t-5.9811645\t2\tPNTEPTHHFI\tgi|528928354|ref|XP_005193233.1|(pre=R,post=H)\t93\t0\t1.0661531E-5\t0.42148226\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1217 experiment=4\t-1\tHCD\t571.8232\t1\t-41.180023\t2\tQLEDILVLAK\tgi|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)\t59\t-1\t1.18926155E-5\t0.47015077\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1223 experiment=3\t-1\tHCD\t478.24365\t0\t-42.496838\t2\tAAQGALQPSL\tgi|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)\t56\t-16\t1.2600591E-5\t0.49813917\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1214 experiment=5\t-1\tHCD\t519.65906\t0\t35.002014\t3\tVNPVTALTLLEKMK\tgi|528968106|ref|XP_005212568.1|(pre=R,post=D)\t56\t-5\t1.9413415E-5\t0.780167\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1231 experiment=2\t-1\tHCD\t490.2488\t1\t4.9017324\t3\tTIFDTEIESTSPK\tgi|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)\t65\t-18\t2.1515163E-5\t0.8612735\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1220 experiment=2\t-1\tHCD\t410.21426\t1\t-45.215214\t3\tQLEGRLQDLR\tgi|528944676|ref|XP_005204734.1|(pre=E,post=A)\t51\t-8\t2.3277607E-5\t0.9202336\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1181 experiment=2\t-1\tHCD\t506.74472\t1\t-13.802416\t2\tLECTNLYR\tgi|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)\t35\t-17\t2.9523253E-5\t1.1555992\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1202 experiment=2\t-1\tHCD\t489.23615\t0\t-25.636705\t3\tLMLLSRDDSGSGSK\tgi|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)\t75\t-17\t3.1620126E-5\t1.270718\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1222 experiment=2\t-1\tHCD\t582.2852\t0\t-48.73894\t3\tIQNGALNCEEKLTLAK\tgi|528944676|ref|XP_005204734.1|(pre='..b'CD\t545.8876\t1\t-31.845514\t3\tQSFGLSQEEYGFDGA\tgi|28849955|ref|NP_788795.1|(pre=K,post=P);gi|119924469|ref|XP_001252524.1|(pre=K,post=P)\t120\t-12\t3.4639085E-4\t13.972368\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1225 experiment=2\t-1\tHCD\t550.7279\t0\t-4.211383\t2\tAEDEPEWPQ\tgi|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)\t46\t-39\t3.8618056E-4\t15.193888\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1218 experiment=5\t-1\tHCD\t587.7718\t1\t-4.5191565\t2\tKQEESAEAGAPG\tgi|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)\t52\t-31\t4.938522E-4\t19.69137\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1201 experiment=3\t-1\tHCD\t512.217\t0\t-47.184654\t2\tPFVCLECGR\tgi|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)\t44\t-26\t5.290015E-4\t20.813036\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1208 experiment=3\t-1\tHCD\t490.20404\t0\t-36.60451\t2\tENLEQAFE\tgi|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)\t76\t-34\t5.55107E-4\t21.727999\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1204 experiment=4\t-1\tHCD\t464.18753\t1\t-3.946628\t2\tHYCGKCCL\tgi|528968221|ref|XP_005212615.1|(pre=R,post=T);gi|27807503|ref|NP_777203.1|(pre=R,post=T)\t32\t-44\t6.305883E-4\t24.682487\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1200 experiment=2\t-1\tHCD\t563.21234\t0\t15.388735\t2\tEEDASSCQEQ\tgi|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)\t79\t-44\t9.1590727E-4\t36.20856\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1183 experiment=2\t-1\tHCD\t416.16492\t0\t8.50641\t2\tDENYYQ\tgi|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)\t52\t-39\t9.4161194E-4\t36.417786\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1228 experiment=2\t-1\tHCD\t500.6953\t1\t-1.0961035\t2\tMCNFHYQG\tgi|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)\t54\t-36\t0.0011096081\t43.43228\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1236 experiment=3\t-1\tHCD\t673.7862\t0\t-47.91735\t2\tEDLVPWIEDCK\tgi|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)\t56\t-52\t0.0015187213\t60.30387\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1199 experiment=3\t-1\tHCD\t495.18527\t0\t-25.883345\t2\tYNCDKMIC\tgi|528954392|ref|XP_005208526.1|(pre=K,post=R);gi|115496708|ref|NP_001069831.1|(pre=K,post=R)\t40\t-41\t0.0025026577\t97.95903\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1199 experiment=3\t-1\tHCD\t495.18527\t1\t-8.696244\t2\tCGDCKFNVC\tgi|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)\t40\t-41\t0.0025026577\t98.46456\t1.0\t1.0\n+201208-378803.mzML\tsample=1 period=1 cycle=1188 experiment=2\t-1\tHCD\t489.16623\t0\t-47.910866\t3\tCTNFSSCWSDGKM\tgi|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)\t64\t-61\t0.0058590886\t234.54517\t1.0\t1.0\n' |
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| diff -r 058a2ab1d462 -r b4ccaf21855d tool_dependencies.xml --- a/tool_dependencies.xml Wed Dec 07 16:43:17 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="msgfplus" version="10089"> - <repository changeset_revision="c1863143aa2a" name="package_msgfplus_v10089" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |