Mercurial > repos > workflow4metabolomics > skyline2isocor
changeset 0:d45fffedc467 draft
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>
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--- /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 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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 +1Cc.raw ATP 1 331956160 +1Bc.raw ATP 2 14031760 +1Cc.raw ATP 2 90597680 +1Bc.raw ATP 3 2838365 +1Cc.raw ATP 3 22771812 +1Bc.raw ATP 4 2316501 +1Cc.raw ATP 4 2131422 +1Bc.raw ATP 5 23784890 +1Cc.raw ATP 5 4392749 +1Bc.raw ATP 6 1430278 +1Cc.raw ATP 6 151160 +1Bc.raw ATP 7 448952 +1Cc.raw ATP 7 95579 +1Bc.raw ATP 8 139656 +1Cc.raw ATP 8 66479 +1Bc.raw ATP 9 24315 +1Cc.raw ATP 9 159731 +1Bc.raw ATP 10 824445 +1Cc.raw ATP 10 242683 +1Bc.raw CDP 0 277854432 +1Cc.raw CDP 0 180155776 +1Bc.raw CDP 1 25613546 +1Cc.raw CDP 1 17352972 +1Bc.raw CDP 2 6720281 +1Cc.raw CDP 2 4084237 +1Bc.raw CDP 3 595503 +1Cc.raw CDP 3 378573 +1Bc.raw CDP 4 822431 +1Cc.raw CDP 4 345580 +1Bc.raw CDP 5 15691563 +1Cc.raw CDP 5 874316 +1Bc.raw CDP 6 2569059 +1Cc.raw CDP 6 1719445 +1Bc.raw CDP 7 3205500 +1Cc.raw CDP 7 2595231 +1Bc.raw CDP 8 2198661 +1Cc.raw CDP 8 1984864 +1Bc.raw CDP 9 1912321 +1Cc.raw CDP 9 981080 +1Bc.raw CTP 0 97752376 +1Cc.raw CTP 0 354104640 +1Bc.raw CTP 1 9014061 +1Cc.raw CTP 1 37810844 +1Bc.raw CTP 2 2637210 +1Cc.raw CTP 2 12270652 +1Bc.raw CTP 3 493995 +1Cc.raw CTP 3 1147615 +1Bc.raw CTP 4 225668 +1Cc.raw CTP 4 374674 +1Bc.raw CTP 5 3881030 +1Cc.raw CTP 5 530041 +1Bc.raw CTP 6 321278 +1Cc.raw CTP 6 445751 +1Bc.raw CTP 7 567000 +1Cc.raw CTP 7 497650 +1Bc.raw CTP 8 436078 +1Cc.raw CTP 8 503947 +1Bc.raw CTP 9 379632 +1Cc.raw CTP 9 171234 +1Bc.raw Cytidine 0 110500024 +1Cc.raw Cytidine 0 94952984 +1Bc.raw Cytidine 1 6917021 +1Cc.raw Cytidine 1 6293648 +1Bc.raw Cytidine 2 253535 +1Cc.raw Cytidine 2 219137 +1Bc.raw Cytidine 3 91008 +1Cc.raw Cytidine 3 0 +1Bc.raw Cytidine 4 0 +1Cc.raw Cytidine 4 0 +1Bc.raw Cytidine 5 3953760 +1Cc.raw Cytidine 5 1140258 +1Bc.raw Cytidine 6 0 +1Cc.raw Cytidine 6 0 +1Bc.raw Cytidine 7 0 +1Cc.raw Cytidine 7 0 +1Bc.raw Cytidine 8 0 +1Cc.raw Cytidine 8 0 +1Bc.raw Cytidine 9 0 +1Cc.raw Cytidine 9 0 +1Bc.raw GDP 0 183419200 +1Cc.raw GDP 0 5829401 +1Bc.raw GDP 1 20590900 +1Cc.raw GDP 1 422107 +1Bc.raw GDP 2 7804884 +1Cc.raw GDP 2 92678 +1Bc.raw GDP 3 1823927 +1Cc.raw GDP 3 236742 +1Bc.raw GDP 4 2016415 +1Cc.raw GDP 4 13772 +1Bc.raw GDP 5 19619284 +1Cc.raw GDP 5 31978 +1Bc.raw GDP 6 1194784 +1Cc.raw GDP 6 26256 +1Bc.raw GDP 7 201536 +1Cc.raw GDP 7 36826 +1Bc.raw GDP 8 309616 +1Cc.raw GDP 8 43431 +1Bc.raw GDP 9 268794 +1Cc.raw GDP 9 0 +1Bc.raw GDP 10 77674 +1Cc.raw GDP 10 33280 +1Bc.raw GMP 0 131522216 +1Cc.raw GMP 0 397354 +1Bc.raw GMP 1 13938626 +1Cc.raw GMP 1 213919 +1Bc.raw GMP 2 3637522 +1Cc.raw GMP 2 0 +1Bc.raw GMP 3 606319 +1Cc.raw GMP 3 0 +1Bc.raw GMP 4 963454 +1Cc.raw GMP 4 0 +1Bc.raw GMP 5 13534815 +1Cc.raw GMP 5 0 +1Bc.raw GMP 6 134354 +1Cc.raw GMP 6 0 +1Bc.raw GMP 7 0 +1Cc.raw GMP 7 0 +1Bc.raw GMP 8 0 +1Cc.raw GMP 8 0 +1Bc.raw GMP 9 0 +1Cc.raw GMP 9 0 +1Bc.raw GMP 10 0 +1Cc.raw GMP 10 0 +1Bc.raw GTP 0 1377586 +1Cc.raw GTP 0 685898 +1Bc.raw GTP 1 169988 +1Cc.raw GTP 1 60237 +1Bc.raw GTP 2 338539 +1Cc.raw GTP 2 89532 +1Bc.raw GTP 3 15879 +1Cc.raw GTP 3 39374 +1Bc.raw GTP 4 10927 +1Cc.raw GTP 4 0 +1Bc.raw GTP 5 130142 +1Cc.raw GTP 5 25645 +1Bc.raw GTP 6 124400 +1Cc.raw GTP 6 16310 +1Bc.raw GTP 7 115268 +1Cc.raw GTP 7 4394 +1Bc.raw GTP 8 99669 +1Cc.raw GTP 8 14385 +1Bc.raw GTP 9 102146 +1Cc.raw GTP 9 44732 +1Bc.raw GTP 10 61715 +1Cc.raw GTP 10 31661 +1Bc.raw IMP 0 21731700 +1Cc.raw IMP 0 29553942 +1Bc.raw IMP 1 2046580 +1Cc.raw IMP 1 2483813 +1Bc.raw IMP 2 1102702 +1Cc.raw IMP 2 59175 +1Bc.raw IMP 3 750858 +1Cc.raw IMP 3 127272 +1Bc.raw IMP 4 798244 +1Cc.raw IMP 4 0 +1Bc.raw IMP 5 10917623 +1Cc.raw IMP 5 0 +1Bc.raw IMP 6 134071 +1Cc.raw IMP 6 0 +1Bc.raw IMP 7 102530 +1Cc.raw IMP 7 46581 +1Bc.raw IMP 8 0 +1Cc.raw IMP 8 0 +1Bc.raw IMP 9 0 +1Cc.raw IMP 9 0 +1Bc.raw IMP 10 0 +1Cc.raw IMP 10 0 +1Bc.raw UDP 0 414451744 +1Cc.raw UDP 0 701342400 +1Bc.raw UDP 1 47638556 +1Cc.raw UDP 1 115244616 +1Bc.raw UDP 2 47647284 +1Cc.raw UDP 2 59672152 +1Bc.raw UDP 3 23283766 +1Cc.raw UDP 3 28410322 +1Bc.raw UDP 4 31764274 +1Cc.raw UDP 4 5940255 +1Bc.raw UDP 5 312608064 +1Cc.raw UDP 5 8335464 +1Bc.raw UDP 6 25615516 +1Cc.raw UDP 6 716107 +1Bc.raw UDP 7 12679936 +1Cc.raw UDP 7 53200 +1Bc.raw UDP 8 962342 +1Cc.raw UDP 8 13484 +1Bc.raw UDP 9 134556 +1Cc.raw UDP 9 66458 +1Bc.raw UDPAcGlcN 0 147400880 +1Cc.raw UDPAcGlcN 0 497737888 +1Bc.raw UDPAcGlcN 1 34547192 +1Cc.raw UDPAcGlcN 1 124516552 +1Bc.raw UDPAcGlcN 2 23484704 +1Cc.raw UDPAcGlcN 2 209956608 +1Bc.raw UDPAcGlcN 3 25758670 +1Cc.raw UDPAcGlcN 3 65518868 +1Bc.raw UDPAcGlcN 4 20443204 +1Cc.raw UDPAcGlcN 4 24415836 +1Bc.raw UDPAcGlcN 5 108661952 +1Cc.raw UDPAcGlcN 5 15392614 +1Bc.raw UDPAcGlcN 6 230854064 +1Cc.raw UDPAcGlcN 6 6333184 +1Bc.raw UDPAcGlcN 7 45257816 +1Cc.raw UDPAcGlcN 7 4478011 +1Bc.raw UDPAcGlcN 8 47845764 +1Cc.raw UDPAcGlcN 8 4448550 +1Bc.raw UDPAcGlcN 9 20391152 +1Cc.raw UDPAcGlcN 9 3971238 +1Bc.raw UDPAcGlcN 10 30479670 +1Cc.raw UDPAcGlcN 10 3172275 +1Bc.raw UDPAcGlcN 11 141836016 +1Cc.raw UDPAcGlcN 11 4611530 +1Bc.raw UDPAcGlcN 12 19285690 +1Cc.raw UDPAcGlcN 12 3801463 +1Bc.raw UDPAcGlcN 13 18404962 +1Cc.raw UDPAcGlcN 13 4689228 +1Bc.raw UDPAcGlcN 14 4729885 +1Cc.raw UDPAcGlcN 14 3879133 +1Bc.raw UDPAcGlcN 15 4016577 +1Cc.raw UDPAcGlcN 15 5293326 +1Bc.raw UDPAcGlcN 16 3331716 +1Cc.raw UDPAcGlcN 16 3679576 +1Bc.raw UDPAcGlcN 17 4362360 +1Cc.raw UDPAcGlcN 17 4082185 +1Bc.raw UMP 0 492295488 +1Cc.raw UMP 0 678773184 +1Bc.raw UMP 1 54854400 +1Cc.raw UMP 1 106707688 +1Bc.raw UMP 2 48958356 +1Cc.raw UMP 2 48354456 +1Bc.raw UMP 3 24356038 +1Cc.raw UMP 3 24149268 +1Bc.raw UMP 4 34483400 +1Cc.raw UMP 4 4240274 +1Bc.raw UMP 5 354854400 +1Cc.raw UMP 5 2430849 +1Bc.raw UMP 6 27630432 +1Cc.raw UMP 6 60106 +1Bc.raw UMP 7 10287202 +1Cc.raw UMP 7 0 +1Bc.raw UMP 8 256329 +1Cc.raw UMP 8 0 +1Bc.raw UMP 9 0 +1Cc.raw UMP 9 0