# HG changeset patch # User galaxyp # Date 1615812723 0 # Node ID 5b5a9f59e2c78eafc6bb70f1c734679373f6c00a # Parent 528bcf03e56125ccdc568b02e9056b4225793ddc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407" diff -r 528bcf03e561 -r 5b5a9f59e2c7 macros.xml --- a/macros.xml Fri Jul 17 17:05:41 2020 -0400 +++ b/macros.xml Mon Mar 15 12:52:03 2021 +0000 @@ -1,5 +1,6 @@ - 1.6.0 + 1.6.2 + 0 diff -r 528bcf03e561 -r 5b5a9f59e2c7 pepquery.xml --- a/pepquery.xml Fri Jul 17 17:05:41 2020 -0400 +++ b/pepquery.xml Mon Mar 15 12:52:03 2021 +0000 @@ -1,10 +1,10 @@ - + Peptide-centric search engine for novel peptide identification and validation. macros.xml - pepquery + pepquery @@ -19,6 +19,9 @@ #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_file.display_name.split('/')[-1])) + ".fa" ln -s '$req_inputs.spectrum_file' '$spectrum_file' && ln -s '$req_inputs.db_file' '$db_file' && + #if $req_inputs.tags.tagType == 'pFind': + pepquery main.java.util.generateTags '$req_inputs.tags.qry_res' > qry.tags && + #end if pepquery -ms '$spectrum_file' -db '$db_file' @@ -42,6 +45,13 @@ #end if #end if -indexType $req_inputs.indexType + #if $req_inputs.tags.tagType == 'PepQuery': + -tag '$req_inputs.tags.tag_file' + -tagIndexType $req_inputs.tags.tagIndexType + #elif $req_inputs.tags.tagType == 'pFind': + -tag qry.tags + -tagIndexType 2 + #end if #if $modifications.fixed_mod -fixMod '$modifications.fixed_mod' #end if @@ -73,11 +83,11 @@
- + - - - - + + + + + + + + + + + + + + + + + + + + +
+ +
- + - + - - - + + +
- - + + - +
- + @@ -185,55 +219,59 @@ - +
- + - + - - - - - - + + + + + +
- + + req_inputs['tags']['tagType'] in ['pFind'] + + - + - + - + - + +
@@ -278,10 +316,12 @@ + +
@@ -327,10 +367,63 @@ + + + +
+ + + + + + + + + +
+
+ + + + + +
+
+
+ + + +
+
+ + +
+
+ + + + + + + + +
+
+ + + + + + + + +
+ +
@@ -380,6 +473,7 @@ +
@@ -425,9 +519,125 @@ + + +
+ + + + + + + + + + + + + + + +
+
+ + + + + +
+
+
+ + + +
+
+ + +
+
+ + + + + + + + +
+
+ + + + + + + +
+ + + +
+ + + + + + + + + + + + + + +
+
+ + + + + +
+
+
+ + + +
+
+ + +
+
+ + + + + + + + +
+
+ + + + + + + + + +
+ 10.1101/gr.235028.118 + 10.1038/s41467-020-15456-w diff -r 528bcf03e561 -r 5b5a9f59e2c7 test-data/immunopeptidomics.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/immunopeptidomics.mgf Mon Mar 15 12:52:03 2021 +0000 @@ -0,0 +1,464 @@ +BEGIN IONS +TITLE=controllerType=0 controllerNumber=1 scan=19846 +RTINSECONDS=2320.06458 +PEPMASS=383.529876708984 +CHARGE=3+ +84.0449677 46347.0703125 +84.0813446 85493.9453125 +86.0719299 7175.7060546875 +86.0969772 135316.21875 +87.0795746 57686.53515625 +89.5852509 6013.955078125 +91.0547638 26870.0390625 +100.0871506 10508.3408203125 +101.0712357 8028.2236328125 +102.0548477 7109.3364257813 +110.071434 72448.5390625 +112.0872192 68537.90625 +116.0708847 66026.75 +116.6829987 7043.2426757813 +119.0492325 28436.21484375 +120.0808487 28182.986328125 +123.0442657 6282.2768554688 +127.0979004 32528.88671875 +129.1026154 74929.3046875 +129.1124268 15517.341796875 +132.1023407 7616.8291015625 +136.075592 267654.46875 +137.0793915 44604.71484375 +140.0816498 8406.1591796875 +145.4732819 7887.0209960938 +147.0440521 10594.44921875 +147.1123962 10032.357421875 +155.0816803 6984.1274414063 +157.1085968 34948.90234375 +165.0540466 39318.01953125 +167.0815887 29707.244140625 +168.085022 6312.9848632813 +182.0816193 28942.546875 +183.1242371 7433.0512695313 +183.1487885 8203.357421875 +193.0978699 6826.6010742188 +195.0764313 23284.12109375 +195.1120148 9413.0185546875 +197.1287689 31395.33203125 +198.132309 9345.76953125 +199.7877808 5461.4345703125 +213.0883179 6907.8862304688 +217.1338043 13646.8583984375 +219.1365814 28881.201171875 +226.1663971 13425.7822265625 +244.165451 62294.3984375 +245.1695709 14033.3974609375 +249.673233 32895.77734375 +254.1607361 72503.140625 +255.1666107 6893.8310546875 +259.0739441 12570.2685546875 +260.0770569 6460.126953125 +271.1891785 9831.76953125 +275.1358337 11066.83984375 +304.6169434 9695.1650390625 +308.5368347 10936.181640625 +308.8744507 6715.9243164063 +311.181427 8423.06640625 +326.7102356 8839.98828125 +328.2081909 21860.5078125 +329.8709106 7965.8657226563 +330.2044983 8398.9033203125 +331.1609192 7686.9453125 +333.8371277 25565.46484375 +334.1699219 7952.1284179688 +339.8395081 31163.154296875 +340.1759949 26240.822265625 +340.6808167 36919.71484375 +342.1118774 7167.1025390625 +342.1811218 10171.65234375 +346.5349731 7574.7329101563 +347.7381592 9350.056640625 +348.4993286 7552.921875 +353.6708679 38643.10546875 +354.1769409 6889.3901367188 +354.2250671 21217.833984375 +361.6572571 6491.6513671875 +362.1836853 6020.7607421875 +363.1853333 8824.9462890625 +377.2033691 6569.89453125 +381.2067871 7040.6538085938 +383.2186279 68377.4609375 +383.3130188 116036.234375 +383.526886 42512.03125 +385.2560425 10095.142578125 +398.2119751 25488.392578125 +401.2857666 10739.900390625 +410.2869873 10938.7431640625 +417.2008667 6045.6533203125 +417.696991 8364.318359375 +418.2027893 8019.1762695313 +426.2158203 9391.662109375 +428.8858948 6009.2065429688 +431.206543 9535.4150390625 +451.2514343 6296.6337890625 +465.7139282 6659.9360351563 +466.2247925 8575.556640625 +475.2226257 6292.1694335938 +488.2868042 7346.7373046875 +489.2886047 30622.896484375 +491.2367249 8038.7392578125 +492.2262268 27380.2578125 +496.3111572 9502.2919921875 +498.3398438 83627.8203125 +499.348114 9477.421875 +502.2510376 7497.5302734375 +502.8083191 7691.1728515625 +518.2723389 29630.49609375 +519.2763672 13119.953125 +656.3309937 6904.6923828125 +673.3564453 8458.634765625 +END IONS +BEGIN IONS +TITLE=controllerType=0 controllerNumber=1 scan=19905 +RTINSECONDS=2325.98454 +PEPMASS=534.22802734375 +CHARGE=2+ +74.0607834 11525.5478515625 +80.820961 1134.3864746094 +84.0448685 11916.904296875 +84.0813599 24140.73046875 +86.0719757 1059.546875 +86.0969696 48334.11328125 +87.0556259 2711.1242675781 +87.0794067 2536.3103027344 +87.099884 1441.4647216797 +88.0397949 1339.0686035156 +89.0711365 5940.744140625 +95.5842514 960.4934692383 +100.0871887 1435.1180419922 +101.0711517 11117.935546875 +102.0551834 7843.828125 +104.0528793 2629.0866699219 +107.0505447 1256.6583251953 +107.47509 1007.3388061523 +110.0714264 24055.96484375 +112.087204 2137.0339355469 +115.0872574 2242.5446777344 +119.0812531 1181.8509521484 +120.0808029 19385.041015625 +127.0867386 5999.564453125 +129.065918 4383.1904296875 +129.1022491 33245.55859375 +130.0497742 1252.8232421875 +131.0811462 1228.9758300781 +136.0639343 1478.1802978516 +136.0756531 41457.83203125 +137.0790558 2168.0249023438 +141.0658417 2161.6188964844 +141.1025543 1396.7373046875 +145.0974884 1154.3653564453 +152.0713348 1227.7298583984 +155.0810394 2207.4116210938 +157.0602112 1539.4930419922 +157.08461 1485.4039306641 +157.1333466 2088.0070800781 +159.0758057 2233.6645507813 +159.1125183 1578.9256591797 +165.0541687 14583.548828125 +166.085968 18895.611328125 +169.1333466 10393.7421875 +171.0764618 1893.2116699219 +172.1085052 1334.9647216797 +180.0661316 2653.572265625 +182.0809937 32101.177734375 +183.076828 2454.3715820313 +183.1490936 1469.2236328125 +185.077774 2541.4504394531 +185.0941162 1574.8117675781 +185.1289368 1785.0300292969 +186.087677 2044.2495117188 +187.1076813 2141.6088867188 +198.0757141 1864.1412353516 +199.0702972 1590.9162597656 +200.10289 5724.33203125 +201.1239624 2084.2858886719 +203.0672455 1515.2619628906 +207.1134491 2512.40625 +213.0875549 1643.7739257813 +215.1399994 2060.5869140625 +216.0997772 1206.705078125 +216.1348419 1320.7780761719 +217.1352234 8159.3056640625 +220.1828613 3609.7250976563 +220.2030029 1611.9375 +221.1286774 11386.6640625 +223.1070251 5323.6176757813 +226.1182861 4679.68359375 +230.1152496 2067.7849121094 +235.1436768 2349.3061523438 +236.1468964 1393.5037841797 +237.1257629 2463.6643066406 +240.1340179 1668.9652099609 +245.13237 1704.8936767578 +247.1428375 1828.2724609375 +249.0960083 1496.8309326172 +249.1233063 1982.8770751953 +254.1599274 1287.4233398438 +262.6038818 2132.6999511719 +267.1069946 1409.6979980469 +267.1347351 4155.18359375 +270.1081848 2705.4152832031 +270.6130981 2401.3571777344 +271.1154175 1773.4208984375 +277.6126709 1322.0480957031 +283.1292419 6684.1733398438 +285.2037659 1555.5247802734 +290.6115112 1747.0528564453 +293.1127625 1832.3509521484 +295.0375366 1139.5216064453 +298.6217346 2137.7734375 +299.1255493 1164.4644775391 +299.6296692 5615.0180664063 +304.6210938 1524.0411376953 +313.6674805 1478.9112548828 +314.6342773 1185.4146728516 +341.1139832 1686.7280273438 +350.1498108 2248.2668457031 +350.6541443 9815.0107421875 +351.1555786 4738.2700195313 +351.6599426 1457.0270996094 +355.647583 1925.8502197266 +358.1459961 1697.1291503906 +364.1647644 2035.076171875 +364.6515198 2264.7180175781 +365.6571045 2539.4509277344 +366.1519775 1271.5914306641 +368.1899719 2488.8234863281 +370.1492615 1207.8226318359 +372.6609192 1450.5041503906 +373.1611023 15705.77734375 +373.6647339 6134.396484375 +376.5512695 1535.8891601563 +379.1600952 1519.6890869141 +379.6573486 1735.7387695313 +382.6697693 1877.0784912109 +384.6668396 1368.4975585938 +386.1818542 4932.7622070313 +388.0981445 1814.0821533203 +388.1616516 1639.3973388672 +391.6724243 1722.4331054688 +394.6583252 2745.8254394531 +395.1569519 1794.5734863281 +399.1826477 1813.751953125 +399.6832886 2202.8469238281 +400.1859131 27261.03515625 +400.6886902 11703.2177734375 +405.1769714 1845.1595458984 +406.1872559 5626.5249023438 +409.1769714 1553.7102050781 +410.2037659 9268.25390625 +410.7049255 2537.4650878906 +412.1827393 2462.1599121094 +415.1905518 4857.001953125 +417.1824646 2098.9926757813 +423.1886902 1632.6658935547 +428.6966248 5038.703125 +429.1943359 2628.6257324219 +430.1769409 2335.6350097656 +438.2408752 2383.4521484375 +439.1846313 18274.087890625 +439.6879578 7237.6088867188 +443.2449951 1595.5926513672 +445.186676 4973.349609375 +445.6867676 2095.1735839844 +446.1969604 1545.0024414063 +450.6947937 2427.0949707031 +452.2566528 1537.7886962891 +454.1917114 1963.4315185547 +458.1747131 1448.1218261719 +461.2607727 1722.7113037109 +465.6973877 1562.3093261719 +466.1947937 2171.53515625 +467.2056274 10621.619140625 +467.7023621 9091.3349609375 +468.1976929 1944.4018554688 +468.267395 4734.5639648438 +469.273468 1822.9508056641 +473.1994934 1352.2316894531 +473.6989746 1343.6881103516 +475.1999512 5885.4248046875 +475.7026672 6054.9418945313 +476.2094421 4897.3432617188 +476.7133789 1982.70703125 +478.2355347 5131.12109375 +481.1903992 2123.00390625 +481.7055664 2059.3818359375 +482.2129822 6752.0048828125 +482.7108459 2522.6437988281 +487.3049316 2514.1276855469 +490.7094421 2462.6801757813 +495.70578 5170.00390625 +501.7067566 1650.3034667969 +501.7937622 7237.1142578125 +502.296875 2418.212890625 +504.21698 9748.248046875 +504.7191772 6072.6821289063 +510.2188721 6962.052734375 +519.2223511 8869.3369140625 +519.7225342 4718.7387695313 +520.2103271 16541.169921875 +520.7109985 2730.8581542969 +524.7560425 1626.7911376953 +526.2027588 2263.7565917969 +526.7091675 1732.9114990234 +533.8047485 10959.140625 +534.2905273 10083.3759765625 +534.7897339 30336.474609375 +535.220459 1591.669921875 +539.1575928 2096.6694335938 +551.1583862 2616.3996582031 +569.1661377 2812.7487792969 +641.3411255 4872.2426757813 +643.3137207 1385.0288085938 +652.3312378 1978.6364746094 +668.3342896 1452.5230712891 +682.3339233 1898.4290771484 +683.3429565 1458.1762695313 +696.3226318 1923.4722900391 +784.5008545 6190.7158203125 +790.3800659 2451.6320800781 +819.3933716 4207.2880859375 +820.4173584 2018.9385986328 +824.4292603 11264.025390625 +869.4186401 2067.2492675781 +882.4277954 1771.7611083984 +884.423584 1570.5802001953 +885.4588623 2440.49609375 +955.4633789 7311.4379882813 +969.456604 2234.6115722656 +END IONS +BEGIN IONS +TITLE=controllerType=0 controllerNumber=1 scan=19944 +RTINSECONDS=2329.22502 +PEPMASS=516.783386230469 +CHARGE=2+ +72.0815811 27197.671875 +74.0610199 4197.1069335938 +84.0451736 15634.2109375 +84.0815887 26392.96875 +86.0969391 88900.34375 +87.0557785 6371.4975585938 +87.1004715 5257.353515625 +88.0400085 4621.7041015625 +101.0712738 5125.9956054688 +102.0554962 23467.248046875 +107.0487747 4362.7963867188 +110.0715256 339710.21875 +111.0756683 11064.5341796875 +112.0868912 4111.2602539063 +116.0706635 55538.3046875 +120.080925 26441.748046875 +127.0875549 4627.248046875 +129.102829 26702.419921875 +132.1021881 5254.7578125 +133.0611267 3728.3393554688 +136.0756378 91992.3203125 +137.0794525 4378.3774414063 +138.0666656 7507.4252929688 +145.5386963 6195.8090820313 +157.1097717 3760.1879882813 +159.0761414 3559.2092285156 +166.086441 5174.974609375 +169.0968933 6497.8017578125 +173.09198 66982.4140625 +180.113205 6698.7612304688 +181.0975647 20135.044921875 +182.081604 7997.3110351563 +183.1493378 16863.73046875 +197.1275787 6301.8452148438 +202.0863037 3530.7102050781 +208.1073456 25956.681640625 +209.0920258 14764.1796875 +218.0425568 28767.90234375 +229.1558533 5750.8208007813 +233.0927124 4071.7492675781 +235.1186981 36820.6640625 +243.1336212 24782.921875 +267.1106567 5503.90625 +278.1124878 4135.1215820313 +286.1757813 15374.74609375 +304.1647339 5803.3159179688 +306.0768738 3530.1059570313 +318.1595459 5520.9609375 +330.1925964 14000.76171875 +344.6773376 3574.6950683594 +356.2409973 12024.30078125 +360.2006531 46041.26171875 +360.7026062 19602.333984375 +363.6889648 16339.1533203125 +364.1605225 3471.5439453125 +365.1912537 6514.8598632813 +365.6857605 3434.3635253906 +372.6929016 23375.6328125 +374.1980286 240148.9375 +374.6990051 88531.46875 +377.6847839 18261.869140625 +378.1841431 4990.4458007813 +384.2341614 28763.40234375 +386.6903687 14500.7939453125 +398.2019958 16223.544921875 +416.7427673 8074.5288085938 +423.2320251 4371.8520507813 +425.1813965 4210.1938476563 +430.7402344 27642.935546875 +431.2440491 13417.583984375 +442.2075195 7980.6059570313 +442.2713928 4595.1391601563 +442.7108459 5553.3310546875 +448.2337952 8279.3447265625 +448.7311707 5624.8461914063 +451.2121582 8333.0185546875 +451.7119141 4570.4624023438 +457.7275391 17480.1015625 +459.2512817 48900.5546875 +459.7523804 29497.771484375 +460.2167053 5359.6381835938 +498.7574158 3551.4931640625 +499.2520752 4235.8666992188 +507.2600708 53245.89453125 +507.7609253 46670.12890625 +508.2612305 19332.828125 +516.2666626 4137.541015625 +516.7805176 58299.46875 +517.281189 36883.984375 +529.3075562 16754.47265625 +556.2666626 3977.314453125 +582.3347168 7930.2817382813 +599.2963867 5640.9077148438 +610.3297729 130150.6640625 +611.3359375 27716.517578125 +617.3026733 19406.369140625 +618.3014526 5174.8359375 +626.3168335 4723.9135742188 +635.3135986 17860.3515625 +636.3198853 4314.6948242188 +643.3532715 23298.431640625 +644.3613892 4250.1220703125 +667.2992554 8192.587890625 +685.3235474 3758.7578125 +719.3981934 13301.7373046875 +720.395752 4378.724609375 +729.3352051 7709.2412109375 +747.3901367 84267.8828125 +748.3964233 29535.37109375 +754.3642578 5714.333984375 +755.3690186 3943.5083007813 +764.3662109 6421.2250976563 +772.3707886 3762.69140625 +789.3843384 4607.880859375 +791.3812256 3588.5078125 +798.3960571 6360.8334960938 +806.4115601 30085.07421875 +832.4921875 4568.6284179688 +833.508728 4909.1865234375 +860.4714355 13005.275390625 +895.4536743 16561.779296875 +896.4584961 4322.0971679688 +END IONS diff -r 528bcf03e561 -r 5b5a9f59e2c7 test-data/novel_peptides --- a/test-data/novel_peptides Fri Jul 17 17:05:41 2020 -0400 +++ b/test-data/novel_peptides Mon Mar 15 12:52:03 2021 +0000 @@ -1,3 +1,6 @@ DSGASGSILEASAAR ELGSSDLTAR SPYREFTDHLVK +RQVPEHLGP +RPGPGTRKSL +MTDRHAGTY diff -r 528bcf03e561 -r 5b5a9f59e2c7 test-data/pFind.qry.res --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pFind.qry.res Mon Mar 15 12:52:03 2021 +0000 @@ -0,0 +1,32 @@ +S 1148.575077 3 +controllerType=0 controllerNumber=1 scan=19846 +1 FACNGTGGIIVP 1148.576804 3.554176 0.977448 0.268814 0 0 1 0 1 11340;1979;S;V 0 -0.001047 0.000000 5.000000 0.145238 1.000000 18 0 0 0 1344 0 0 0 +2 TLMEQTLPVT 1148.586699 4.380692 0.986473 0.268814 1 3 Oxidation[M]#0 0 0 0 2 32727;102;F;V 93939;102;F;V 0 0.005119 1.000000 2.000000 0.157397 2.000000 109 0 0 0 384 0 0 0 +3 RSDALGGCLSL 1148.572781 3.598858 0.991751 0.268814 1 8 Carbamidomethyl[C]#0 0 1 0 1 5598;401;D;A 0 0.000261 1.000000 6.000000 0.087418 2.000000 1 0 0 0 800 0 0 0 +4 SETLSIVCPSI 1148.586698 4.274827 0.995714 0.268814 0 0 0 0 1 120267;1812;Q;I 0 0.000569 1.000000 4.000000 0.131591 2.000000 648 0 0 0 800 0 0 0 +5 RPSTASGSSVVT 1148.590536 3.900134 0.995843 0.268814 0 0 0 0 1 33405;1207;H;A 0 0.001153 1.000000 6.000000 0.155589 2.000000 3 0 0 0 1568 0 0 0 +6 FGQVAASTAPSL 1148.594562 3.942397 0.997807 0.268814 0 0 0 0 7 18779;1673;V;F 57765;21;V;F 68677;499;V;F 72305;1102;V;F 106433;450;V;F 118259;1661;V;F 149057;526;V;F 0 0.002566 1.000000 7.000000 0.115885 2.000000 1088 0 0 0 1600 0 0 0 +7 QDGPGFKSISL 1148.594562 3.621902 0.997928 0.268814 0 0 1 0 3 25722;229;V;R 46484;120;V;R 119316;229;V;R 0 0.002473 1.000000 6.000000 0.127843 2.000000 512 0 0 0 800 0 0 0 +S 1067.448778 2 +controllerType=0 controllerNumber=1 scan=19905 +1 VDQEGANSMT 1067.430933 3.505104 0.997174 0.444184 1 9 Oxidation[M]#0 0 0 0 3 20025;195;D;A 133965;196;D;A 138831;195;D;A 0 0.006154 1.000000 4.000000 0.098087 2.000000 1 0 0 0 408 0 0 0 +2 FYGNSISIS 1067.444476 3.014719 0.998504 0.444184 1 7 Phospho[S]#0 0 0 0 1 11805;412;S;A 0 0.006294 1.000000 3.000000 0.054075 2.000000 32 0 0 0 70 0 0 0 +3 KDPGMGAMGGM 1067.431801 3.263346 0.998586 0.444184 1 11 Oxidation[M]#0 0 0 0 1 23457;553;E;G 0 -0.000013 1.000000 5.000000 0.087146 2.000000 261 0 0 0 400 0 0 0 +4 FYGNSISIS 1067.444476 3.028426 0.998621 0.444184 1 9 Phospho[S]#0 0 0 0 1 11805;412;S;A 0 0.003416 1.000000 3.000000 0.032929 2.000000 160 0 0 0 134 0 0 0 +S 1142.501268 2 +controllerType=0 controllerNumber=1 scan=19907 +1 MQSSQSMSKL 1142.517968 3.710725 0.978768 0.276033 1 7 Oxidation[M]#0 0 0 0 1 33;841;I;T 0 -0.001474 0.000000 3.000000 0.145364 3.000000 0 0 0 0 302 0 0 0 +2 MQSSQSMSKL 1142.517968 1.886902 0.998416 0.276033 1 1 Oxidation[M]#0 0 0 0 1 33;841;I;T 0 0.003725 0.000000 6.000000 0.104444 1.000000 5 0 0 0 256 0 0 0 +3 DTITQKVEE 1142.497627 1.828102 0.999712 0.276033 1 4 Phospho[T]#0 0 0 0 5 6567;5813;S;I 65345;3767;S;I 73025;5704;S;I 100015;919;S;I 103069;3727;S;I 0 -0.011066 1.000000 5.000000 0.145552 1.000000 130 0 0 0 0 0 0 0 +S 928.482124 2 +controllerType=0 controllerNumber=1 scan=19946 +1 GPRLPGSSSA 928.484626 7.710279 0.421887 0.011383 0 0 0 0 1 26031;290;E;A 0 0.001328 1.000000 0.000000 0.207882 8.000000 510 0 0 0 488 0 0 0 +2 PLGRPGSSGT 928.484626 5.893959 0.818989 0.011383 0 0 1 0 4 23498;63;G;G 50106;66;G;G 69602;63;G;G 147656;118;G;G 0 0.002600 1.000000 1.000000 0.212426 5.000000 250 0 0 0 488 0 0 0 +3 IVNPGRDSA 928.484626 4.782812 0.975088 0.011383 0 0 0 0 8 8187;441;A;T 50181;441;A;T 50183;441;A;T 54737;441;A;T 61191;441;A;T 73135;441;A;T 85927;441;A;T 133089;441;A;T 0 0.000119 1.000000 3.000000 0.149306 3.000000 232 0 0 0 200 0 0 0 +4 PRLPGSSSA 928.484629 8.003373 0.979251 0.011383 1 0 Carbamidomethyl[AnyN-term]#0 0 0 0 1 26031;291;G;A 0 0.001326 1.000000 0.000000 0.207882 8.000000 255 0 0 0 244 0 0 0 +5 GAPLAAPFGGA 928.488651 4.541935 0.980862 0.011383 0 0 1 0 1 7256;3036;P;G 0 0.002595 1.000000 3.000000 0.134447 4.000000 582 0 0 0 960 0 0 0 +6 RKAPDPSGT 928.484626 3.961262 0.983572 0.011383 0 0 0 0 1 26911;595;S;G 0 0.003601 1.000000 3.000000 0.147253 3.000000 99 0 0 0 224 0 0 0 +7 RPVGASPSSA 928.484626 4.484990 0.987448 0.011383 0 0 1 0 1 680;164;A;Q 0 0.000146 1.000000 5.000000 0.155946 3.000000 449 0 0 0 448 0 0 0 +8 HLLFGPSSA 928.488651 4.685283 0.989669 0.011383 0 0 0 0 4 23883;190;Y;L 58837;221;Y;L 77055;191;Y;L 117305;220;Y;L 0 -0.003066 1.000000 4.000000 0.200977 3.000000 225 0 0 0 224 0 0 0 +9 QLQPKSSSA 928.473392 4.929118 0.990178 0.011383 1 0 Gln->pyro-Glu[AnyN-termQ]#0 0 0 0 2 6245;3970;I;G 136775;870;I;G 0 0.007494 1.000000 3.000000 0.156720 4.000000 240 0 0 0 240 0 0 0 +10 NAHISKTSA 928.484626 3.752999 0.992705 0.011383 0 0 1 0 6 25928;751;F;P 42420;742;F;P 47934;768;F;P 58152;692;F;P 101556;692;F;P 141526;759;F;P 0 -0.000622 1.000000 4.000000 0.126520 2.000000 193 0 0 0 208 0 0 0 diff -r 528bcf03e561 -r 5b5a9f59e2c7 test-data/test.tags --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.tags Mon Mar 15 12:52:03 2021 +0000 @@ -0,0 +1,3 @@ +controllerType=0 controllerNumber=1 scan=19846 FACNGTGGIIVP;TLMEQTLPVT;RSDALGGCLSL;SETLSIVCPSI;RPSTASGSSVVT;FGQVAASTAPSL;QDGPGFKSISL +controllerType=0 controllerNumber=1 scan=19905 VDQEGANSMT;FYGNSISIS;KDPGMGAMGGM;FYGNSISIS +controllerType=0 controllerNumber=1 scan=19907 MQSSQSMSKL;MQSSQSMSKL;DTITQKVEE