| Previous changeset 4:79818ce5a8bf (2024-02-22) Next changeset 6:af25aa61c611 (2024-05-07) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit 4b8a43b863ff8a0ff1d5a08e516068853adf358d |
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modified:
riassigner.xml |
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added:
test-data/nist_to_ri_2mols_output.tsv test-data/results.tsv |
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removed:
test-data/nist_to_ri_2mols_output.csv test-data/results.csv |
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| diff -r 79818ce5a8bf -r 4abc4359b978 riassigner.xml --- a/riassigner.xml Thu Feb 22 10:40:24 2024 +0000 +++ b/riassigner.xml Tue Apr 16 11:30:33 2024 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy4" profile="21.09"> +<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy5" profile="21.09"> <description>compute retention indices</description> <macros> <import>macros.xml</import> @@ -14,8 +14,8 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ - python -m RIAssigner --reference "$reference_section.reference" "$reference_section.reference.ext" "$reference_section.reference_rt_units" --query "$query_section.query" "$query_section.query.ext" "$query_section.query_rt_units" --method "$method" --output "output.${query_section.query.ext}" && - cp -r 'output.${query_section.query.ext}' '${output}' + python -m RIAssigner --reference "$reference_section.reference" "$reference_section.reference.ext" "$reference_section.reference_rt_units" --query "$query_section.query" "$query_section.query.ext" "$query_section.query_rt_units" --method "$method" --output "output.${output.ext}" && + cp -r 'output.${output.ext}' '${output}' ]]> </command> @@ -55,8 +55,12 @@ </inputs> <outputs> - <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query" - metadata_source="query"/> + <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format="tsv" + metadata_source="query"> + <change_format> + <when input="query_section.query.ext" value="msp" format="msp" /> + </change_format> + </data> </outputs> <tests> @@ -66,7 +70,7 @@ <param name="reference" value="Alkanes_20210325.csv" ftype="csv"/> <param name="reference_rt_units" value="seconds"/> <param name="method" value="kovats"/> - <output name="output" file="results.csv" ftype="csv"/> + <output name="output" file="results.tsv" ftype="tsv"/> </test> </tests> |
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| diff -r 79818ce5a8bf -r 4abc4359b978 test-data/nist_to_ri_2mols_output.csv --- a/test-data/nist_to_ri_2mols_output.csv Thu Feb 22 10:40:24 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -casno,num_peaks,compound_name,retention_index,formula,id,comment,inchi,smiles,nominal_mass,unnamed: 10 -7732185,5,Water,317.0,H2O,9,"SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67",InChI=1S/H2O/h1H2,O,18, -67561,16,Methyl Alcohol,354.0,CH4O,32,"SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806","InChI=1S/CH4O/c1-2/h2H,1H3",CO,32, |
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| diff -r 79818ce5a8bf -r 4abc4359b978 test-data/nist_to_ri_2mols_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nist_to_ri_2mols_output.tsv Tue Apr 16 11:30:33 2024 +0000 |
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| @@ -0,0 +1,3 @@ +casno num_peaks compound_name retention_index formula id comment inchi smiles nominal_mass unnamed: 10 +7732185 5 Water 317.0 H2O 9 SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67 InChI=1S/H2O/h1H2 O 18 +67561 16 Methyl Alcohol 354.0 CH4O 32 SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806 InChI=1S/CH4O/c1-2/h2H,1H3 CO 32 |
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| diff -r 79818ce5a8bf -r 4abc4359b978 test-data/results.csv --- a/test-data/results.csv Thu Feb 22 10:40:24 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,139 +0,0 @@\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-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-0,100.00745893371972,150.8464679272933,1226.2836871213192,100.00735567072928,100.0076216379324,0.0,0.0,0.0,0.0,343727.1821962064,1190536.8233104984,0.0,583751.5160698479,0.0,0.0,0.0,0.0,0.0,0.0,0.0,344070.99328295107,1235766.0989206864,0.0,0.0,0.0,1386250.730736992,302723.34407143085,0.0,0.0,0.0,0.0,,,,,149.79663744165728,152.85886804073365,,152.08111089155872,,,,,,,,160.61341924128226,149.51726998686647,,,,151.21712108386745,130.07389749109836,,,,\n-19,102.00457480699318,152.71810107630537,1236.0317764390904,102.00457437738012,102.00457545359384,0.0,0.0,0.0,0.0,0.0,401776.5410071658,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,405551.0191800205,0.0,0.0,0.0,483600.4138013043,0.0,0.0,0.0,0.0,0.0,,,,,,153.75213685855582,,,,,,,,,,,151.52351426303477,,,,152.87865210732542,,,,,\n-17,101.09168025140154,153.0891462648851,1237.9643034629432,101.09166621605507,101.09169498689182,2243772.00898847,2245442.805897871,2202837.759411076,2400412.347176022,2328623.48943265,2172980.8252230017,2303641.624591576,1883073.1640696805,2326876.3560613613,2319161.9913469306,2195992.851287496,2051403.435804971,2087888.1702773408,2147256.4225186,2236065.5599120394,1803952.417306124,1837840.0561802448,2464608.236924318,2287740.0949162217,2402185.340292664,2247200.670206981,2170378.8875550795,2489012.4802597985,2246595.00367897,2414966.263956461,2674111.172234478,177.193933635369,160.40776578227548,161.510268582435,159.52741368102852,140.26589392139266,143.88984092982076,155.5549779397553,143.73741924037088,145.6465368875498,155.05865618861412,152.05379099265411,156.5215268354318,154.16942936489684,149.9130432928564,153.06243670806356,144.47582960972943,142.25440940177367,158.66227281250974,156.7969410779646,154.13641197726767,142.65505757945357,121.0780825641391,160.67819591700527,154.8544928523361,154.44435148607258,157.66403625576288\n-130,114.04245791237447,163.90869300550122,1294.3161094036523,114.04245611859233,114.0424591228148,0.0,0.0,0.0,0.0,342186.4331953138,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,219711.3634527797,0.0,0.0,0.0,0.0,0.0,243816.3758712958,0.0,0.0,0.0,0.0,,,,,163.46392905347628,,,,,,,,,,,173.97267054671062,,,,,,154.2894794163168,,,,\n-2,100.03933181643292,164.93401089576156,1299.6563067487582,100.'..b'65,3132586.893793458,18615445.518081523,8779519.892811857,7821265.817516655,7318231.363423373,17052944.124547847,17705601.12003027,7381842.8791467855,7507751.434472027,5614165.229928601,5083043.448356966,6014819.599957343,7677652.840119992,9525720.204986677,13124010.32727464,4449216.396456121,5084409.041402683,7068918.492463864,8903492.552417388,11129457.16284126,3586726.5429585357,4683877.06537885,4789317.530727295,16848200.39817579,572.9208755811804,561.9264538296106,560.313697648783,569.0451336253075,597.0486469160259,618.5960499003095,599.966720224376,570.3598693954336,572.5640600858902,590.4551444599642,604.5271558220973,645.9576586722352,562.272401541715,566.2111552350638,563.4756712415398,616.8285067769766,572.7797532655906,584.8243251027727,615.7734815974779,562.1740268915122,615.953211382121,612.4507135732015,565.617486815423,562.3080599992253,563.3539465984826,577.1104493740121\n-60,107.03121146809325,588.7951918374481,3829.8444161022503,107.03114828040049,107.0314693172737,3592694.359616667,3201839.723883349,2809483.466349844,7287076.472859506,4076969.0803328967,7029899.495354267,5500270.238107461,6221697.554288604,5264593.750631485,5876275.365380479,4361444.671168931,3492300.122580127,3078916.644584559,2818982.6561914533,8235956.393522463,2054051.5464090493,6771656.745539739,4207910.655709444,4740197.27889004,7238621.646492192,6531166.712362954,2297608.5779429786,3470734.405118296,4692098.998246031,5055681.060515234,7979671.029318698,580.1309338282904,577.0280485482859,566.8875065854336,577.7988873733879,598.310680692563,625.1203075772064,592.5549795547977,614.2600710330929,613.2059897472199,579.3151796178922,582.7154652052899,574.844897867262,573.7293081051322,569.814345243441,609.1529630112135,643.5599998779851,616.9141435428556,587.0352742747373,594.9653236312654,581.4812506628166,618.241520867545,665.9466049948514,558.016476476157,564.8777455795679,584.717887909236,557.8997683708424\n-25,102.96661658005064,589.4677348297056,3832.1796348253665,102.96647017471294,102.96689769936218,4390103.463842012,4297462.349741759,3666496.691904214,6109458.33845109,24699822.497650385,21883678.585728675,8321212.074083056,27084446.364938512,39891388.04324441,8450354.113045298,8961273.900970176,7597127.2100914335,6131056.216352236,10496145.104503464,9867530.033086907,23079398.081929285,24082512.297955677,4552467.976478131,5210666.404323116,6757120.128719496,24164153.01004557,24599594.38737598,3849090.457527556,4522132.278562568,4680511.068344637,7171169.435551958,570.5577266885095,559.630687847809,610.9860152440048,593.847919251615,568.3530419120924,583.1954203251123,604.9460474055132,618.0936306620558,640.5081095224386,614.8754014139106,600.9438265583838,561.4322206699607,568.7322619534058,630.7576354463617,601.6891512389441,598.424661621581,609.097793329469,600.8466770552002,600.4834858917224,595.934367349452,610.8096099041106,583.0502354694186,560.4224870025323,583.8368911394255,591.7464181271113,578.1189738872687\n-47,105.0654967035496,597.071228690364,3858.580655174875,105.06544015836654,105.06582254184346,5890430.979752225,5264847.276383639,5380791.188066957,5354329.935690502,4400302.753252647,8473726.514058117,6692693.523824933,13247555.018905131,11265651.753295217,6877125.93417878,6766538.824502002,6575361.3145988425,5567743.973156313,6155754.966110237,7484333.711424559,5229336.955787514,12227057.591904985,6639941.720103377,7243488.961927972,7598904.729928684,9260373.02863242,5202574.599313867,6694747.816617744,4849764.183904009,7144883.916904502,8720928.225414202,634.5363928550748,593.6242807976413,650.9087373103761,558.4780831137844,626.6068290705708,631.2271561531859,571.2878155314747,592.6180526626691,613.4857740346071,619.8891274044084,606.5431263781306,558.8066755698802,582.7700076782212,649.4284635943173,610.5636277377373,638.7233651937364,618.7913869634958,561.9085470732589,573.3456225254384,594.4751922242256,635.8339811173981,661.7062221006969,570.2211862433658,657.5180134546628,571.5197555432308,610.4378977103438\n' 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| diff -r 79818ce5a8bf -r 4abc4359b978 test-data/results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results.tsv Tue Apr 16 11:30:33 2024 +0000 |
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| b'@@ -0,0 +1,139 @@\n+unnamed: 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