Repository 'riassigner'
hg clone https://toolshed.g2.bx.psu.edu/repos/recetox/riassigner

Changeset 4:79818ce5a8bf (2024-02-22)
Previous changeset 3:8c5e65adf694 (2023-10-12) Next changeset 5:4abc4359b978 (2024-04-16)
Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit de7fd0986bce8d42bc7e63f9e4caf3c23862e497
modified:
macros.xml
test-data/aplcms_aligned_peaks.csv
test-data/results.csv
added:
test-data/nist_ei_ms_2mols_input.msp
test-data/nist_ei_ms_2mols_output.msp
test-data/nist_to_ri_2mols_input.csv
test-data/nist_to_ri_2mols_output.csv
b
diff -r 8c5e65adf694 -r 79818ce5a8bf macros.xml
--- a/macros.xml Thu Oct 12 13:31:32 2023 +0000
+++ b/macros.xml Thu Feb 22 10:40:24 2024 +0000
[
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.3.4</token>
+    <token name="@TOOL_VERSION@">0.4.0</token>
     <xml name="creator">
         <creator>
             <person
@@ -7,13 +7,18 @@
                 familyName="Hecht"
                 url="https://github.com/hechth"
                 identifier="0000-0001-6744-996X" />
+            <person
+                givenName="Wudmir"
+                familyName="Rojas"
+                url="https://github.com/wverastegui"
+                identifier="0000-0001-7036-9987" />
             <organization
                 url="https://www.recetox.muni.cz/"
                 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
                 name="RECETOX MUNI" />
         </creator>
     </xml>
-

     <token name="@HELP@">
         <![CDATA[
         RIAssigner can be used to read data from .msp, .csv and .tsv files using matchms and pandas and to compute the
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diff -r 8c5e65adf694 -r 79818ce5a8bf test-data/aplcms_aligned_peaks.csv
--- a/test-data/aplcms_aligned_peaks.csv Thu Oct 12 13:31:32 2023 +0000
+++ b/test-data/aplcms_aligned_peaks.csv Thu Feb 22 10:40:24 2024 +0000
b
b'@@ -137,3708 +137,3 @@\n 135,114.09144293859883,265.60351157826926,114.0911760766588,114.09158792525542,129027.76903427429,130619.98638380914,0.0,0.0,11530279.096086023,16980186.872445803,276795.3684628808,8491063.887341969,5861799.424869677,0.0,150156.66803051005,0.0,0.0,0.0,0.0,14725387.19836813,14811930.666669158,199175.8040038576,0.0,214934.86125822476,13946613.278805176,9188826.516077751,0.0,304383.0494282061,0.0,161024.4543312735,202.21916459891202,200.6985721312973,,,384.59325963380905,274.43916724968096,197.54446497787208,273.0142969007856,382.5385670136834,,192.67733092146648,,,,,369.7602913693222,297.0592993019821,197.41021220908036,,192.2807977328864,188.19297870413723,262.5392638451808,,196.08428245990413,,195.67528582359628\n 136,114.09944253761691,200.47961357948955,114.09933363233942,114.09972773253178,14808795.40568619,13886728.76025565,13341187.090367349,5485303.532407128,12943123.102444654,20422349.930797063,15312720.36236665,17337225.101026427,11714187.098007612,15175049.829150911,16903155.481412828,15357501.064697113,9537116.131320074,6481419.879089968,16931713.73834524,20872708.47199452,11614763.53543789,17196203.837594435,16101100.215647385,4864831.987739311,22327893.02683804,19237542.489511136,15968016.961772969,14784530.938506646,5586276.379468718,15453334.620554592,233.9306579513754,188.68589348735216,165.5063483655187,157.43741555389985,220.2138144038685,197.96033252588245,221.12160996710838,190.37599302896007,221.43921321874967,157.67208080656218,211.37613702558346,219.65532076808893,154.66900788226286,149.30192653322493,182.24448888967763,189.72435438141142,219.99766139270392,229.34406878645146,219.52650299542262,152.88456690323528,192.8635698475792,208.44547397117458,225.82642488189506,234.10120660984484,153.28384607950653,220.3766871853425\n 137,114.10395997068004,561.9674320429314,114.1039320362002,114.10426180703531,0.0,0.0,0.0,0.0,0.0,7339151.616426367,452899.15536075423,0.0,2904922.3975132303,2624885.953505421,0.0,0.0,0.0,0.0,9010735.421077048,7871933.021147243,0.0,0.0,0.0,733574.0727629781,6019974.448970871,7443686.11028591,0.0,0.0,0.0,750520.6198502594,,,,,,636.2628383179406,450.43851343994913,,619.9211442319021,512.1811050690386,,,,,549.847245597565,625.7595828639008,,,,452.2630173175957,638.0944956316572,649.9286783853316,,,,455.4708355830752\n-138,114.13597952981634,424.0730786705588,114.1356724767337,114.13600731441092,0.0,0.0,0.0,3412573.315883216,52376767.72694673,42720083.61726981,0.0,40238451.145565055,24423428.788158454,248284.92360648373,0.0,0.0,0.0,0.0,1206437.6960909972,51313966.33485706,40968621.29495897,0.0,0.0,493554.27489507664,40073015.74391687,51396255.73910617,0.0,618034.5455745418,0.0,792582.8467146866,,,,416.6096053981309,403.6653321361223,409.10412597844015,,407.36983049548166,411.15200467547646,441.3128400754634,,,,,454.92237466013023,405.659649893447,407.93702124272255,,,445.83202504777495,408.50034369595824,399.0074845687168,,410.81404302845226,,454.1801015862469\n-139,115.002953859016,576.8148955756255,115.00277504001737,115.00324193182273,4919862.294719368,6073758.714979382,4806050.471897105,7063096.797451094,26953062.90459062,26470663.711730637,12397791.566220956,8792877.3922927,12225352.449372265,12368102.23922802,13534619.462491224,9369301.387691142,8534816.877707051,10608142.696927572,13814196.214642057,31286802.584094536,27345039.417819183,6075056.925097361,7364531.95955749,8393554.468364373,25810175.09588961,28962506.762544613,5173097.739552991,6145004.047203733,5592072.497390192,8425064.449806679,573.5685602794252,568.2159781003286,594.8126858294347,554.4585468634884,566.8649856591538,573.8166725909625,574.9403940337945,501.0856658243425,566.0319012765868,559.411273348691,629.153126090325,559.7519988101286,565.6148636771026,649.1890897905118,564.9710034353639,624.6218545173319,570.260781115662,552.9450788245302,572.4110062733714,569.4005560033418,579.747329879878,671.3676440861595,554.3531339459263,586.9719154312027,594.6124244845739,601.0867044042641\n-140,115.0'..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'
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diff -r 8c5e65adf694 -r 79818ce5a8bf test-data/nist_ei_ms_2mols_input.msp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nist_ei_ms_2mols_input.msp Thu Feb 22 10:40:24 2024 +0000
b
@@ -0,0 +1,40 @@
+NAME: Water
+FORMULA: H2O
+MW: 18
+CASNO: 7732185
+ID: 9
+COMMENT: SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67
+NUM PEAKS: 5
+STDINCHI: InChI=1S/H2O/h1H2
+SMILES: O
+16.0 8.99
+17.0 211.81
+18.0 999.0
+19.0 5.0
+20.0 3.0
+
+NAME: Methyl Alcohol
+FORMULA: CH4O
+MW: 32
+CASNO: 67561
+ID: 32
+COMMENT: SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806
+NUM PEAKS: 16
+STDINCHI: InChI=1S/CH4O/c1-2/h2H,1H3
+SMILES: CO
+2.0 3.0
+12.0 2.0
+13.0 5.99
+14.0 15.99
+15.0 122.89
+16.0 1.0
+17.0 3.0
+18.0 6.99
+19.0 1.0
+28.0 44.96
+29.0 444.6
+30.0 63.94
+31.0 999.0
+32.0 742.33
+33.0 10.99
+34.0 1.0
b
diff -r 8c5e65adf694 -r 79818ce5a8bf test-data/nist_ei_ms_2mols_output.msp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nist_ei_ms_2mols_output.msp Thu Feb 22 10:40:24 2024 +0000
b
@@ -0,0 +1,43 @@
+FORMULA: H2O
+CASNO: 7732185
+ID: 9
+COMMENT: SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67
+SMILES: O
+COMPOUND_NAME: Water
+NOMINAL_MASS: 18
+INCHI: InChI=1S/H2O/h1H2
+RETENTION_INDEX: 317
+NUM PEAKS: 5
+16.0        8.99
+17.0        211.81
+18.0        999.0
+19.0        5.0
+20.0        3.0
+
+FORMULA: CH4O
+CASNO: 67561
+ID: 32
+COMMENT: SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806
+SMILES: CO
+COMPOUND_NAME: Methyl Alcohol
+NOMINAL_MASS: 32
+INCHI: InChI=1S/CH4O/c1-2/h2H,1H3
+RETENTION_INDEX: 354
+NUM PEAKS: 16
+2.0         3.0
+12.0        2.0
+13.0        5.99
+14.0        15.99
+15.0        122.89
+16.0        1.0
+17.0        3.0
+18.0        6.99
+19.0        1.0
+28.0        44.96
+29.0        444.6
+30.0        63.94
+31.0        999.0
+32.0        742.33
+33.0        10.99
+34.0        1.0
+
b
diff -r 8c5e65adf694 -r 79818ce5a8bf test-data/nist_to_ri_2mols_input.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nist_to_ri_2mols_input.csv Thu Feb 22 10:40:24 2024 +0000
b
@@ -0,0 +1,3 @@
+casno,num_peaks,compound_name,retention_index,formula,id,comment,inchi,smiles,nominal_mass,
+7732185,5,Water,,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,,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
b
diff -r 8c5e65adf694 -r 79818ce5a8bf test-data/nist_to_ri_2mols_output.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nist_to_ri_2mols_output.csv Thu Feb 22 10:40:24 2024 +0000
b
@@ -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,
b
diff -r 8c5e65adf694 -r 79818ce5a8bf test-data/results.csv
--- a/test-data/results.csv Thu Oct 12 13:31:32 2023 +0000
+++ b/test-data/results.csv Thu Feb 22 10:40:24 2024 +0000
b
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