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changeset 1:9ee2e2ceb2c9 draft

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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 4378d616c184a24ef8cf8671bd7d68d9ce3876ac"
author computational-metabolomics
date Thu, 19 Mar 2020 06:04:18 -0400
parents fd5c0b39569a
children f151ee133612
files metfrag.py metfrag.xml test-data/RP022611_suspect_default.txt
diffstat 3 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/metfrag.py	Wed Feb 05 12:30:06 2020 -0500
+++ b/metfrag.py	Thu Mar 19 06:04:18 2020 -0400
@@ -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)
--- a/metfrag.xml	Wed Feb 05 12:30:06 2020 -0500
+++ b/metfrag.xml	Thu Mar 19 06:04:18 2020 -0400
@@ -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>
--- 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
@@ -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