| Previous changeset 2:4e47a0fa9287 (2023-06-22) Next changeset 4:79818ce5a8bf (2024-02-22) |
|
Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a |
|
modified:
riassigner.xml |
|
added:
test-data/Alkanes_20210325.csv test-data/aplcms_aligned_peaks.csv test-data/results.csv |
| b |
| diff -r 4e47a0fa9287 -r 8c5e65adf694 riassigner.xml --- a/riassigner.xml Thu Jun 22 15:19:27 2023 +0000 +++ b/riassigner.xml Thu Oct 12 13:31:32 2023 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy2" profile="21.09"> +<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy4" profile="21.09"> <description>compute retention indices</description> <macros> <import>macros.xml</import> @@ -75,4 +75,8 @@ @HELP@ ]]> </help> + + <citations> + <citation type="doi">10.21105/joss.04337</citation> + </citations> </tool> |
| b |
| diff -r 4e47a0fa9287 -r 8c5e65adf694 test-data/Alkanes_20210325.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Alkanes_20210325.csv Thu Oct 12 13:31:32 2023 +0000 |
| b |
| @@ -0,0 +1,31 @@ +Compound_Name,Carbon_Number,RT +Undecane,11,124.8 +Dodecane,12,145.8 +Tridecane,13,165 +Tetradecane,14,184.8 +Pentadecane,15,204 +Hexadecane,16,222.6 +Heptadecane,17,245.4 +Octadecane,18,268.8 +Nonadecane,19,288 +Eicosane,20,307.2 +Uncosane,21,325.2 +Docosane,22,341.4 +Tricosane,23,359.4 +Tetracosane,24,377.4 +Pentacosane,25,393.6 +Hexacosane,26,408 +Heptacosane,27,420.6 +Octacosane,28,432 +Nonacosane,29,442.2 +Triacontane,30,453 +Untriacontane,31,463.2 +Dotriacontane,32,474.6 +Tritriacontane,33,487.2 +Tetrtriacontane,34,501 +Pentatriacontane,35,517.2 +Hexatricontane,36,535.2 +Heptatriacontane,37,556.2 +Octatriacontane,38,580.2 +Nonatriacontane,39,609 +Tetracontane,40,642.6 |
| b |
| diff -r 4e47a0fa9287 -r 8c5e65adf694 test-data/aplcms_aligned_peaks.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aplcms_aligned_peaks.csv Thu Oct 12 13:31:32 2023 +0000 |
| b |
| b'@@ -0,0 +1,3844 @@\n+,mz,rt,mz_min,mz_max,intensity.dataset_23283.dat,intensity.dataset_23284.dat,intensity.dataset_23285.dat,intensity.dataset_23286.dat,intensity.dataset_23287.dat,intensity.dataset_23288.dat,intensity.dataset_23289.dat,intensity.dataset_23290.dat,intensity.dataset_23291.dat,intensity.dataset_23292.dat,intensity.dataset_23293.dat,intensity.dataset_23294.dat,intensity.dataset_23295.dat,intensity.dataset_23296.dat,intensity.dataset_23297.dat,intensity.dataset_23298.dat,intensity.dataset_23299.dat,intensity.dataset_23300.dat,intensity.dataset_23301.dat,intensity.dataset_23302.dat,intensity.dataset_23303.dat,intensity.dataset_23304.dat,intensity.dataset_23305.dat,intensity.dataset_23306.dat,intensity.dataset_23307.dat,intensity.dataset_23308.dat,time.dataset_23283.dat,time.dataset_23284.dat,time.dataset_23285.dat,time.dataset_23286.dat,time.dataset_23287.dat,time.dataset_23288.dat,time.dataset_23289.dat,time.dataset_23290.dat,time.dataset_23291.dat,time.dataset_23292.dat,time.dataset_23293.dat,time.dataset_23294.dat,time.dataset_23295.dat,time.dataset_23296.dat,time.dataset_23297.dat,time.dataset_23298.dat,time.dataset_23299.dat,time.dataset_23300.dat,time.dataset_23301.dat,time.dataset_23302.dat,time.dataset_23303.dat,time.dataset_23304.dat,time.dataset_23305.dat,time.dataset_23306.dat,time.dataset_23307.dat,time.dataset_23308.dat\n+0,100.00745893371973,150.8464679272933,100.00735567072928,100.0076216379324,0.0,0.0,0.0,0.0,343727.1821962064,1190536.8233104984,0.0,583751.5160698479,0.0,0.0,0.0,0.0,0.0,0.0,0.0,344070.99328295107,1235766.0989206864,0.0,0.0,0.0,1386250.730736992,302723.34407143085,0.0,0.0,0.0,0.0,,,,,149.79663744165728,152.85886804073365,,152.08111089155872,,,,,,,,160.61341924128226,149.51726998686647,,,,151.21712108386745,130.07389749109836,,,,\n+1,100.01554827903911,240.61628599549996,100.01541629015878,100.01567718306735,0.0,0.0,0.0,0.0,0.0,706286.7339961977,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,5113054.199441888,0.0,0.0,0.0,0.0,246053.399905149,0.0,0.0,0.0,0.0,,,,,,211.5819214590982,,,,,,,,,,,285.33934807712035,,,,,180.20452636866096,,,,\n+2,100.03933181643292,164.93401089576156,100.03930056665979,100.039571954246,0.0,0.0,0.0,0.0,1014222.2638757358,1000440.7691426005,0.0,123670.32256446578,195153.73453303738,0.0,0.0,0.0,0.0,0.0,0.0,1344128.502448579,433607.05931785295,0.0,0.0,0.0,428627.37262419506,1331546.0116389373,0.0,0.0,0.0,0.0,,,,,146.17649076035352,202.46453853007532,,150.910109664791,154.97400419466447,,,,,,,158.60737095475594,177.29606351633862,,,,177.1313269036101,146.14341245441983,,,,\n+3,100.04738519978878,203.52466558949374,100.04734238158571,100.04764962252936,322644.88554933376,268778.8613923998,213753.6183592096,336891.728304994,5813000.819404766,3274751.0190586047,460819.84557681164,2197523.7344056605,3257375.74232179,383470.66100774385,345856.53193509544,318251.96724663663,377187.54249823553,366450.60474631866,460787.02786689583,6610334.439601819,3508484.0377538535,567191.0583320381,331316.60261793085,513827.3793023971,4007399.3894778895,5835386.507655533,442563.8750421949,476708.5075964048,476404.83513589343,540480.8256741092,185.69374355978255,193.8851995676775,186.8909182218055,182.66354765323095,218.64111985310822,202.6329822395296,189.9534176594962,230.00709074746962,249.02569783866932,177.79659229010957,173.1962612753376,175.10597844094386,175.87250604762727,173.02617298288163,174.60027538643007,314.30621958557884,187.89536507501032,175.82287781616472,174.4964563323785,170.1026918470606,214.68507160875373,304.7848879617386,183.4111778298676,176.6742918115503,171.70214402935198,173.92504712698107\n+4,100.05192737202083,378.874546561913,100.05165900931391,100.05199489207028,3036304.3852898898,3290495.542546281,3029574.7237072503,7027558.595532235,100366491.25350536,34274438.76548687,7776901.350912492,8554664.495363595,51833625.988015346,7991666.965216131,4125401.424539689,2250034.769434525,1718367.745571977,4492170.4747321205,18056775.759979792,105914134.08671731,21414694.968'..b'6782362,,445.3581908193953,,,,606.0066238984979,161.760306444314,163.71207616612895,,,554.4492943797621,238.74176794918034,208.25030658594872,,,,554.0409899800429\n+3839,99.07606329121175,456.47832848607703,99.07580010817104,99.07620872555974,538225.7109273394,492864.10643724154,537789.4551108466,7464554.093965235,101710082.23899822,46779794.061436124,5074104.1153983,9791865.108230101,52374681.10770606,7923955.492344107,3028775.0312884673,1781782.6162001614,2346367.0212637335,1902939.0657454103,21511368.85222672,115765209.36244734,28776871.93050168,2836075.207137374,3742060.918972687,11432967.29468203,45477232.57296493,109468210.60724396,835142.07094789,3091337.867397372,4510272.6216480015,12891168.649497904,192.39288550344895,183.62111777998038,193.67698204834488,503.0281070634392,483.62062235045084,491.48058860872817,517.6236539484887,418.38457846043593,483.7052052824214,535.167823220549,514.6305894468724,482.53787575123243,318.14869770769127,297.68200041216363,536.8562336578553,529.4611787828466,516.9944410772723,620.0728669053556,547.1675699306842,499.90635026567355,493.444488226441,468.45985181241394,382.4121745132595,539.9576442004043,515.4638031343356,504.966933602456\n+3840,99.08056739919397,532.9782992243934,99.0803726615214,99.08064971765278,0.0,0.0,0.0,39054457.93050379,103471393.43388967,128961189.32907483,8482721.906002827,29863488.755565464,60864601.994179524,28780010.616306458,2938068.9943430503,0.0,0.0,0.0,44493274.08770076,151782399.15886715,70504467.49865471,0.0,3651726.407702397,48407750.76992002,77287541.67400235,101247776.40030646,0.0,0.0,4408142.55481681,49593636.12893212,,,,597.8924762533137,529.1027568240761,518.3225631262479,497.63167828535893,454.3202566911999,515.9885151171484,587.7104307193763,473.4172199917479,,,,517.5781666957765,497.02713325302113,534.4829624441827,,554.2519948891664,488.75967682794357,586.7631242193713,525.2092574315548,,,548.904178075678,582.5825719901595\n+3841,99.11236482763735,165.43921308450473,99.11232308702678,99.11261668830147,514728.2348741879,759959.417355987,542858.0879739128,435864.43741913245,553172.1384020299,461856.59535662015,737029.5884742055,393809.6612605471,427799.9487440314,714654.6469534417,679050.050953298,592336.0270316459,543100.4111342217,579620.1192761657,710230.5340571136,397306.10898318526,422744.0971923534,611297.5300363423,777737.3166927565,701218.3657212163,561811.0182356834,535904.1660740478,739645.3964949858,709816.4523091213,506948.37125092436,947600.4477664935,187.54663484678667,173.52860341704607,188.8898839462118,163.15760207871057,140.26589392139266,146.10492803584276,171.9491144793201,146.2312458159697,148.46653586261053,167.62558510643518,169.6998141370289,169.14090023092007,153.75818279088742,165.93339955820724,165.6284035943987,147.1333049487116,168.0289322727685,158.68357830661125,168.5935367119472,169.31000511423397,143.76694073406753,123.30914820092423,173.90819975357854,169.41398184273893,208.3640083701994,166.76009459388754\n+3842,99.11685288466634,436.9686084640473,99.1167860421713,99.1169370307429,8702167.918399934,6540425.102141567,6321631.77686023,100933001.16464725,895750254.632205,1541176575.7419136,27062615.175575197,778325018.9733388,462241584.46593845,28759198.58311829,11064134.68059317,6019268.029023882,5803775.228034632,4994108.225936754,81026673.40968122,887881447.5139393,1451820317.6599944,12590402.377886878,13511583.026233023,54307674.81548672,1532872589.9636302,889853144.365722,7164408.7342861425,17979055.60801024,21226258.68546369,61546272.514614604,175.82831388288702,229.9215059724905,238.31534303766486,412.417780022125,424.39180544204453,417.0984121223902,536.7629297800115,421.2988896601585,434.04340350233804,510.01873030697163,494.1620900564951,307.3176555900867,300.16146053477644,311.25369305695364,556.1778555414872,431.8785784505268,418.8438326453146,543.7533243279508,496.54780631396045,502.1948162678692,416.27957925048713,424.22982907679625,465.19502762155184,299.3382197642626,529.8820661347211,528.0058375360394\n' |
| b |
| diff -r 4e47a0fa9287 -r 8c5e65adf694 test-data/results.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results.csv Thu Oct 12 13:31:32 2023 +0000 |
| b |
| b'@@ -0,0 +1,3844 @@\n+Unnamed: 0,mz,rt,retention_index,mz_min,mz_max,intensity.dataset_23283.dat,intensity.dataset_23284.dat,intensity.dataset_23285.dat,intensity.dataset_23286.dat,intensity.dataset_23287.dat,intensity.dataset_23288.dat,intensity.dataset_23289.dat,intensity.dataset_23290.dat,intensity.dataset_23291.dat,intensity.dataset_23292.dat,intensity.dataset_23293.dat,intensity.dataset_23294.dat,intensity.dataset_23295.dat,intensity.dataset_23296.dat,intensity.dataset_23297.dat,intensity.dataset_23298.dat,intensity.dataset_23299.dat,intensity.dataset_23300.dat,intensity.dataset_23301.dat,intensity.dataset_23302.dat,intensity.dataset_23303.dat,intensity.dataset_23304.dat,intensity.dataset_23305.dat,intensity.dataset_23306.dat,intensity.dataset_23307.dat,intensity.dataset_23308.dat,time.dataset_23283.dat,time.dataset_23284.dat,time.dataset_23285.dat,time.dataset_23286.dat,time.dataset_23287.dat,time.dataset_23288.dat,time.dataset_23289.dat,time.dataset_23290.dat,time.dataset_23291.dat,time.dataset_23292.dat,time.dataset_23293.dat,time.dataset_23294.dat,time.dataset_23295.dat,time.dataset_23296.dat,time.dataset_23297.dat,time.dataset_23298.dat,time.dataset_23299.dat,time.dataset_23300.dat,time.dataset_23301.dat,time.dataset_23302.dat,time.dataset_23303.dat,time.dataset_23304.dat,time.dataset_23305.dat,time.dataset_23306.dat,time.dataset_23307.dat,time.dataset_23308.dat\n+3835,99.03162030799956,142.67379366183633,1185.1133031516015,99.03161686937968,99.03162445630808,0.0,0.0,0.0,0.0,1124023.5414198886,0.0,0.0,0.0,302811.79369835946,0.0,0.0,0.0,0.0,0.0,0.0,689466.2692573667,0.0,0.0,0.0,0.0,0.0,1185293.3404002658,0.0,0.0,0.0,0.0,,,,,140.7677080635659,,,,148.14892015326652,,,,,,,160.31743543051294,,,,,,121.461111,,,,\n+798,169.0314087180851,143.0311614429152,1186.8150544900723,169.03127206136165,169.0316819389772,0.0,0.0,0.0,0.0,305244.92965288245,0.0,0.0,12538844.289546728,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,668804.8639133602,0.0,0.0,0.0,0.0,,,,,148.17622517287128,,,151.30544042838676,,,,,,,,,,,,,,129.6118187274875,,,,\n+78,109.00492907059838,143.68682488560978,1189.9372613600465,109.00492721060658,109.0049302044596,0.0,0.0,0.0,0.0,387414.4182122475,463239.19886551664,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,462236.3507863071,0.0,0.0,0.0,492413.733649669,399820.6922610059,0.0,0.0,0.0,0.0,,,,,143.77939636976086,149.54889043214672,,,,,,,,,,,148.41804574766948,,,,148.6747370599136,128.0130548185582,,,,\n+629,155.0466908284799,144.1940338735765,1192.352542255126,155.0465960159991,155.04680960708157,0.0,0.0,0.0,0.0,481903.4259434357,703533.909202827,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,553038.2457900472,612054.5412496057,0.0,0.0,0.0,652745.3943256153,479513.4813412025,0.0,0.0,0.0,0.0,,,,,144.1783529211089,148.97702498912713,,,,,,,,,,149.51183575898546,148.1880205624459,,,,146.98702981137984,127.3219391984118,,,,\n+1229,206.90526899749815,146.9760009755798,1206.1250050811448,206.90526103874345,206.9052832278356,0.0,0.0,0.0,0.0,0.0,0.0,0.0,894992.1586137018,1342804.5796392127,0.0,0.0,0.0,0.0,747303.2873156482,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,,,,,,,,144.19461709026095,146.33083681853836,,,,,150.40254901794015,,,,,,,,,,,,\n+3677,81.98144188683492,147.9671441305876,1211.287209013477,81.98144088848625,81.98144279113436,0.0,0.0,0.0,0.0,0.0,253699.015608638,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,259894.1644246692,0.0,0.0,0.0,268279.0812923885,0.0,0.0,0.0,0.0,0.0,,,,,,149.697389482583,,,,,,,,,,,144.65752139764447,,,,149.54652151153533,,,,,\n+1039,191.055454152838,148.47415300759937,1213.9278802479134,191.0554484145863,191.05545859198415,0.0,0.0,0.0,0.0,0.0,0.0,0.0,209251.29726182952,418432.1085526457,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,228432.31184552168,0.0,0.0,0.0,0.0,,,,,,,,154.77102987211398,156.91670777392326,,,,,,,,,,,,,133.73472137676086,,,,\n+543,148.9176308667527,148.68550079771873,1215.0286499881183,148.91738994562775,148.91786336584133,0.0,0.0,0.0,0.0,0.0,0.0,0.0,798691.4557159346,1358627.69767623'..b'.232681805,0.0,0.0,0.0,2181156.8931490085,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,486280.521442894,0.0,,,,650.0371016972144,,,648.3319531465992,,,,651.5748135466148,,,,,,,,,,,,,,648.0470619489781,\n+3195,463.0888849434387,650.8246263935703,4024.4780547427686,463.0888764290204,463.0888945646882,1665462.8852622574,0.0,0.0,0.0,0.0,0.0,2787506.42967796,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,2677063.55348658,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,652.4599330780792,,,,,,647.0007109717561,,,,,,,,,,,653.0132351308756,,,,,,,,\n+3388,534.5386455716197,652.19595514262,4028.559390305417,534.5382526354327,534.5388980107543,0.0,0.0,0.0,0.0,4567710.582079917,0.0,0.0,0.0,2666460.1068839496,0.0,0.0,0.0,0.0,0.0,0.0,6533670.165672642,0.0,0.0,0.0,0.0,0.0,6534724.505807184,0.0,0.0,0.0,0.0,,,,,645.9043301620057,,,,643.7420165723186,,,,,,,645.839778264491,,,,,,670.1518830813577,,,,\n+2630,357.29091613592834,652.2606060387114,4028.7518036866413,357.2909119303794,357.2909183392246,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1005034.9780591392,1234940.905759689,0.0,0.0,0.0,0.0,1059344.8341987878,0.0,0.0,0.0,0.0,,,,,,,,,,,,,,,,656.7700626749433,611.741375270128,,,,,688.270380171063,,,,\n+3476,573.0877453536401,653.0143831885092,4030.9951880610392,573.0877328023662,573.0877750716893,0.0,0.0,0.0,0.0,3205105.0784855485,0.0,0.0,0.0,1296461.0518279276,0.0,0.0,0.0,0.0,0.0,0.0,3534226.3136434774,0.0,0.0,0.0,0.0,0.0,3404611.365840343,0.0,0.0,0.0,0.0,,,,,644.5789286397387,,,,645.1288080258456,,,,,,,648.6236620189509,,,,,,673.7261340695015,,,,\n+2430,329.3045018130326,655.2004045800634,4037.5012041073314,329.3044928529303,329.3045128559214,0.0,0.0,0.0,0.0,2337898.389705523,0.0,0.0,0.0,856847.8907710246,0.0,0.0,0.0,0.0,0.0,0.0,2223961.718494521,638425.7424802145,0.0,0.0,0.0,0.0,2175951.802131959,0.0,0.0,0.0,0.0,,,,,647.1489450707796,,,,647.8622593854034,,,,,,,651.4770292549206,652.7141605856102,,,,,676.7996286036033,,,,\n+3477,574.094263583205,655.7494385959299,4039.1352339164578,574.0942567867738,574.0942735957009,0.0,0.0,0.0,0.0,2410328.573559394,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,2423864.091818226,0.0,0.0,0.0,0.0,0.0,2250526.276622361,0.0,0.0,0.0,0.0,,,,,644.9260366233736,,,,,,,,,,,648.4462226416501,,,,,,673.8760565227657,,,,\n+1011,188.09994324748567,660.8186642962881,4054.222215167524,188.09994026414608,188.09994519760832,0.0,0.0,0.0,0.0,0.0,671102.3017674579,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,739490.7703412201,658299.6231906784,0.0,0.0,0.0,915828.7659944702,0.0,0.0,0.0,0.0,0.0,,,,,,660.8239220413193,,,,,,,,,,660.2041943996575,661.0372599343855,,,,661.2092808097904,,,,,\n+3426,549.1624860526152,661.5098365908839,4056.2792755681066,549.1623240045401,549.162739861546,0.0,0.0,0.0,0.0,0.0,0.0,8256775.858559255,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,9367209.764957776,0.0,0.0,22546661.004421216,0.0,0.0,0.0,0.0,,,,,,,647.3170124513354,,,,,,,,,,,,647.7370773213164,,,689.47542,,,,\n+1759,256.1307926180016,663.4429458256153,4062.0325768619505,256.1306622019853,256.1310028841874,0.0,0.0,0.0,0.0,1480892.5836203618,1637872.2095444708,0.0,548621.0944454535,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1628498.975773744,1133986.5420280446,0.0,0.0,0.0,1641552.9159746228,1291983.0444011367,0.0,0.0,0.0,0.0,,,,,657.4350761055546,661.5487529418958,,655.7079610596141,,,,,,,,660.6605361068878,659.7968593870798,,,,661.7847760673579,687.1666591109171,,,,\n+675,159.06075304118465,668.0630689658807,4075.782943350835,159.06040305085887,159.06092858172207,0.0,0.0,0.0,0.0,2871204.4688100237,0.0,0.0,0.0,2102848.868974304,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,767276.9717977985,0.0,0.0,0.0,0.0,,,,,657.7464647659501,,,,657.371422131692,,,,,,,,,,,,,689.07132,,,,\n+1293,212.1045024440408,669.7505895768605,4080.8053261216087,212.1045007003065,212.10450434038157,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,745350.9671837527,0.0,0.0,0.0,687390.8061591205,859509.7942086764,0.0,0.0,0.0,0.0,,,,,,,,,,,,,,,,,660.641822804564,,,,660.8595039238884,687.7504420021291,,,,\n' |