| Previous changeset 0:fd5c0b39569a (2020-02-05) Next changeset 2:f151ee133612 (2020-07-14) |
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Commit message:
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 4378d616c184a24ef8cf8671bd7d68d9ce3876ac" |
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modified:
metfrag.py metfrag.xml test-data/RP022611_suspect_default.txt |
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| diff -r fd5c0b39569a -r 9ee2e2ceb2c9 metfrag.py --- a/metfrag.py Wed Feb 05 12:30:06 2020 -0500 +++ b/metfrag.py Thu Mar 19 06:04:18 2020 -0400 |
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| @@ -481,12 +481,12 @@ for key, value in line.items(): # Filter when no MS/MS peak matched if key == "ExplPeaks": - if float(args.pctexplpeak_thrshld) > 0 and \ - "NA" in value: + if float(args.pctexplpeak_thrshld) > 0 \ + and value and "NA" in value: bewrite = False # Filter with a score threshold elif key == "Score": - if float(value) <= float(args.score_thrshld): + if value and float(value) <= float(args.score_thrshld): bewrite = False elif key == "NoExplPeaks": nbfindpeak = float(value) |
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| diff -r fd5c0b39569a -r 9ee2e2ceb2c9 metfrag.xml --- a/metfrag.xml Wed Feb 05 12:30:06 2020 -0500 +++ b/metfrag.xml Thu Mar 19 06:04:18 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="metfrag" name="MetFrag" version="2.4.5+galaxy1"> +<tool id="metfrag" name="MetFrag" version="2.4.5+galaxy2" profile="18.01"> <description> in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra </description> |
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| diff -r fd5c0b39569a -r 9ee2e2ceb2c9 test-data/RP022611_suspect_default.txt --- a/test-data/RP022611_suspect_default.txt Wed Feb 05 12:30:06 2020 -0500 +++ b/test-data/RP022611_suspect_default.txt Thu Mar 19 06:04:18 2020 -0400 |
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| @@ -192,7 +192,6 @@ [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 59.0138_715.8;71.014_679.7;72.9928_77.2;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;72.9928:[C2H3O3-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 112.04692311490557 696.0;1156.0;1156.0;696.0;1156.0 (4R,5S)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol 91654167 InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3-,4+,5?,6?/m0/s1 LKDRXBCSQODPBY-KKHOPBGESA-N LKDRXBCSQODPBY KKHOPBGESA 2 C6H12O6 180.063388 5 5 2.69015731859903 C1[C@@H]([C@H](C(C(O1)(CO)O)O)O)O 1.807282351045528 1.0 -2.8 [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 59.0138_715.8;71.014_679.7;72.9928_77.2;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;72.9928:[C2H3O3-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 112.04692311490557 696.0;1156.0;1156.0;696.0;1156.0 (2S,5R)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol 129275707 InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3-,4?,5?,6+/m1/s1 LKDRXBCSQODPBY-IHKGAJJJSA-N LKDRXBCSQODPBY IHKGAJJJSA 2 C6H12O6 180.063388 5 5 2.69015731859903 C1[C@H](C(C([C@@](O1)(CO)O)O)O)O 1.807282351045528 1.0 -2.8 [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 59.0138_715.8;71.014_679.7;72.9928_77.2;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;72.9928:[C2H3O3-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 112.04692311490557 696.0;1156.0;1156.0;696.0;1156.0 (3S,4R)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol 130839859 InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3?,4-,5+,6?/m1/s1 LKDRXBCSQODPBY-RBIOSCOISA-N LKDRXBCSQODPBY RBIOSCOISA 2 C6H12O6 180.063388 5 5 2.69015731859903 C1C([C@H]([C@@H](C(O1)(CO)O)O)O)O 1.807282351045528 1.0 -2.8 -[M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 59.0138_715.8;71.014_679.7;72.9928_77.2;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;72.9928:[C2H3O3-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 112.04692311490557 696.0;1156.0;1156.0;696.0;1156.0 (2S)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol 132399063 InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3?,4?,5?,6-/m0/s1 LKDRXBCSQODPBY-XIURSDRTSA-N LKDRXBCSQODPBY XIURSDRTSA 2 C6H12O6 180.063388 5 5 2.69015731859903 C1C(C(C([C@@](O1)(CO)O)O)O)O 1.807282351045528 1.0 -2.8 [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 59.0138_715.8;71.014_679.7;72.9928_77.2;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;72.9928:[C2H3O3-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 112.04692311490557 696.0;1156.0;1156.0;696.0;1156.0 (2S,5S)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol 133621853 InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3-,4?,5?,6-/m0/s1 LKDRXBCSQODPBY-FYCPLRARSA-N LKDRXBCSQODPBY FYCPLRARSA 2 C6H12O6 180.063388 5 5 2.69015731859903 C1[C@@H](C(C([C@@](O1)(CO)O)O)O)O 1.807282351045528 1.0 -2.8 [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 59.0138_715.8;71.014_679.7;72.9928_77.2;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;72.9928:[C2H3O3-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 112.04692311490557 696.0;1156.0;1156.0;696.0;1156.0 (3R)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol 134546532 InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3?,4?,5-,6?/m1/s1 LKDRXBCSQODPBY-SZIDTYJOSA-N LKDRXBCSQODPBY SZIDTYJOSA 2 C6H12O6 180.063388 5 5 2.69015731859903 C1C(C([C@H](C(O1)(CO)O)O)O)O 1.807282351045528 1.0 -2.8 [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 59.0138_715.8;71.014_679.7;72.9928_77.2;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;72.9928:[C2H3O3-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 112.04692311490557 696.0;1156.0;1156.0;696.0;1156.0 (2R,4R,5R)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol 135041916 InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3-,4-,5?,6-/m1/s1 LKDRXBCSQODPBY-DUVQVXGLSA-N LKDRXBCSQODPBY DUVQVXGLSA 2 C6H12O6 180.063388 5 5 2.69015731859903 C1[C@H]([C@H](C([C@](O1)(CO)O)O)O)O 1.807282351045528 1.0 -2.8 @@ -1489,6 +1488,7 @@ [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result NA NA 0.0 NA 2-([1,2]oxazolo[5,4-d]pyrimidin-4-ylamino)ethanol 130608923 InChI=1S/C7H8N4O2/c12-2-1-8-6-5-3-11-13-7(5)10-4-9-6/h3-4,12H,1-2H2,(H,8,9,10) XZPRYOZZYDRABV-UHFFFAOYSA-N XZPRYOZZYDRABV UHFFFAOYSA 2 C7H8N4O2 180.064726 0 5 0.6198963831464734 C1=NOC2=NC=NC(=C21)NCCO 0.13070315747891742 0.0 0.0 [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result NA NA 0.0 NA 3-(1H-imidazol-2-ylamino)pyrrolidine-2,5-dione 63563868 InChI=1S/C7H8N4O2/c12-5-3-4(6(13)11-5)10-7-8-1-2-9-7/h1-2,4H,3H2,(H2,8,9,10)(H,11,12,13) CYRYTONKLVUKMZ-UHFFFAOYSA-N CYRYTONKLVUKMZ UHFFFAOYSA 2 C7H8N4O2 180.064726 0 5 0.6197650920608329 C1C(C(=O)NC1=O)NC2=NC=CN2 0.13067547517602196 0.0 -0.8 [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 101.0234_103.0 101.0234:[C2H2N3O2+H]- 13.93860878029479 1058.0 1-methyl-4-nitro-N-prop-2-ynylpyrazol-3-amine 103079866 InChI=1S/C7H8N4O2/c1-3-4-8-7-6(11(12)13)5-10(2)9-7/h1,5H,4H2,2H3,(H,8,9) XCNFBKKSEWYTLH-UHFFFAOYSA-N XCNFBKKSEWYTLH UHFFFAOYSA 2 C7H8N4O2 180.064726 1 5 0.47791449086055554 CN1C=C(C(=N1)NCC#C)[N+](=O)[O-] 0.1306315458481384 0.0 1.0 +[M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result NA NA 0.0 NA 2-(hydroxymethyl)-5-methyl-6H-[1,2,4]triazolo[1,5-a]pyrimidin-7-one 125268082 InChI=1S/C7H8N4O2/c1-4-2-6(13)11-7(8-4)9-5(3-12)10-11/h12H,2-3H2,1H3 CYKZZSFJVCWECT-UHFFFAOYSA-N CYKZZSFJVCWECT UHFFFAOYSA 2 C7H8N4O2 180.064726 0 5 0.61904418082746 CC1=NC2=NC(=NN2C(=O)C1)CO 0.13052347336245182 0.0 -1.0 [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result NA NA 0.0 NA 3-oxa-1,8,10,12-tetrazatricyclo[7.3.0.02,6]dodeca-9,11-dien-7-one 138976721 InChI=1S/C7H8N4O2/c12-5-4-1-2-13-6(4)11-7(10-5)8-3-9-11/h3-4,6H,1-2H2,(H,8,9,10,12) HLQFTGPOADVHPI-UHFFFAOYSA-N HLQFTGPOADVHPI UHFFFAOYSA 2 C7H8N4O2 180.064726 0 5 0.6189748953994755 C1COC2C1C(=O)NC3=NC=NN23 0.13050886475293083 0.0 -0.7 [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result NA NA 0.0 NA 1-methyl-8-methylidene-7,9-dihydro-3H-purine-2,6-dione 90749597 InChI=1S/C7H8N4O2/c1-3-8-4-5(9-3)10-7(13)11(2)6(4)12/h8-9H,1H2,2H3,(H,10,13) HFLNWPJJNBUFFQ-UHFFFAOYSA-N HFLNWPJJNBUFFQ UHFFFAOYSA 2 C7H8N4O2 180.064726 0 5 0.6184620764417207 CN1C(=O)C2=C(NC(=C)N2)NC1=O 0.13040073852600662 0.0 -0.1 [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result NA NA 0.0 NA 3-amino-2-methyl-7H-pyrazolo[4,3-c]pyridine-4,6-dione 60103973 InChI=1S/C7H8N4O2/c1-11-6(8)5-3(10-11)2-4(12)9-7(5)13/h2,8H2,1H3,(H,9,12,13) WJRVALFBYBWECZ-UHFFFAOYSA-N WJRVALFBYBWECZ UHFFFAOYSA 2 C7H8N4O2 180.064726 0 5 0.6181966089929742 CN1C(=C2C(=N1)CC(=O)NC2=O)N 0.13034476556874733 0.0 -0.8 |