Mercurial > repos > workflow4metabolomics > skyline2isocor

changeset 0:d45fffedc467 draft

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planemo upload for repository https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m commit 23cfca443338f5ae8eed54b44a5b0d7b02563334
author workflow4metabolomics
date Tue, 19 Mar 2024 14:49:27 +0000
parents
children cdb4564fcb68
files skyline2isocor.xml test-data/skyline_output.csv test-data/test_output.tsv
diffstat 3 files changed, 865 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/skyline2isocor.xml	Tue Mar 19 14:49:27 2024 +0000
@@ -0,0 +1,39 @@
+<tool id='skyline2isocor' name='Skyline2Isocor: converting skyling outputs into IsoCor inputs' version='@TOOL_VERSION@+galaxy0' profile='20.5'>
+    <macros>
+        <token name='@TOOL_VERSION@'>0.3.0</token>
+    </macros>
+    <requirements>
+        <requirement type='package' version='@TOOL_VERSION@'>skyline2isocor</requirement>
+    </requirements>
+    <command detect_errors='exit_code'><![CDATA[
+    skyline2isocor -i '$skyline_output' -o '$isocor_input' > '$stdout' 2> '$stderr'
+    ]]></command>
+    <inputs>
+        <param type='data' format='tabular, txt' name='skyline_output' label='Skyline output file' help='Skyline output to convert'/>
+    </inputs>
+    <outputs>
+        <data format='txt' name='stdout' label='Log'/>
+        <data format='txt' name='stderr' label='Error log' />
+        <data format='tabular,txt' name='isocor_input' label='IsoCor input file' />
+    </outputs>
+    <tests>
+        <test>
+            <param name='skyline_output' value='skyline_output.csv' />
+            <output name='isocor_input' value='test_output.tsv' />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Preparing skyline output data for use in IsoCor software for natural abundance isotope correction. Can be directly linked to Isocor in a workflow.
+        Input is the skyline output. Necessary columns: File Name, Molecule Name, Product Adduct, Total Area.
+        ]]></help>
+    <citations>
+        <citation type='bibtex'>
+                @misc{
+                githubskyline2isocor,
+                author = {Le Gregam, Loic},
+                year = {2024},
+                title = {Skyline2IsoCor,
+            }
+        </citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/skyline_output.csv	Tue Mar 19 14:49:27 2024 +0000
@@ -0,0 +1,413 @@
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+1Bc.raw;Cytidine;[M9C13-1H];251.108438;0
+1Cc.raw;Cytidine;[M9C13-1H];251.108438;0
+1Bc.raw;GDP;[M-H];442.017054;183419200
+1Cc.raw;GDP;[M-H];442.017054;5829401
+1Bc.raw;GDP;[M1C13-1H];443.020409;20590900
+1Cc.raw;GDP;[M1C13-1H];443.020409;422107
+1Bc.raw;GDP;[M2C13-1H];444.023764;7804884
+1Cc.raw;GDP;[M2C13-1H];444.023764;92678
+1Bc.raw;GDP;[M3C13-1H];445.027119;1823927
+1Cc.raw;GDP;[M3C13-1H];445.027119;236742
+1Bc.raw;GDP;[M4C13-1H];446.030474;2016415
+1Cc.raw;GDP;[M4C13-1H];446.030474;13772
+1Bc.raw;GDP;[M5C13-1H];447.033829;19619284
+1Cc.raw;GDP;[M5C13-1H];447.033829;31978
+1Bc.raw;GDP;[M6C13-1H];448.037183;1194784
+1Cc.raw;GDP;[M6C13-1H];448.037183;26256
+1Bc.raw;GDP;[M7C13-1H];449.040538;201536
+1Cc.raw;GDP;[M7C13-1H];449.040538;36826
+1Bc.raw;GDP;[M8C13-1H];450.043893;309616
+1Cc.raw;GDP;[M8C13-1H];450.043893;43431
+1Bc.raw;GDP;[M9C13-1H];451.047248;268794
+1Cc.raw;GDP;[M9C13-1H];451.047248;0
+1Bc.raw;GDP;[M10C13-1H];452.050603;77674
+1Cc.raw;GDP;[M10C13-1H];452.050603;33280
+1Bc.raw;GMP;[M-H];362.050724;131522216
+1Cc.raw;GMP;[M-H];362.050724;397354
+1Bc.raw;GMP;[M1C13-1H];363.054078;13938626
+1Cc.raw;GMP;[M1C13-1H];363.054078;213919
+1Bc.raw;GMP;[M2C13-1H];364.057433;3637522
+1Cc.raw;GMP;[M2C13-1H];364.057433;0
+1Bc.raw;GMP;[M3C13-1H];365.060788;606319
+1Cc.raw;GMP;[M3C13-1H];365.060788;0
+1Bc.raw;GMP;[M4C13-1H];366.064143;963454
+1Cc.raw;GMP;[M4C13-1H];366.064143;0
+1Bc.raw;GMP;[M5C13-1H];367.067498;13534815
+1Cc.raw;GMP;[M5C13-1H];367.067498;0
+1Bc.raw;GMP;[M6C13-1H];368.070853;134354
+1Cc.raw;GMP;[M6C13-1H];368.070853;0
+1Bc.raw;GMP;[M7C13-1H];369.074207;0
+1Cc.raw;GMP;[M7C13-1H];369.074207;0
+1Bc.raw;GMP;[M8C13-1H];370.077562;0
+1Cc.raw;GMP;[M8C13-1H];370.077562;0
+1Bc.raw;GMP;[M9C13-1H];371.080917;0
+1Cc.raw;GMP;[M9C13-1H];371.080917;0
+1Bc.raw;GMP;[M10C13-1H];372.084272;0
+1Cc.raw;GMP;[M10C13-1H];372.084272;0
+1Bc.raw;GTP;[M-H];442.017054;1377586
+1Cc.raw;GTP;[M-H];442.017054;685898
+1Bc.raw;GTP;[M1C13-1H];443.020409;169988
+1Cc.raw;GTP;[M1C13-1H];443.020409;60237
+1Bc.raw;GTP;[M2C13-1H];444.023764;338539
+1Cc.raw;GTP;[M2C13-1H];444.023764;89532
+1Bc.raw;GTP;[M3C13-1H];445.027119;15879
+1Cc.raw;GTP;[M3C13-1H];445.027119;39374
+1Bc.raw;GTP;[M4C13-1H];446.030474;10927
+1Cc.raw;GTP;[M4C13-1H];446.030474;0
+1Bc.raw;GTP;[M5C13-1H];447.033829;130142
+1Cc.raw;GTP;[M5C13-1H];447.033829;25645
+1Bc.raw;GTP;[M6C13-1H];448.037183;124400
+1Cc.raw;GTP;[M6C13-1H];448.037183;16310
+1Bc.raw;GTP;[M7C13-1H];449.040538;115268
+1Cc.raw;GTP;[M7C13-1H];449.040538;4394
+1Bc.raw;GTP;[M8C13-1H];450.043893;99669
+1Cc.raw;GTP;[M8C13-1H];450.043893;14385
+1Bc.raw;GTP;[M9C13-1H];451.047248;102146
+1Cc.raw;GTP;[M9C13-1H];451.047248;44732
+1Bc.raw;GTP;[M10C13-1H];452.050603;61715
+1Cc.raw;GTP;[M10C13-1H];452.050603;31661
+1Bc.raw;IMP;[M-H];347.039824;21731700
+1Cc.raw;IMP;[M-H];347.039824;29553942
+1Bc.raw;IMP;[M1C13-1H];348.043179;2046580
+1Cc.raw;IMP;[M1C13-1H];348.043179;2483813
+1Bc.raw;IMP;[M2C13-1H];349.046534;1102702
+1Cc.raw;IMP;[M2C13-1H];349.046534;59175
+1Bc.raw;IMP;[M3C13-1H];350.049889;750858
+1Cc.raw;IMP;[M3C13-1H];350.049889;127272
+1Bc.raw;IMP;[M4C13-1H];351.053244;798244
+1Cc.raw;IMP;[M4C13-1H];351.053244;0
+1Bc.raw;IMP;[M5C13-1H];352.056599;10917623
+1Cc.raw;IMP;[M5C13-1H];352.056599;0
+1Bc.raw;IMP;[M6C13-1H];353.059954;134071
+1Cc.raw;IMP;[M6C13-1H];353.059954;0
+1Bc.raw;IMP;[M7C13-1H];354.063308;102530
+1Cc.raw;IMP;[M7C13-1H];354.063308;46581
+1Bc.raw;IMP;[M8C13-1H];355.066663;0
+1Cc.raw;IMP;[M8C13-1H];355.066663;0
+1Bc.raw;IMP;[M9C13-1H];356.070018;0
+1Cc.raw;IMP;[M9C13-1H];356.070018;0
+1Bc.raw;IMP;[M10C13-1H];357.073373;0
+1Cc.raw;IMP;[M10C13-1H];357.073373;0
+1Bc.raw;UDP;[M-H];402.994922;414451744
+1Cc.raw;UDP;[M-H];402.994922;701342400
+1Bc.raw;UDP;[M1C13-1H];403.998277;47638556
+1Cc.raw;UDP;[M1C13-1H];403.998277;115244616
+1Bc.raw;UDP;[M2C13-1H];405.001632;47647284
+1Cc.raw;UDP;[M2C13-1H];405.001632;59672152
+1Bc.raw;UDP;[M3C13-1H];406.004987;23283766
+1Cc.raw;UDP;[M3C13-1H];406.004987;28410322
+1Bc.raw;UDP;[M4C13-1H];407.008341;31764274
+1Cc.raw;UDP;[M4C13-1H];407.008341;5940255
+1Bc.raw;UDP;[M5C13-1H];408.011696;312608064
+1Cc.raw;UDP;[M5C13-1H];408.011696;8335464
+1Bc.raw;UDP;[M6C13-1H];409.015051;25615516
+1Cc.raw;UDP;[M6C13-1H];409.015051;716107
+1Bc.raw;UDP;[M7C13-1H];410.018406;12679936
+1Cc.raw;UDP;[M7C13-1H];410.018406;53200
+1Bc.raw;UDP;[M8C13-1H];411.021761;962342
+1Cc.raw;UDP;[M8C13-1H];411.021761;13484
+1Bc.raw;UDP;[M9C13-1H];412.025116;134556
+1Cc.raw;UDP;[M9C13-1H];412.025116;66458
+1Bc.raw;UDPAcGlcN;[M-H];606.074295;147400880
+1Cc.raw;UDPAcGlcN;[M-H];606.074295;497737888
+1Bc.raw;UDPAcGlcN;[M1C13-1H];607.077649;34547192
+1Cc.raw;UDPAcGlcN;[M1C13-1H];607.077649;124516552
+1Bc.raw;UDPAcGlcN;[M2C13-1H];608.081004;23484704
+1Cc.raw;UDPAcGlcN;[M2C13-1H];608.081004;209956608
+1Bc.raw;UDPAcGlcN;[M3C13-1H];609.084359;25758670
+1Cc.raw;UDPAcGlcN;[M3C13-1H];609.084359;65518868
+1Bc.raw;UDPAcGlcN;[M4C13-1H];610.087714;20443204
+1Cc.raw;UDPAcGlcN;[M4C13-1H];610.087714;24415836
+1Bc.raw;UDPAcGlcN;[M5C13-1H];611.091069;108661952
+1Cc.raw;UDPAcGlcN;[M5C13-1H];611.091069;15392614
+1Bc.raw;UDPAcGlcN;[M6C13-1H];612.094424;230854064
+1Cc.raw;UDPAcGlcN;[M6C13-1H];612.094424;6333184
+1Bc.raw;UDPAcGlcN;[M7C13-1H];613.097779;45257816
+1Cc.raw;UDPAcGlcN;[M7C13-1H];613.097779;4478011
+1Bc.raw;UDPAcGlcN;[M8C13-1H];614.101133;47845764
+1Cc.raw;UDPAcGlcN;[M8C13-1H];614.101133;4448550
+1Bc.raw;UDPAcGlcN;[M9C13-1H];615.104488;20391152
+1Cc.raw;UDPAcGlcN;[M9C13-1H];615.104488;3971238
+1Bc.raw;UDPAcGlcN;[M10C13-1H];616.107843;30479670
+1Cc.raw;UDPAcGlcN;[M10C13-1H];616.107843;3172275
+1Bc.raw;UDPAcGlcN;[M11C13-1H];617.111198;141836016
+1Cc.raw;UDPAcGlcN;[M11C13-1H];617.111198;4611530
+1Bc.raw;UDPAcGlcN;[M12C13-1H];618.114553;19285690
+1Cc.raw;UDPAcGlcN;[M12C13-1H];618.114553;3801463
+1Bc.raw;UDPAcGlcN;[M13C13-1H];619.117908;18404962
+1Cc.raw;UDPAcGlcN;[M13C13-1H];619.117908;4689228
+1Bc.raw;UDPAcGlcN;[M14C13-1H];620.121262;4729885
+1Cc.raw;UDPAcGlcN;[M14C13-1H];620.121262;3879133
+1Bc.raw;UDPAcGlcN;[M15C13-1H];621.124617;4016577
+1Cc.raw;UDPAcGlcN;[M15C13-1H];621.124617;5293326
+1Bc.raw;UDPAcGlcN;[M16C13-1H];622.127972;3331716
+1Cc.raw;UDPAcGlcN;[M16C13-1H];622.127972;3679576
+1Bc.raw;UDPAcGlcN;[M17C13-1H];623.131327;4362360
+1Cc.raw;UDPAcGlcN;[M17C13-1H];623.131327;4082185
+1Bc.raw;UMP;[M-H];323.028591;492295488
+1Cc.raw;UMP;[M-H];323.028591;678773184
+1Bc.raw;UMP;[M1C13-1H];324.031946;54854400
+1Cc.raw;UMP;[M1C13-1H];324.031946;106707688
+1Bc.raw;UMP;[M2C13-1H];325.035301;48958356
+1Cc.raw;UMP;[M2C13-1H];325.035301;48354456
+1Bc.raw;UMP;[M3C13-1H];326.038656;24356038
+1Cc.raw;UMP;[M3C13-1H];326.038656;24149268
+1Bc.raw;UMP;[M4C13-1H];327.04201;34483400
+1Cc.raw;UMP;[M4C13-1H];327.04201;4240274
+1Bc.raw;UMP;[M5C13-1H];328.045365;354854400
+1Cc.raw;UMP;[M5C13-1H];328.045365;2430849
+1Bc.raw;UMP;[M6C13-1H];329.04872;27630432
+1Cc.raw;UMP;[M6C13-1H];329.04872;60106
+1Bc.raw;UMP;[M7C13-1H];330.052075;10287202
+1Cc.raw;UMP;[M7C13-1H];330.052075;0
+1Bc.raw;UMP;[M8C13-1H];331.05543;256329
+1Cc.raw;UMP;[M8C13-1H];331.05543;0
+1Bc.raw;UMP;[M9C13-1H];332.058785;0
+1Cc.raw;UMP;[M9C13-1H];332.058785;0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_output.tsv	Tue Mar 19 14:49:27 2024 +0000
@@ -0,0 +1,413 @@
+sample	metabolite	derivative	isotopologue	area
+1Bc.raw	2PG_3PG		0	295079
+1Cc.raw	2PG_3PG		0	43339152
+1Bc.raw	2PG_3PG		1	21721
+1Cc.raw	2PG_3PG		1	384440
+1Bc.raw	2PG_3PG		2	0
+1Cc.raw	2PG_3PG		2	20673
+1Bc.raw	2PG_3PG		3	817336
+1Cc.raw	2PG_3PG		3	717032
+1Bc.raw	6PG		0	20488444
+1Cc.raw	6PG		0	174559680
+1Bc.raw	6PG		1	1353794
+1Cc.raw	6PG		1	9204649
+1Bc.raw	6PG		2	2034893
+1Cc.raw	6PG		2	715170
+1Bc.raw	6PG		3	3868554
+1Cc.raw	6PG		3	1536649
+1Bc.raw	6PG		4	1407862
+1Cc.raw	6PG		4	80192
+1Bc.raw	6PG		5	14516783
+1Cc.raw	6PG		5	101574
+1Bc.raw	6PG		6	149455936
+1Cc.raw	6PG		6	3293361
+1Bc.raw	FruBP		0	43524440
+1Cc.raw	FruBP		0	343385984
+1Bc.raw	FruBP		1	5018922
+1Cc.raw	FruBP		1	23490898
+1Bc.raw	FruBP		2	5249852
+1Cc.raw	FruBP		2	7612326
+1Bc.raw	FruBP		3	23203430
+1Cc.raw	FruBP		3	4299920
+1Bc.raw	FruBP		4	5899907
+1Cc.raw	FruBP		4	15122
+1Bc.raw	FruBP		5	30436672
+1Cc.raw	FruBP		5	84067
+1Bc.raw	FruBP		6	331211488
+1Cc.raw	FruBP		6	4920671
+1Bc.raw	F6P		0	7924251
+1Cc.raw	F6P		0	41230904
+1Bc.raw	F6P		1	162158
+1Cc.raw	F6P		1	2986936
+1Bc.raw	F6P		2	59431
+1Cc.raw	F6P		2	243332
+1Bc.raw	F6P		3	2732191
+1Cc.raw	F6P		3	103702
+1Bc.raw	F6P		4	172443
+1Cc.raw	F6P		4	18357
+1Bc.raw	F6P		5	3695150
+1Cc.raw	F6P		5	0
+1Bc.raw	F6P		6	47925972
+1Cc.raw	F6P		6	0
+1Bc.raw	Glc6P		0	5363725
+1Cc.raw	Glc6P		0	109423144
+1Bc.raw	Glc6P		1	50205
+1Cc.raw	Glc6P		1	6682065
+1Bc.raw	Glc6P		2	28468
+1Cc.raw	Glc6P		2	827495
+1Bc.raw	Glc6P		3	728908
+1Cc.raw	Glc6P		3	124630
+1Bc.raw	Glc6P		4	114192
+1Cc.raw	Glc6P		4	0
+1Bc.raw	Glc6P		5	5325325
+1Cc.raw	Glc6P		5	0
+1Bc.raw	Glc6P		6	71047344
+1Cc.raw	Glc6P		6	14839
+1Bc.raw	Glycerol3P		0	27313730
+1Cc.raw	Glycerol3P		0	22702250
+1Bc.raw	Glycerol3P		1	194608
+1Cc.raw	Glycerol3P		1	226523
+1Bc.raw	Glycerol3P		2	0
+1Cc.raw	Glycerol3P		2	0
+1Bc.raw	Glycerol3P		3	2109259
+1Cc.raw	Glycerol3P		3	0
+1Bc.raw	Man6P		0	7415886
+1Cc.raw	Man6P		0	29522790
+1Bc.raw	Man6P		1	164595
+1Cc.raw	Man6P		1	1846092
+1Bc.raw	Man6P		2	189478
+1Cc.raw	Man6P		2	76491
+1Bc.raw	Man6P		3	2058744
+1Cc.raw	Man6P		3	403253
+1Bc.raw	Man6P		4	210092
+1Cc.raw	Man6P		4	12494
+1Bc.raw	Man6P		5	2233690
+1Cc.raw	Man6P		5	0
+1Bc.raw	Man6P		6	25720328
+1Cc.raw	Man6P		6	0
+1Bc.raw	Rib1P		0	1159334
+1Cc.raw	Rib1P		0	9710056
+1Bc.raw	Rib1P		1	45995
+1Cc.raw	Rib1P		1	153362
+1Bc.raw	Rib1P		2	1315014
+1Cc.raw	Rib1P		2	10469
+1Bc.raw	Rib1P		3	176568
+1Cc.raw	Rib1P		3	246750
+1Bc.raw	Rib1P		4	596625
+1Cc.raw	Rib1P		4	0
+1Bc.raw	Rib1P		5	10429096
+1Cc.raw	Rib1P		5	0
+1Bc.raw	RibuBP		0	2230721
+1Cc.raw	RibuBP		0	23132056
+1Bc.raw	RibuBP		1	293094
+1Cc.raw	RibuBP		1	476256
+1Bc.raw	RibuBP		2	3889052
+1Cc.raw	RibuBP		2	22399
+1Bc.raw	RibuBP		3	821719
+1Cc.raw	RibuBP		3	1036051
+1Bc.raw	RibuBP		4	1959176
+1Cc.raw	RibuBP		4	0
+1Bc.raw	RibuBP		5	21985638
+1Cc.raw	RibuBP		5	15252
+1Bc.raw	CitIsocit		0	838341120
+1Cc.raw	CitIsocit		0	468549376
+1Bc.raw	CitIsocit		1	101047488
+1Cc.raw	CitIsocit		1	108765856
+1Bc.raw	CitIsocit		2	92395712
+1Cc.raw	CitIsocit		2	285495552
+1Bc.raw	CitIsocit		3	7150959
+1Cc.raw	CitIsocit		3	109556672
+1Bc.raw	CitIsocit		4	688004
+1Cc.raw	CitIsocit		4	77349936
+1Bc.raw	CitIsocit		5	151768
+1Cc.raw	CitIsocit		5	28082652
+1Bc.raw	CitIsocit		6	17839710
+1Cc.raw	CitIsocit		6	23705252
+1Bc.raw	Malate		0	22269720
+1Cc.raw	Malate		0	391202752
+1Bc.raw	Malate		1	2951479
+1Cc.raw	Malate		1	92022056
+1Bc.raw	Malate		2	151174
+1Cc.raw	Malate		2	119120744
+1Bc.raw	Malate		3	11304
+1Cc.raw	Malate		3	54604696
+1Bc.raw	Malate		4	15523
+1Cc.raw	Malate		4	9230890
+1Bc.raw	Succ		0	45289940
+1Cc.raw	Succ		0	41509728
+1Bc.raw	Succ		1	1848810
+1Cc.raw	Succ		1	2928804
+1Bc.raw	Succ		2	331868
+1Cc.raw	Succ		2	2333543
+1Bc.raw	Succ		3	0
+1Cc.raw	Succ		3	356473
+1Bc.raw	Succ		4	19201
+1Cc.raw	Succ		4	18578
+1Bc.raw	ADP		0	2440984576
+1Cc.raw	ADP		0	2201489152
+1Bc.raw	ADP		1	271398304
+1Cc.raw	ADP		1	237094816
+1Bc.raw	ADP		2	79139232
+1Cc.raw	ADP		2	54469464
+1Bc.raw	ADP		3	21046842
+1Cc.raw	ADP		3	16188251
+1Bc.raw	ADP		4	20803564
+1Cc.raw	ADP		4	1593009
+1Bc.raw	ADP		5	189281952
+1Cc.raw	ADP		5	2258170
+1Bc.raw	ADP		6	12261620
+1Cc.raw	ADP		6	1380628
+1Bc.raw	ADP		7	4199929
+1Cc.raw	ADP		7	1013611
+1Bc.raw	ADP		8	1020241
+1Cc.raw	ADP		8	344656
+1Bc.raw	ADP		9	707909
+1Cc.raw	ADP		9	420721
+1Bc.raw	ADP		10	286802
+1Cc.raw	ADP		10	365821
+1Bc.raw	ATP		0	352560256
+1Cc.raw	ATP		0	2799310848
+1Bc.raw	ATP		1	41379616
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+1Bc.raw	IMP		10	0
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