Previous changeset 4:ae66b58846cd (2023-12-01) |
Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit c6bc00f50c232c1c7cbb2e6f838c14a0c1c20e05 |
modified:
macros.xml recetox_msfinder.xml test-data/log_smiles.smi |
added:
test-data/test2_out.msp |
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diff -r ae66b58846cd -r e7eff0c9baa3 macros.xml --- a/macros.xml Fri Dec 01 09:23:21 2023 +0000 +++ b/macros.xml Wed Jan 24 13:26:32 2024 +0000 |
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@@ -2,7 +2,7 @@ <token name="@TOOL_VERSION@">v3.5.2</token> <xml name="requirements"> <requirements> - <container type="docker">recetox/recetox-msfinder:v3.5.2-rcx1</container> + <container type="docker">recetox/recetox-msfinder:v3.5.2-rcx2</container> </requirements> </xml> <xml name="creator"> @@ -31,7 +31,7 @@ <param type="float" value="0.01" name="Ms2Tolerance" label="Ms2Tolerance" help="The mass tolerance used for fragment peak matching and annotation." /> <param name="IsTmsMeoxDerivative" type="boolean" checked="False" truevalue="True" falsevalue="False" label="IsTmsMeoxDerivative" help="Check TMS-MeOX derivative to use EIMS database; otherwise, MSMS database is used." /> - <param type="integer" value="1" name="RelativeAbundanceCutOff" label="RelativeAbundanceCutOff" + <param type="integer" value="1" min="0" max="100" name="RelativeAbundanceCutOff" label="RelativeAbundanceCutOff" help="Remove peaks with less than specified % relative intensity from the spectra." /> <param type="float" value="0.001" name="Ms1Tolerance" label="Ms1Tolerance" help="The precursor m/z tolerance to generate formula candidates." /> <param type="select" name="MassToleranceType" label="MassToleranceType" help="Da stands for Daltons (amu), and Ppm stands for parts per million"> @@ -39,20 +39,38 @@ <option value="Ppm">Ppm</option> </param> <param type="integer" value="-1" name="StructurePredictionTimeOut" label="StructurePredictionTimeOut" help="Time out parameter, value of -1 means no timeout" /> - <param name="LewisAndSeniorCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="LewisAndSeniorCheck" - help="Generate formula candidates that match the valence rules of formula elements." /> + <param name="LewisAndSeniorCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="LEWIS and SENIOR rules check" + help="Generate formula candidates that match the valence rules of formula elements. For an explanation of those rules see 'Seven Golden Rules for heuristic + filtering of molecular formulas obtained by accurate mass spectrometry'" /> + <param name="element_ratio_check" type="select" value="CommonRange=TRUE" label="element ratio check." + help="Generate formula candidates that satisfy every element ratios (ex. H/C ratio should be between 0 and 3.33 for Common range (99.7%) restriction.)"> + <option value="CommonRange=TRUE" selected="true">Common Range</option> + <option value="ExtendedRange=TRUE">Extended Range</option> + <option value="ExtremeRange=TRUE">No restriction</option> + </param> + <param type="integer" value="2" min="1" max="3" name="TreeDepth" label="Tree Depth" + help="The limitation of in silico cleavages, i.e. if the user sets '2', the MS-FINDER program generates fragments up to the second level of product ions."/> + <param type="integer" value="20" min="0" max="100" name="IsotopicAbundanceTolerance" label="Isotopic Ratio Tolerance" + help="Calculate the isotopic score. The tolerance should be utilized as the sigma value for the Gaussian scoring."/> + <param name="ElementProbabilityCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Element probability check" + help="Generate formula candidates that satisfy the heuristic rules as described in the Seven Golden Rules paper. For example, if a formula + candidate contains the following element counts, i.e. NOPS all > 1, the element counts of N, O, P, and S should be less than 9, 19, 3, and 2, respectively."/> + <param name="IsUseEiFragmentDB" type="boolean" checked="False" truevalue="True" falsevalue="False" label="Use EI fragment database" + help="Utilize the fragment ion library for EI-MS spectral mining"/> </xml> - <!-- Element Checks <xml name="element_check_parameter"> - <param name="Ocheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Ocheck" /> - <param name="Ncheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Ncheck" /> - <param name="Pcheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Pcheck" /> - <param name="Scheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Scheck" /> - <param name="Fcheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Fcheck" /> - <param name="ClCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="ClCheck" /> - <param name="BrCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="BrCheck" /> - <param name="Icheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Icheck" /> - <param name="SiCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="SiCheck" /> - </xml> --> + + <xml name="element_select"> + <option value="Ocheck=True">Oxygen check</option> + <option value="Ncheck=True">Nitrogen check</option> + <option value="Pcheck=True">Phosphorus check</option> + <option value="Scheck=True">Sulfur check</option> + <option value="Fcheck=True">Fluorine check</option> + <option value="ClCheck=True">Chlorine Check</option> + <option value="BrCheck=True">Bromine Check</option> + <option value="Icheck=True">Iodine check</option> + <option value="SiCheck=True">Silicon Check</option> + </xml> + <xml name="output"> <collection type="list" format="txt" name="output" label="${tool.name} on ${on_string}"> <discover_datasets pattern="(?P<designation>.+)\.smi" directory="output" ext="smi" /> @@ -74,7 +92,7 @@ FORMULA, PRECURSORMZ and SMILES (or INCHI) metadata entries are required to be present in the input mass spectral library file. Each spectrum has to be separated by a single blank line. - For detailed documentation of the tool please visit https://mtbinfo-team.github.io/mtbinfo.github.io/MS-FINDER/tutorial + For detailed documentation of the tool please visit https://systemsomicslab.github.io/mtbinfo.github.io/MS-FINDER/tutorial ]]> </token> |
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diff -r ae66b58846cd -r e7eff0c9baa3 recetox_msfinder.xml --- a/recetox_msfinder.xml Fri Dec 01 09:23:21 2023 +0000 +++ b/recetox_msfinder.xml Wed Jan 24 13:26:32 2024 +0000 |
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@@ -1,4 +1,4 @@ -<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy3"> +<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy4"> <description>Annotation of fragment peaks in mass spectral libraries.</description> <macros> <import>macros.xml</import> @@ -7,13 +7,13 @@ <expand macro="creator" /> <expand macro="requirements" /> - <command> + <command detect_errors="exit_code"> <![CDATA[ mkdir output; sh ${write_param}; - mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o 'output/result.msp'; + mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i '$input_data' -m 'MSFINDER.INI' -o 'output/result.msp'; + [ -f output/log_smiles.smi ] && sed -i '1s/^/smiles\n/' output/log_smiles.smi; [ -s output/result.msp ] || rm output/result.msp; - ]]> </command> @@ -36,16 +36,25 @@ "IsUseCcsForFilteringCandidates=True" \ "CcsToleranceForStructureElucidation=10" \ "CanExcuteMS2AdductSearch=False" \ - "IsUseXlogpPrediction=False" >MSFINDER.INI + "IsUseXlogpPrediction=False" \ + "ElementProbabilityCheck=$ElementProbabilityCheck" \ + "IsotopicAbundanceTolerance=$IsotopicAbundanceTolerance" \ + "TreeDepth=$TreeDepth" \ + "$element_ratio_check" \ + "IsUseEiFragmentDB=$IsUseEiFragmentDB" >MSFINDER.INI + + #set element_selected = "\n".join([str($element) for $element in str($element_selection_option).split(",")]) + printf "%s\n" "$element_selected" >> MSFINDER.INI </configfile> </configfiles> <inputs> <expand macro="input" /> <expand macro="parameter" /> - <!-- <section name="element_selection" title="Element Selection" expanded="true" help="Generate formula candidates that just contain the elements selected by the users."> - <expand macro="element_check_parameter" /> - </section> --> + <param name="element_selection_option" type="select" label="Element selection" multiple="true" optional="true" + help="Generate formula candidates that just contain the elements selected by the users. Check 'IsTmsMeoxDerivative' if you want to annotate EI-MS spectra."> + <expand macro="element_select" /> + </param> </inputs> <outputs> @@ -61,6 +70,15 @@ <!-- This is set to 16 since msfinder sometimes places double bonds between certain atoms and sometimes not - there are 16 such cases in this file. --> </test> <test> + <param name="input_data" value="test.msp" ftype="msp" /> + <param name="element_ratio_check" value="ExtendedRange=TRUE"/> + <param name="TreeDepth" value="3"/> + <param name="element_selection_option" value="Ocheck=True,Ncheck=True,Pcheck=True,Scheck=True,Fcheck=True,ClCheck=True,BrCheck=True,Icheck=True,SiCheck=True"/> + <output_collection name="output" type="list"> + <element name="result" file="test2_out.msp" lines_diff="24"/> + </output_collection> + </test> + <test> <param name="input_data" value="test_log.msp" ftype="msp" /> <output_collection name="output" type="list"> <element name="log_smiles" file="log_smiles.smi" /> |
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diff -r ae66b58846cd -r e7eff0c9baa3 test-data/log_smiles.smi --- a/test-data/log_smiles.smi Fri Dec 01 09:23:21 2023 +0000 +++ b/test-data/log_smiles.smi Wed Jan 24 13:26:32 2024 +0000 |
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@@ -1,1 +1,2 @@ +smiles Cl[Si]1Oc2ccccc2O1.[C-]#[O+].[C-]#[O+].[CH]1C=CC=C1.[Fe] |
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diff -r ae66b58846cd -r e7eff0c9baa3 test-data/test2_out.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_out.msp Wed Jan 24 13:26:32 2024 +0000 |
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@@ -0,0 +1,105 @@ +NAME: Acetylserotonin_2TMS isomer 2 +SCANNUMBER: -1 +RETENTIONTIME: -1 +RETENTIONINDEX: 2520.736 +PRECURSORMZ: 362.18381 +PRECURSORTYPE: [M]+ +IONMODE: Positive +SPECTRUMTYPE: Centroid +FORMULA: C18H30N2O2Si2 +INCHIKEY: BITJWWNGDAOCJT-UHFFFAOYSA-N +INCHI: +SMILES: C[Si](C)(C)Oc1cc2c(cc1)n(cc2CC\N=C(/C)O)[Si](C)(C)C +AUTHORS: Price et al., RECETOX, Masaryk University (CZ) +COLLISIONENERGY: 70 +INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS +INSTRUMENTTYPE: GC-EI-Orbitrap +IONIZATION: +LICENSE: CC BY-NC +COMMENT: +Num Peaks: 84 +73.04681 6882 "Theoretical m/z 73.046802, Mass diff 0 (0.11 ppm), SMILES C[Si](C)C, Annotation [C3H10Si-H]+, Rule of HR True" +74.04642 3441 +76.01821 5005 "Theoretical m/z 76.018724, Mass diff 0 (0 ppm), Formula C5H2N" +77.02173 4634 +78.03387 2401 +78.91781 4925 +79.04164 36910 "Theoretical m/z 79.042199, Mass diff 0 (0 ppm), Formula C5H5N" +80.91575 12768 +81.06992 1588 "Theoretical m/z 81.070425, Mass diff 0 (0 ppm), Formula C6H9" +89.03854 1372 "Theoretical m/z 89.041721, Mass diff 0.003 (35.73 ppm), SMILES O[Si](C)(C)C, Annotation [C3H10OSi-H]+, Rule of HR True" +91.05424 1324 "Theoretical m/z 91.057371, Mass diff 0.003 (34.39 ppm), SMILES O[Si](C)(C)C, Annotation [C3H10OSi+H]+, Rule of HR True" +92.06213 3591 "Theoretical m/z 92.0626, Mass diff 0 (0 ppm), Formula C7H8" +93.03666 8343 "Theoretical m/z 93.03404, Mass diff -0.003 (0 ppm), Formula C6H5O" +94.93144 2656 +95.04466 8498 "Theoretical m/z 95.04969, Mass diff 0.004 (0 ppm), Formula C6H7O" +95.93922 1565 +103.05418 2844 "Theoretical m/z 103.054775, Mass diff 0 (0 ppm), Formula C8H7" +104.06204 1384 +105.06992 2211 "Theoretical m/z 105.070425, Mass diff 0 (0 ppm), Formula C8H9" +106.89473 3073 +106.94908 3532 +108.94706 3679 "Theoretical m/z 108.956593, Mass diff 0.009 (0 ppm), Formula C3HOSi2" +111.04412 1592 "Theoretical m/z 111.044604, Mass diff 0 (0 ppm), Formula C6H7O2" +113.03857 1585 "Theoretical m/z 113.039125, Mass diff 0 (0 ppm), Formula C9H5" +115.05422 7216 "Theoretical m/z 115.054775, Mass diff 0 (0 ppm), Formula C9H7" +120.05695 3247 "Theoretical m/z 120.057515, Mass diff 0 (0 ppm), Formula C8H8O" +120.94707 4091 "Theoretical m/z 120.956593, Mass diff 0.009 (0 ppm), Formula C4HOSi2" +120.96468 3380 "Theoretical m/z 120.967826, Mass diff 0.003 (0 ppm), Formula C3HN2Si2" +122.06804 4192 "Theoretical m/z 122.073165, Mass diff 0.005 (0 ppm), Formula C8H10O" +123.93423 1315 "Theoretical m/z 123.943682, Mass diff 0.009 (0 ppm), Formula C3O2Si2" +124.94194 4725 "Theoretical m/z 124.951507, Mass diff 0.009 (0 ppm), Formula C3HO2Si2" +127.02392 3504 "Theoretical m/z 127.021531, Mass diff -0.003 (0 ppm), Formula C5H7O2Si" +129.06982 2726 "Theoretical m/z 129.070425, Mass diff 0 (0 ppm), Formula C10H9" +130.06831 4067 "Theoretical m/z 130.065128, Mass diff 0.003 (24.46 ppm), SMILES C1=CC=C2C(=C1)NCC2C, Annotation [C9H9N-H]+, Rule of HR True" +141.06976 3435 "Theoretical m/z 141.070425, Mass diff 0 (0 ppm), Formula C11H9" +145.06465 1876 "Theoretical m/z 145.06534, Mass diff 0 (0 ppm), Formula C10H9O" +149.06238 3354 "Theoretical m/z 149.060255, Mass diff -0.003 (0 ppm), Formula C9H9O2" +152.06189 6328 "Theoretical m/z 152.071154, Mass diff 0.009 (0 ppm), Formula C8H10NO2" +164.94904 1697 "Theoretical m/z 164.957655, Mass diff 0.008 (0 ppm), Formula C4HN2O2Si2" +167.05533 3051 "Theoretical m/z 167.060378, Mass diff 0.005 (30.22 ppm), SMILES N(=C)CCC2CNC1=CC=CC=C12, Annotation [C11H12N2-5H]+, Rule of HR True" +170.0343 2446 "Theoretical m/z 170.042052, Mass diff 0.008 (45.59 ppm), SMILES C1=CC=C2C(=C1)CCN2[Si](C)C, Annotation [C10H13NSi-5H]+, Rule of HR True" +171.95171 10548 "Theoretical m/z 171.943682, Mass diff -0.009 (0 ppm), Formula C7O2Si2" +172.95517 1555 +173.94968 10065 "Theoretical m/z 173.946756, Mass diff -0.003 (0 ppm), Formula C6NO2Si2" +174.95305 1284 +178.07762 1953 "Theoretical m/z 178.07825, Mass diff 0 (0 ppm), Formula C14H10" +183.08034 6206 "Theoretical m/z 183.08099, Mass diff 0 (0 ppm), Formula C13H11O" +184.08812 6315 "Theoretical m/z 184.097778, Mass diff 0.009 (0 ppm), Formula C8H18NSi2" +185.09143 2274 +192.98021 1819 "Theoretical m/z 192.985814, Mass diff 0.005 (0 ppm), Formula C10HN2OSi" +194.07246 1646 "Theoretical m/z 194.073165, Mass diff 0 (0 ppm), Formula C14H10O" +197.97484 2121 "Theoretical m/z 197.980001, Mass diff 0.005 (0 ppm), Formula C13NSi" +198.97534 5042 "Theoretical m/z 198.978391, Mass diff 0.003 (0 ppm), Formula C8H3N2OSi2" +204.08408 1545 "Theoretical m/z 204.083912, Mass diff 0 (0.83 ppm), SMILES O(C1=CC=C2NCCC2(=C1))[Si](C)(C)C, Annotation [C11H15NOSi-H]+, Rule of HR True" +208.03126 3799 "Theoretical m/z 208.025007, Mass diff -0.007 (0 ppm), Formula C8H10NO2Si2" +209.01154 5448 "Theoretical m/z 209.013973, Mass diff 0.002 (0 ppm), Formula C15HN2" +210.99068 3675 "Theoretical m/z 210.996379, Mass diff 0.005 (0 ppm), Formula C10H3N2O2Si" +211.06046 5392 "Theoretical m/z 211.061058, Mass diff 0 (0 ppm), Formula C9H15O2Si2" +214.10466 3080 "Theoretical m/z 214.104654, Mass diff 0 (0.03 ppm), SMILES C1=CC=C2C(=C1)C(CN2[Si](C)(C)C)CC, Annotation [C13H19NSi-3H]+, Rule of HR True" +220.07869 6462 "Theoretical m/z 220.07938, Mass diff 0 (0 ppm), Formula C11H14NO2Si" +226.0417 4848 "Theoretical m/z 226.050827, Mass diff 0.009 (0 ppm), Formula C12H12NSi2" +227.02208 14828 "Theoretical m/z 227.024538, Mass diff 0.002 (0 ppm), Formula C15H3N2O" +230.00099 2388 "Theoretical m/z 230.003074, Mass diff 0.002 (0 ppm), Formula C18N" +230.09961 2241 "Theoretical m/z 230.099573, Mass diff 0 (0.16 ppm), SMILES O(C1=CC=C2NCC(C2(=C1))CC)[Si](C)(C)C, Annotation [C13H19NOSi-3H]+, Rule of HR True" +240.94661 1761 "Theoretical m/z 240.956593, Mass diff 0.009 (0 ppm), Formula C14HOSi2" +254.96269 2484 "Theoretical m/z 254.972243, Mass diff 0.009 (0 ppm), Formula C15H3OSi2" +257.06641 1341 "Theoretical m/z 257.074096, Mass diff 0.008 (29.9 ppm), SMILES OC(=NCCC2CNC1=CC=C(O[Si]C)C=C12)C, Annotation [C13H18N2O2Si-5H]+, Rule of HR True" +273.14221 1338 "Theoretical m/z 273.141773, Mass diff 0 (1.6 ppm), SMILES OC(=NCCC2CN(C1=CC=CC=C12)[Si](C)(C)C)C, Annotation [C15H22N2OSi-H]+, Rule of HR True" +288.12326 15718 "Theoretical m/z 288.123437, Mass diff 0 (0.62 ppm), SMILES O(C1=CC=C2C(=C1)C(CN2[Si](C)(C)C)CC)[Si](C)C, Annotation [C15H25NOSi2-3H]+, Rule of HR True" +289.12668 5715 +290.13898 125444 "Theoretical m/z 290.139087, Mass diff 0 (0.37 ppm), SMILES O(C1=CC=C2C(=C1)C(CN2[Si](C)(C)C)C)[Si](C)(C)C, Annotation [C15H25NOSi2-H]+, Rule of HR True" +291.14282 16150 +292.1355 12595 +293.13925 1290 "Theoretical m/z 293.139308, Mass diff 0 (0 ppm), Formula C15H25O2Si2" +302.1391 2508 "Theoretical m/z 302.139642, Mass diff 0 (0 ppm), Formula C16H24NOSi2" +303.14676 109060 "Theoretical m/z 303.146918, Mass diff 0 (0.52 ppm), SMILES O(C1=CC=C2C(=C1)C(CN2[Si](C)(C)C)CC)[Si](C)(C)C, Annotation [C16H27NOSi2-2H]+, Rule of HR False" +304.1492 19700 +305.143 7792 +306.13388 4148 "Theoretical m/z 306.134557, Mass diff 0 (0 ppm), Formula C15H24NO2Si2" +328.98126 2010 +345.1445 7128 "Theoretical m/z 345.145456, Mass diff 0 (0 ppm), Formula C17H25N2O2Si2" +360.16812 2877 +362.18381 10542 "Theoretical m/z 362.184022, Mass diff 0 (0.58 ppm), SMILES OC(=NCCC2CN(C1=CC=C(O[Si](C)(C)C)C=C12)[Si](C)(C)C)C, Annotation [C18H30N2O2Si2]+, Rule of HR False" +363.18671 4306 + |