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Changeset 0:3cb0128a59a6 (2024-03-28)

Next changeset 1:ea6ea4029c47 (2024-08-22)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590

added:
macros.xml
test-data/Absolute_isotopologue_abundances.tsv
test-data/AbundanceCorrected.tsv
test-data/CorrectedIsotopologues.tsv
test-data/Corrected_isotope_abundances.tsv
test-data/FracContribution_C.tsv
test-data/Isotopologue_proportional_abundances.tsv
test-data/IsotopologuesAbs.tsv
test-data/IsotopologuesProp.tsv
test-data/MeanEnrichment13C.tsv
test-data/Mean_enrichment_data.tsv
test-data/TRACER_IsoCor_out_example.tsv
test-data/TRACER_dataMatrix.tsv
test-data/TRACER_generic_sheet.xlsx
test-data/TRACER_metabo_4.xlsx
test-data/isotopologuesCorrValues.tsv
test-data/rawAbundances.tsv
test-data/sampleMetadata_1.csv
test-data/sampleMetadata_2.tsv
test-data/sampleMetadata_3.csv
test-data/sampleMetadata_4.csv
test-data/variableMetadata.tsv
tracegroomer.xml

diff -r 000000000000 -r 3cb0128a59a6 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Mar 28 13:19:21 2024 +0000

b'@@ -0,0 +1,109 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">0.1.3</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">tracegroomer</requirement>\n+ </requirements>\n+ </xml>\n+ <xml name="input_datasets">\n+ <param name="labeled_metabo_file" type="data" optional="false" format="tabular,xlsx" label="Labeled metabolomics file"/>\n+ <param name="sample_metadata_path" type="data" format="tabular" label="sample metadata file" help="The metadata, a unique file with the description of the samples in your measures files. This is compulsory, see section Metadata File Information."/>\n+ <param name="amount_material" type="data" optional="true" format="interval" label="amount material" help="Absolute path to the file having the amount of material by sample, for the normalization. This file must be a tab delimited file with exactly 2 columns with a header: the first column contains the original names of the samples, and the second column the numbers (tissue weight, number of cells, volume, etc)"/>\n+ <param name="remove_these_metabolites" type="data" optional="true" format="interval" label="remove metabolites using this file" help="Absolute path to the tab delimited file with columns: compartment, metabolite. This file lists the metabolites to be completely excluded, compartment specific. Defining such exclusion list requires deep knowledge of the data by the user (measurements coherence/quality, etc)"/>\n+ <conditional name="type_of_file">\n+ <param name="type_of_file_selector" type="select" label="Choose which type of input file is used" help="One of the following: IsoCor_out_tsv|rule_tsv|VIBMEC_xlsx|generic_xlsx">\n+ <option value="IsoCor_out_tsv" selected="true">isocor output file</option>\n+ <option value="VIBMEC_xlsx">VIBMEC xlsx file</option>\n+ <option value="generic_xlsx">generic xlsx file</option>\n+ <option value="rule_tsv">rule tsv file</option>\n+ </param>\n+ <when value="IsoCor_out_tsv">\n+ </when>\n+ <when value="generic_xlsx">\n+ <param name="sheetname" type="text" value="isotopologuesCorrValues" optional="false" label="name of the sheet containing the isotopologues corrected values" >\n+ <sanitizer invalid_char="">\n+ <valid initial="string.ascii_letters,string.digits">\n+ <add value="_" />\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ <when value="VIBMEC_xlsx">\n+ <param name="raw_abundance_sheet_name" type="text" value="rawAbundances" optional="false" label="name of the sheet containing the raw abundances values" >\n+ <sanitizer invalid_char="">\n+ <valid initial="string.ascii_letters,string.digits">\n+ <add value="_" />\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="frac_contribution_sheet_name" type="text" value="FracContribution_C" optional="false" label="name of the sheet containing the mean enrichment values" >\n+ <sanitizer invalid_char="">\n+ <valid initial="string.ascii_letters,string.digits">\n+ <add value="_" />\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="corrected_isotopologues_sheet_name" type="text" value="CorrectedIsotopologues" optional="false" label="name of the sheet containing the isotopologues corrected values" >\n+ <sanitizer invalid_char="">\n+ <vali'..b'isotopologue number in variable metadata file" >\n+ <sanitizer invalid_char="">\n+ <valid initial="string.ascii_letters,string.digits">\n+ <add value="_" />\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ </section>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="advanced_options">\n+ <section name="advanced_options" title="Advanced options" expanded="false">\n+\n+ <param name="alternative_div_amount_material" type="boolean" truevalue="--alternative_div_amount_material" falsevalue="" label="alternative isotopologues division by amount material" help="In the normalisation by the amount of material, not only the division of the given absolute values by these amounts is performed, but also the product of the resulting quotients and the averaged amount of material is computed"/>\n+ <param name="div_isotopologues_by_amount_material" type="boolean" truevalue="--div_isotopologues_by_amount_material" falsevalue="" label="isotopologues by amount material" help="Apply normalization by the amount of material at the level of isotopologue absolute values. Immediately after this, and before any other computation, tracegroomer re-computes all derived (thus normalized) metrics"/>\n+ <param name="isotopologues_preview" type="boolean" truevalue="--isotopologues_preview" falsevalue="" label="Plot isotopologue" help="Generate simple plots that give a general overview of the isotopologue proportions given by the user. Performs a scatter plot of the individual isotopologue proportions for all metabolites, as well as a plot of the sums of isotopologue proportions (the sum must be equal to 1 for each metabolite and sample)"/>\n+ <param name="fractions_stomp_values" type="boolean" truevalue="--fractions_stomp_values" falsevalue="" label="Stomps fractional contributions" help="Stomps fractional contributions (synonym: mean enrichment), and isotopologue proportions, to max 1.0 and min 0.0"/>\n+ <param name="subtract_blankavg" type="boolean" truevalue="--subtract_blankavg" falsevalue="" label="" help="from samples\' abundances, subtracts the average of the blanks for all metabolites across all samples. Note that the Internal Standards are not subjected to this operation, as recommended by VIB platform"/>\n+ <param name="under_detection_limit_set_nan" type="boolean" truevalue="--under_detection_limit_set_nan" falsevalue="" label="Limit Of Detection" help="The Limit Of Detection, LOD, corresponds to the averaged blanks abundance values, multiplied by three times the blanks standard deviation. By default, any value that is strictly inferior to its corresponding LOD, is converted into NaN"/>\n+ <param name="use_internal_standard" type="text" optional="true" help="The name of the internal standard, which is a compound or metabolite that has been stated as reference signal. By providing this name, the normalization by the internal standard is automatically performed" label="internal standard" />\n+ <param name="isosprop_min_admitted" type="float" min="-1.0" max="1.0" value="-0.5" label="isotopologues cutoff" help="Metabolites whose isotopologue proportions are less or equal to this cutoff, are removed"/>\n+ </section>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="bibtex">\n+ @software{Galvis_Rodriguez_DIMet,\n+ author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},\n+ license = {MIT},\n+ title = {{DIMet}},\n+ url = {https://github.com/cbib/DIMet}\n+ }\n+ </citation>\n+ </citations>\n+\n+ </xml>\n+</macros>\n\\ No newline at end of file\n'

diff -r 000000000000 -r 3cb0128a59a6 test-data/Absolute_isotopologue_abundances.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Absolute_isotopologue_abundances.tsv Thu Mar 28 13:19:21 2024 +0000

@@ -0,0 +1,24 @@
+ID A_T0_endo-1 A_T0_endo-2 Cont_T0_endo-1 Cont_T0_endo-2 A_T24_endo-1 A_T24_endo-2 Cont_T24_endo-1 Cont_T24_endo-2 A_T0_exo-1 A_T0_exo-2 Cont_T0_exo-1 Cont_T0_exo-2 A_T24_exo-1 A_T24_exo-2 Cont_T24_exo-1 Cont_T24_exo-2
+2-OHGLu_m+0 5550339.322 6072872.833 5893256.269 7454336.274 3855047.791 3216178.72 4066632.965 5550339.322 6072872.833 5893256.269 7454336.274 3855047.791 3216178.72 3102049.195 4066632.965
+2-OHGLu_m+1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+2-OHGLu_m+2 62163.30727 108839.8963 9976.217534 53035.94662 3114533.603 2691689.195 1611494.416 62163.30727 108839.8963 9976.217534 53035.94662 3114533.603 2691689.195 1845577.773 1611494.416
+2-OHGLu_m+3 33950.03875 57015.80123 16218.60873 34068.8323 964673.6406 804919.6602 479959.6627 33950.03875 57015.80123 16218.60873 34068.8323 964673.6406 804919.6602 474922.8927 479959.6627
+2-OHGLu_m+4 31513.15643 43506.47502 18965.84568 23046.25122 5436469.924 4706821.45 2732129.436 31513.15643 43506.47502 18965.84568 23046.25122 5436469.924 4706821.45 3200529.756 2732129.436
+2-OHGLu_m+5 27688.74195 43567.73063 0.0 17896.32501 2769721.539 2302254.26 1298081.886 27688.74195 43567.73063 0.0 17896.32501 2769721.539 2302254.26 1488534.123 1298081.886
+2_3-PG_m+0 206171.4626 285834.0353 298441.8262 268050.3636 36413.27637 27367.17784 26381.30429 23698.7623 206171.4626 285834.0353 298441.8262 268050.3636 36413.27637 27367.17784 26381.30429 23698.7623
+2_3-PG_m+1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+2_3-PG_m+2 133780.182 161461.2364 200778.0533 197229.6694 182631.3947 132170.3807 146120.9923 89966.23931 133780.182 161461.2364 200778.0533 197229.6694 182631.3947 132170.3807 146120.9923 89966.23931
+2_3-PG_m+3 8358749.348 10271010.45 11787744.65 11554464.86 10505228.3 8376820.028 9033424.374 6122480.462 8358749.348 10271010.45 11787744.65 11554464.86 10505228.3 8376820.028 9033424.374 6122480.462
+6-PG_m+0 309932.3475 342540.1698 253560.3827 242260.6594 101608.1805 84940.35902 85240.79781 67359.24717 309932.3475 342540.1698 253560.3827 242260.6594 101608.1805 84940.35902 85240.79781 67359.24717
+6-PG_m+1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+6-PG_m+2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+6-PG_m+3 7664.136895 8906.391308 0.0 0.0 0.0 0.0 0.0 0.0 7664.136895 8906.391308 0.0 0.0 0.0 0.0 0.0 0.0
+6-PG_m+4 11950.01113 11674.22491 9922.705217 15475.23458 45346.04708 36334.93958 34524.35854 26037.70094 11950.01113 11674.22491 9922.705217 15475.23458 45346.04708 36334.93958 34524.35854 26037.70094
+6-PG_m+5 520904.6672 608128.1002 405342.3913 815587.5165 2390706.721 1802278.633 1807036.326 1207909.718 520904.6672 608128.1002 405342.3913 815587.5165 2390706.721 1802278.633 1807036.326 1207909.718
+6-PG_m+6 7423820.948 8341569.748 5394323.444 7384800.665 15231875.3 12525321.98 11279297.92 8040213.605 7423820.948 8341569.748 5394323.444 7384800.665 15231875.3 12525321.98 11279297.92 8040213.605
+a-KG_m+0 441807.2042 612669.4773 552526.6043 482434.0877 1476617.063 1056307.521 572619.741 546375.578 441807.2042 612669.4773 552526.6043 482434.0877 1476617.063 1056307.521 572619.741 546375.578
+a-KG_m+1 6581.125045 12456.03716 0.0 2085.213699 77677.31383 46821.38405 28170.23998 32113.8241 6581.125045 12456.03716 0.0 2085.213699 77677.31383 46821.38405 28170.23998 32113.8241
+a-KG_m+2 70778.42058 118643.5176 46309.55877 54983.84668 1907292.33 1596531.466 636158.2851 415566.8382 70778.42058 118643.5176 46309.55877 54983.84668 1907292.33 1596531.466 636158.2851 415566.8382
+a-KG_m+3 22143.37798 32170.99354 13728.65106 12489.92256 623361.4049 483118.3355 149649.632 103268.9093 22143.37798 32170.99354 13728.65106 12489.92256 623361.4049 483118.3355 149649.632 103268.9093
+a-KG_m+4 21225.1587 33085.30969 9561.259531 10809.82522 3267732.931 2762185.304 1099424.672 647876.2431 21225.1587 33085.30969 9561.259531 10809.82522 3267732.931 2762185.304 1099424.672 647876.2431
+a-KG_m+5 0.0 0.0 0.0 0.0 1721462.381 1381372.254 489385.3877 299919.5187 0.0 0.0 0.0 0.0 1721462.381 1381372.254 489385.3877 299919.5187

diff -r 000000000000 -r 3cb0128a59a6 test-data/AbundanceCorrected.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/AbundanceCorrected.tsv Thu Mar 28 13:19:21 2024 +0000

@@ -0,0 +1,39 @@
+ID T0_A_1 T0_A_2 T24_A_1 T24_A_2
+2_3-PG 8698700.9926 10718305.7217 10724272.97107 8536357.58654
+2-OHGLu 5705654.5664 6325802.73618 16140446.4976 13721863.2852
+6-PG 8274272.110725 9312818.634218 17769536.24858 14448875.911600001
+a-KG 562535.286505 809025.3352900001 9074143.42373 7326336.2645499995
+Cit 6104076.527709001 6622207.696758 17362710.7065 15099558.4283
+Fru6P 4798767.932639999 4513233.6544699995 4837930.1953 3290337.21892
+FruBP 38638958.584489994 35926915.2997 15919121.42811 12742908.812899
+Fru1P 8649509.40162 9221146.82622 7263530.71345 6382941.54406
+Fum 849934.584649 1331932.8614599998 2536771.76908 2002385.5281600002
+Glc6P 1371473.29828 1417858.38996 2378469.26438 1566613.8815600001
+Gly3P 2279532.84135 1472280.30519 2323362.4118999997 1159698.9703000002
+IsoCit 686751.7917999999 765537.5006919999 1173628.11465 958226.4224050001
+Mal 16359379.550800001 21696115.306900002 30979835.452200003 28483388.116600007
+P5P 1622226.252397 2101779.62568 4042496.89333 2745142.88324
+PEP 372560.40297 389149.56301800004 901546.463227 300696.507413
+PRPP 3265374.30386 1403175.78537 4685589.198954 1127901.1055990001
+Pyr 8072604.6678 5417572.18565 19414603.972400002 10572949.759383999
+Rib1P 506931.49994 515317.83285 1058757.54637 600209.415023
+Sed7P 405451.02691599994 404632.682093 4256316.13784 3311139.573476
+Suc 16696697.2474 24960174.386 15430602.704 19913145.336999997
+ADP 34025169.109877 37691400.360171005 37723605.076560006 32519284.07825
+AMP 9565403.92 9556049.635 7405683.36312 5000743.872590001
+ATP 41541098.171906 28333872.96799 43782778.395509996 24613580.795915
+CDP 3658703.167 4549519.711 2782262.726477 2433762.26766
+CMP 2104346.331 1898991.26 1261049.8005600001 716871.07791
+CTP 11009149.04 9279476.88 9892652.365619998 6630162.09119
+GDP 9123811.404098999 9618774.8438531 9949031.84874 7448744.72431
+GMP 1040843.97418 983805.82424 955450.71251 624256.36527
+GTP 12846360.211278 8724055.649473 11838142.32576 4862598.134269999
+UDP 19095395.197940003 22041850.9617 26939623.55273 25193602.076109998
+UMP 29113743.746113002 27845070.620795995 31071457.37046 23274629.08901
+UTP 37904488.04698 32947660.03249 41928292.11218999 30037598.8316
+Glutamate 8642056.8426 17149266.2103 47245553.7829 42301398.0359
+Alanine 26433669.23424036 29757276.54221551 114131556.02470112 105304217.6372259
+Aspartate 4153600.4715071535 23560016.546284568 20479103.26962672 28642684.62216362
+Glutamine 15391319.615471464 49113624.6255005 35714798.47397325 26092787.779812228
+Glycine 354765284.35181 292769623.48668975 574309132.522843 468271969.5574398
+Serine 773712972.5683433 1423520249.5635524 1965385721.033115 1753994669.6276615

diff -r 000000000000 -r 3cb0128a59a6 test-data/CorrectedIsotopologues.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CorrectedIsotopologues.tsv Thu Mar 28 13:19:21 2024 +0000

b'@@ -0,0 +1,197 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e_m+4\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\n+L-Tryptophan_m+1\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+10\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+11\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+2\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+3\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+4\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+5\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+6\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+7\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+8\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tryptophan_m+9\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tyrosine_m+0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\n+L-Tyrosine_m+1\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tyrosine_m+2\t0.0004\t0.0\t0.0004\t0.0006\t0.0004\t0.0004\t0.0006\t0.0005\t0.0008\t0.0007\t0.0005\t0.0005\t0.0009\t0.0008\t0.0003\t0.0006\n+L-Tyrosine_m+3\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tyrosine_m+4\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tyrosine_m+5\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tyrosine_m+6\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tyrosine_m+7\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tyrosine_m+8\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Tyrosine_m+9\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Valine_m+0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\n+L-Valine_m+1\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Valine_m+2\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Valine_m+3\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Valine_m+4\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+L-Valine_m+5\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+Oxoglutaric_acid_m+0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Oxoglutaric_acid_m+1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Oxoglutaric_acid_m+2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Oxoglutaric_acid_m+3\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Oxoglutaric_acid_m+4\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Oxoglutaric_acid_m+5\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Phosphoenolpyruvic_acid_m+0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Phosphoenolpyruvic_acid_m+1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Phosphoenolpyruvic_acid_m+2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Phosphoenolpyruvic_acid_m+3\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Pyruvic_acid_m+0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.0\t0.9974\t0.9982\t1.0\t1.0\t0.997\t0.9964\n+Pyruvic_acid_m+1\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+Pyruvic_acid_m+2\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+Pyruvic_acid_m+3\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t1.0\t0.0004\t0.0003\t0.0031\t0.0033\t0.0005\t0.0005\t0.004\t0.0039\n+Succinic_acid_m+0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Succinic_acid_m+1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Succinic_acid_m+2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Succinic_acid_m+3\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+Succinic_acid_m+4\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+cis-Aconitic_acid_m+0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+cis-Aconitic_acid_m+1\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+cis-Aconitic_acid_m+2\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+cis-Aconitic_acid_m+3\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+cis-Aconitic_acid_m+4\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+cis-Aconitic_acid_m+5\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+cis-Aconitic_acid_m+6\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n'

diff -r 000000000000 -r 3cb0128a59a6 test-data/Corrected_isotope_abundances.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Corrected_isotope_abundances.tsv Thu Mar 28 13:19:21 2024 +0000

@@ -0,0 +1,34 @@
+ID MCF001089_TD01 MCF001089_TD02 MCF001089_TD07 MCF001089_TD08 MCF001089_TD19 MCF001089_TD20 MCF001089_TD25 MCF001089_TD26 MCF001089_TD37 MCF001089_TD38 MCF001089_TD43 MCF001089_TD44 MCF001089_TD55 MCF001089_TD56 MCF001089_TD61 MCF001089_TD62
+3-Phosphoglyceric_acid 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Citric_acid
+D-Glyceraldehyde_3-phosphate 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Dihydroxyacetone_phosphate
+Fructose_1,6-bisphosphate 162935.97333333333 94989.17333333334 977244.4733333333 77200.80333333333 217163.87333333332
+Fumaric_acid 2648793.2333333343 4700203.413333334 1696830.2833333388 3272290.323333338 2781852.883333333 5501278.903333336 4164455.0233333334
+Glycine 47009772.21666667 39907004.71666667 45033211.11666667 53735758.81666667 50433589.71666667 49423644.81666667 47224484.31666667 51463639.71666667 21082398.016666666 20528546.116666667 19650482.416666664 19152242.516666666 35768152.41666667 21132662.81666667 21540901.71666667 22233782.916666664
+Hexose 22895288.373333335 21306408.843333334 22860798.743333336 24388352.143333334 23211597.943333335 24961340.313333336 20107687.483333334 23348729.473333333 23812934.643333334 24242428.643333334 22336054.643333334 22906432.643333334 23957348.643333334 23850557.643333334 26889340.643333334 25837975.643333334
+Hexose-phosphate 835186009.5666667 821409929.5666667 646107269.5666667 915363979.5666667 843870509.5666667 818259399.5666667 688064609.5666667 833172229.5666667 1792538.5666666667 1790949.5666666667 1218328.5666666667 1457111.5666666667 2069691.5666666667 1915534.5666666667 1684708.5666666667 1734938.5666666667
+Ile_Leu 1085543492.1333334 1742235058.1333334 1299634032.1333334 1349865884.1333334 1364458522.1333334 1545744172.1333334 1062112159.1333333 1266905279.1333334 2111708660.1333334 2203285239.133333 2037012929.1333334 2023660803.1333334 2311992779.133333 2210982973.133333 2389754947.133333 2339735205.133333
+L-Alanine 21872810.7 15633126.799999999 21168503.7 29253021.3 24452809.599999998 22135270.189999998 24185570.0 26552869.2 1548485.77 1701510.73 1309197.7400000002 1820745.4700000002 1935085.62 1763954.77 1931224.9000000004 2282473.1300000004
+L-Arginine 8520549.7 14932662.400000002 12547158.600000001 8138626.600000001 12848074.600000001 13019470.600000001 8830924.400000002 8993576.3 76704557.1 76562817.1 74284491.1 72162535.1 76269336.1 76291863.1 74652772.1 74944609.1
+L-Asparagine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3617749.87 3435790.2 2756887.13 2910381.68 3513705.7 3293797.9 3311566.8 3892175.2
+L-Aspartic_acid 107230174.01 110752624.0 25085218.509999998 40471356.010000005 85804028.48 80919141.14 22993878.009999998 31233419.71
+L-Glutamic_acid 208787069.89000002 208710973.69 140917516.99 213909793.99 205653213.29000002 195563405.39000002 143617980.99 190106133.99
+L-Glutamine 27909494.383333337 19726522.883333337 13536124.283333335 17913920.783333335 21753742.583333336 18810914.783333335 12284238.233333334 13716599.583333336 1098507.4833333334
+L-Histidine 24630581.03333333 30222238.633333333 24647318.53333333 23434135.833333332 30638205.633333333 28288641.633333333 21809509.233333334 22700730.233333334 66137818.63333333 67607708.63333334 63420421.63333333 61687625.63333333 64943662.63333333 66958084.63333333 67970373.63333334 69607422.63333334
+L-Lactic_acid 1610410544.0933332 3445168544.0933332 2919903764.0933332 1983632154.0933332 2199680624.0933332 2542765424.0933332 1843083224.0933332 1902389044.0933332 9322737799.093334 9302697744.093334 9196079213.093334 8719390692.093334 8901197393.093334 8704911808.093334 9400722189.093334 9863466762.093334
+L-Lysine 17306605.213333335 27612732.113333333 25001333.713333335 17627879.713333335 22933518.813333336 23028350.513333336 19929114.283333335 18884558.213333335 117443154.71333334 121027940.71333334 115723826.71333334 115850611.09333333 119744345.59333333 119004184.71333334 118584270.71333334 117133694.71333334
+L-Malic_acid 125152779.87999988 168222179.57999992 85536019.07999992 153093796.07999992 199415044.87999988 209808502.53999996 111048528.07999992 168084959.07999992
+L-Methionine 76429637.58666667 98173993.58666667 84143963.58666667 90434705.32666667 96650857.58666667 103577905.58666667 76103044.58666667 89472771.65666667 111550662.21666667 114041484.58666667 102236906.58666667 107705253.05666667 118873593.96666667 116214414.89666668 118851523.58666667 123449681.58666667
+L-Phenylalanine 370126893.4666667 588622197.8666667 421973046.1666667 444230948.8666667 473599834.8666667 525083162.8666667 347373413.3666667 417141280.8666667 636990553.8666667 649933157.8666667 607515203.8666667 606053781.8666667 685784788.8666667 665904616.8666667 714741480.8666667 705881485.8666667
+L-Proline 9599080.903333332 9653640.033333333 10532847.213333333 13935072.823333332 10491525.033333333 12535154.033333333 12320625.353333334 13734070.333333334 6433495.033333333 6609824.833333334 5540393.533333333 4245151.533333333 7152407.533333333 6966378.033333333 9268074.033333333 9909521.833333334
+L-Serine 51886840.156666666 55687429.156666666 60878065.156666666 61566987.156666666 60262908.156666666 64646815.156666666 55146456.156666666 61235459.156666666 85713015.15666667 86442185.15666667 80830195.15666667 77735867.15666667 87723164.15666667 84905739.15666667 90456917.15666667 93913089.15666667
+L-Threonine 243276910.8 244437112.15 239746844.79 260796044.54 283078723.92 289486426.92 226742219.26 250548515.2 285717399.29 278341478.49 261018102.39 262753775.69 287841134.94 283733608.09 296904540.79 288355169.29
+L-Tryptophan 6151602.633333334 9627805.133333333 7714718.933333333 5221846.633333334 7438842.333333333 7276985.333333333 6471170.333333333 5357077.223333334 23656601.733333334 24177093.733333334 23401859.733333334 19146747.733333334 22572464.733333334 20887438.733333334 20532655.733333334 21681238.733333334
+L-Tyrosine 324490904.90666664 466056869.90666664 353168947.2066667 378269079.3066666 396880514.3066666 445171883.90666664 296338856.50666666 356363844.90666664 526242843.90666664 541860987.9066666 489041215.90666664 498219681.90666664 554116402.9066666 532238404.90666664 568375310.9066666 574309133.9066666
+L-Valine 307200691.89666665 359678830.37666667 372899784.59666663 366829310.99666667 383925888.89666665 426836324.39666665 308762091.34666663 357769753.69666666 577225423.9966667 578990937.1966666 545903388.7966666 557138987.7966666 606569154.8966666 603361959.6966666 611454433.5966667 621103613.1966666
+Oxoglutaric_acid
+Phosphoenolpyruvic_acid
+Pyruvic_acid 944306.6333333333 2936758.6333333333 3644797.6333333333 5342829.633333333 1875311.6333333333 2239637.6333333333 2881917.6333333333 4024104.6333333333 1917193228.8333335 1800847679.2333333 1898133517.2333333 1831205498.1333334 1954504808.4333334 1917436849.8333335 1873057071.1333334 2047218329.5333335
+Succinic_acid
+cis-Aconitic_acid 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

diff -r 000000000000 -r 3cb0128a59a6 test-data/FracContribution_C.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/FracContribution_C.tsv Thu Mar 28 13:19:21 2024 +0000

@@ -0,0 +1,37 @@
+ID MCF001089_TD01 MCF001089_TD02 MCF001089_TD07 MCF001089_TD08 MCF001089_TD19 MCF001089_TD20 MCF001089_TD25 MCF001089_TD26 MCF001089_TD37 MCF001089_TD38 MCF001089_TD43 MCF001089_TD44 MCF001089_TD55 MCF001089_TD56 MCF001089_TD61 MCF001089_TD62
+Citric_acid
+D.Glyceraldehyde_3.phosphate
+Dihydroxyacetone_phosphate
+Fructose.1.6.bisphosphate
+Fumaric_acid 0.0 0.0 0.0 0.0019 0.0 0.0 0.0005
+Glycine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Hexose 0.0076 0.0017 0.0051 0.0025 0.0058 0.0052 0.0042 0.0046 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+Hexose.phosphate
+Ile_Leu 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+L.Alanine
+L.Arginine
+L.Asparagine
+L.Aspartic_acid
+L.Glutamic_acid
+L.Glutamine
+L.Histidine
+L.Lactic_acid
+L.Lysine
+L.Malic_acid
+L.Methionine
+L.Phenylalanine
+L.Proline
+L.Serine
+L.Threonine
+L.Tryptophan
+L.Tyrosine
+L.Valine
+Oxoglutaric_acid
+Phosphoenolpyruvic_acid
+Pyruvic_acid 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0029 0.0027 0.0001 0.0001 0.0036 0.0038
+Succinic_acid
+X01_Glycolysis
+X02_Krebs.Cycle
+X03_Amino.Acids
+X3.Phosphoglyceric_acid
+cis.Aconitic_acid

diff -r 000000000000 -r 3cb0128a59a6 test-data/Isotopologue_proportional_abundances.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Isotopologue_proportional_abundances.tsv Thu Mar 28 13:19:21 2024 +0000

diff -r 000000000000 -r 3cb0128a59a6 test-data/IsotopologuesAbs.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/IsotopologuesAbs.tsv Thu Mar 28 13:19:21 2024 +0000

b'@@ -0,0 +1,273 @@\n+ID\tT0_A_1\tT0_A_2\tT24_A_1\tT24_A_2\n+2_3-PG_m+0\t206171.4626\t285834.0353\t36413.27637\t27367.17784\n+2_3-PG_m+1\t0.0\t0.0\t0.0\t0.0\n+2_3-PG_m+2\t133780.182\t161461.2364\t182631.3947\t132170.3807\n+2_3-PG_m+3\t8358749.348\t10271010.45\t10505228.3\t8376820.028\n+2-OHGLu_m+0\t5550339.322\t6072872.833\t3855047.791\t3216178.72\n+2-OHGLu_m+1\t0.0\t0.0\t0.0\t0.0\n+2-OHGLu_m+2\t62163.30727\t108839.8963\t3114533.603\t2691689.195\n+2-OHGLu_m+3\t33950.03875\t57015.80123\t964673.6406\t804919.6602\n+2-OHGLu_m+4\t31513.15643\t43506.47502\t5436469.924\t4706821.45\n+2-OHGLu_m+5\t27688.74195\t43567.73063\t2769721.539\t2302254.26\n+6-PG_m+0\t309932.3475\t342540.1698\t101608.1805\t84940.35902\n+6-PG_m+1\t0.0\t0.0\t0.0\t0.0\n+6-PG_m+2\t0.0\t0.0\t0.0\t0.0\n+6-PG_m+3\t7664.136895\t8906.391308\t0.0\t0.0\n+6-PG_m+4\t11950.01113\t11674.22491\t45346.04708\t36334.93958\n+6-PG_m+5\t520904.6672\t608128.1002\t2390706.721\t1802278.633\n+6-PG_m+6\t7423820.948\t8341569.748\t15231875.3\t12525321.98\n+a-KG_m+0\t441807.2042\t612669.4773\t1476617.063\t1056307.521\n+a-KG_m+1\t6581.125045\t12456.03716\t77677.31383\t46821.38405\n+a-KG_m+2\t70778.42058\t118643.5176\t1907292.33\t1596531.466\n+a-KG_m+3\t22143.37798\t32170.99354\t623361.4049\t483118.3355\n+a-KG_m+4\t21225.1587\t33085.30969\t3267732.931\t2762185.304\n+a-KG_m+5\t0.0\t0.0\t1721462.381\t1381372.254\n+Cit_m+0\t3639184.111\t3835186.021\t3350676.17\t2780310.907\n+Cit_m+1\t0.0\t5642.249156\t206041.2034\t167996.5509\n+Cit_m+2\t834839.4782\t924585.3381\t3316645.42\t3032109.913\n+Cit_m+3\t889802.9149\t1013932.124\t1512552.578\t1309751.157\n+Cit_m+4\t215534.0325\t232187.4598\t4401035.422\t3925133.167\n+Cit_m+5\t520405.0021\t605895.3614\t4298813.787\t3745478.97\n+Cit_m+6\t4310.989009\t4779.143302\t276946.1261\t138777.7634\n+Fru6P_m+0\t170520.7743\t166316.6562\t0.0\t0.0\n+Fru6P_m+1\t0.0\t0.0\t0.0\t0.0\n+Fru6P_m+2\t0.0\t0.0\t0.0\t0.0\n+Fru6P_m+3\t25916.65274\t23462.35397\t3.57e-11\t9.08e-12\n+Fru6P_m+4\t0.0\t0.0\t0.0\t0.0\n+Fru6P_m+5\t130538.1956\t140929.0743\t149826.4473\t68739.12792\n+Fru6P_m+6\t4471792.31\t4182525.57\t4688103.748\t3221598.091\n+FruBP_m+0\t187489.9969\t181644.3962\t12286.87822\t8501.84168\n+FruBP_m+1\t0.0\t0.0\t0.0\t0.0\n+FruBP_m+2\t0.0\t865.41032\t0.0\t0.0\n+FruBP_m+3\t863328.265\t786930.0625\t18352.02563\t15569.33664\n+FruBP_m+4\t14882.67759\t14776.22268\t11290.95556\t8166.814379\n+FruBP_m+5\t2184204.485\t2008413.688\t814923.9887\t615276.2002\n+FruBP_m+6\t35389053.16\t32934285.52\t15062267.58\t12095394.62\n+Fru1P_m+0\t3269098.651\t3582721.998\t0.0\t0.0\n+Fru1P_m+1\t0.0\t0.0\t79227.74785\t60896.74846\n+Fru1P_m+2\t0.0\t0.0\t0.0\t0.0\n+Fru1P_m+3\t72494.90812\t78737.83772\t0.0\t0.0\n+Fru1P_m+4\t0.0\t0.0\t0.0\t0.0\n+Fru1P_m+5\t180110.7695\t192583.6675\t262258.5296\t217637.4606\n+Fru1P_m+6\t5127805.073\t5367103.323\t6922044.436\t6104407.335\n+Fum_m+0\t607669.8452\t1025669.59\t1068017.927\t985779.3926\n+Fum_m+1\t5817.345549\t30173.77921\t21432.82565\t74299.66462\n+Fum_m+2\t27633.8473\t58570.49985\t432417.9707\t341705.372\n+Fum_m+3\t208813.5466\t217518.9924\t970861.002\t559981.3751\n+Fum_m+4\t0.0\t0.0\t44042.04373\t40619.72384\n+Glc6P_m+0\t0.0\t0.0\t0.0\t0.0\n+Glc6P_m+1\t0.0\t0.0\t0.0\t0.0\n+Glc6P_m+2\t0.0\t0.0\t0.0\t0.0\n+Glc6P_m+3\t8.24e-12\t8.08e-12\t5.9e-12\t6.97e-12\n+Glc6P_m+4\t0.0\t0.0\t0.0\t0.0\n+Glc6P_m+5\t42042.82428\t43361.96496\t71279.12038\t48538.16956\n+Glc6P_m+6\t1329430.474\t1374496.425\t2307190.144\t1518075.712\n+Gly3P_m+0\t2208557.849\t1383928.659\t1719572.044\t627381.8726\n+Gly3P_m+1\t0.0\t0.0\t0.0\t0.0\n+Gly3P_m+2\t70974.99235\t88351.64619\t603790.3679\t532317.0977\n+Gly3P_m+3\t0.0\t0.0\t0.0\t0.0\n+IsoCit_m+0\t615656.0816\t694840.0737\t356838.4489\t239288.8488\n+IsoCit_m+1\t0.0\t0.0\t0.0\t1292.808105\n+IsoCit_m+2\t27759.10468\t20289.42943\t197334.5792\t166709.5901\n+IsoCit_m+3\t22115.86576\t27343.21092\t56495.29875\t54485.9662\n+IsoCit_m+4\t10599.87698\t6702.555462\t331288.9614\t288846.3519\n+IsoCit_m+5\t10620.86278\t16362.23118\t231670.8264\t207602.8573\n+IsoCit_m+6\t0.0\t0.0\t0.0\t0.0\n+Mal_m+0\t9730217.863\t14206692.82\t10222666.12\t11005711.47\n+Mal_m+1\t611545.6082\t1270294.531\t524640.3452\t1318049.312\n+Mal_m+2\t934087.7991\t1318162.84\t6169579.342\t5554307.727\n+Mal_m+3\t4941880.581\t4769440.201\t12963862.49\t9831574.119\n+Mal_m+4\t141647.6995\t131524.9149\t1099087.155\t773745.4886\n+P5P_m+0\t218078.021\t271462.4692\t96205.24834\t39240.24465\n+P5P_m+1'..b'3\t0.0\t0.0\t0.0\t0.0\n+GMP_m+4\t0.0\t0.0\t11993.58563\t8843.49158\n+GMP_m+5\t15679.58418\t20288.41574\t521715.5958\t336080.3616\n+GMP_m+6\t0.0\t0.0\t30358.60378\t25080.89579\n+GMP_m+7\t0.0\t0.0\t0.0\t0.0\n+GMP_m+8\t0.0\t0.0\t0.0\t0.0\n+GMP_m+9\t0.0\t0.0\t0.0\t0.0\n+GTP_m+0\t12399314.41\t8434826.263\t4201465.761\t1729537.207\n+GTP_m+1\t0.0\t0.0\t0.0\t0.0\n+GTP_m+10\t0.0\t0.0\t0.0\t0.0\n+GTP_m+2\t0.0\t0.0\t0.0\t0.0\n+GTP_m+3\t0.0\t0.0\t0.0\t0.0\n+GTP_m+4\t13922.40107\t9049.86896\t169059.8434\t70725.93719\n+GTP_m+5\t425540.5333\t275295.1407\t6548795.468\t2782073.874\n+GTP_m+6\t7582.866908\t4884.376813\t683935.7446\t189448.0329\n+GTP_m+7\t0.0\t0.0\t171898.6028\t59847.51587\n+GTP_m+8\t0.0\t0.0\t62986.90596\t30965.56731\n+GTP_m+9\t0.0\t0.0\t0.0\t0.0\n+UDP_m+0\t17738999.25\t20258162.45\t8751096.309\t7995093.075\n+UDP_m+1\t0.0\t0.0\t0.0\t0.0\n+UDP_m+2\t0.0\t0.0\t0.0\t0.0\n+UDP_m+3\t20544.6512\t34452.57256\t43224.27853\t41143.60131\n+UDP_m+4\t22500.88887\t25127.19412\t125149.1629\t123796.094\n+UDP_m+5\t573736.6815\t730933.5752\t4653563.201\t4351388.195\n+UDP_m+6\t39416.39887\t44700.42112\t774927.6673\t774837.5878\n+UDP_m+7\t480092.1692\t646545.4959\t8642193.246\t8184232.418\n+UDP_m+8\t220105.1583\t301929.2528\t3949469.688\t3723111.105\n+UDP_m+9\t0.0\t0.0\t0.0\t0.0\n+UMP_m+0\t28673512.42\t27391998.65\t10092857.54\t7472639.169\n+UMP_m+1\t0.0\t0.0\t0.0\t0.0\n+UMP_m+2\t0.0\t0.0\t0.0\t0.0\n+UMP_m+3\t0.0\t0.0\t45292.19686\t34155.08191\n+UMP_m+4\t8137.574403\t8002.531126\t148899.2558\t113794.5688\n+UMP_m+5\t176272.0407\t186757.4143\t5190696.222\t3892543.973\n+UMP_m+6\t21211.0163\t20814.63941\t938686.0928\t648974.0373\n+UMP_m+7\t160911.5657\t163098.8281\t9992123.995\t7657497.326\n+UMP_m+8\t73699.12901\t74398.55786\t4662902.068\t3455024.933\n+UMP_m+9\t0.0\t0.0\t0.0\t0.0\n+UTP_m+0\t34933090.28\t30320273.24\t13874447.33\t9822895.553\n+UTP_m+1\t0.0\t0.0\t0.0\t0.0\n+UTP_m+2\t0.0\t0.0\t0.0\t0.0\n+UTP_m+3\t54733.65501\t41258.5751\t50791.52719\t38104.0243\n+UTP_m+4\t41284.50449\t38339.12847\t196161.81\t145305.8033\n+UTP_m+5\t1149250.73\t1003525.438\t7110363.401\t5132543.055\n+UTP_m+6\t84596.80778\t80341.47212\t1285331.847\t872324.617\n+UTP_m+7\t1134480.491\t1007787.685\t13260305.79\t9679706.825\n+UTP_m+8\t507051.5787\t456134.4938\t6150890.407\t4346718.954\n+UTP_m+9\t0.0\t0.0\t0.0\t0.0\n+Glutamate_m+0\t4373775.126\t9579719.158\t8570247.359\t8038304.389\n+Glutamate_m+1\t102280.3987\t132063.0331\t518730.5369\t125344.8429\n+Glutamate_m+2\t2996893.789\t4821310.693\t11294934.44\t10230644.51\n+Glutamate_m+3\t0.0\t0.0\t0.0\t0.0\n+Glutamate_m+4\t869073.5251\t1921098.995\t17463505.2\t15504153.16\n+Glutamate_m+5\t300034.0038\t695074.3312\t9398136.247\t8402951.134\n+Alanine_m+0\t21089516.4577135\t19744888.5846368\t24358244.7957967\t22142620.8021233\n+Alanine_m+1\t0.0\t0.0\t0.0\t125116.568401705\n+Alanine_m+2\t0.0\t127112.317623622\t2823646.86691813\t2755169.07580148\n+Alanine_m+3\t5344152.77652686\t9885275.63995509\t86949664.3619863\t80281311.1908994\n+Aspartate_m+0\t2508320.60314072\t16249593.3336013\t12558492.2699028\t21649634.1645916\n+Aspartate_m+1\t0.0\t0.0\t0.0\t345790.674931823\n+Aspartate_m+2\t293896.878516743\t867836.953363095\t2456161.54280634\t2408829.36195787\n+Aspartate_m+3\t1351382.98984969\t6275157.18848666\t4744550.04755052\t3904754.8806012\n+Aspartate_m+4\t0.0\t167429.070833514\t719899.409367064\t333675.540081126\n+Glutamine_m+0\t8591809.84097918\t26274341.0632284\t12774710.7633531\t10289593.3087746\n+Glutamine_m+1\t0.0\t0.0\t0.0\t0.0\n+Glutamine_m+2\t3368708.34323401\t11391045.5034577\t6357795.67585396\t4269578.49519186\n+Glutamine_m+3\t1410767.83420093\t4427478.41968074\t2332494.56984921\t1643011.95455286\n+Glutamine_m+4\t1260954.68680199\t4496714.56579442\t9364106.32603213\t6724620.59315617\n+Glutamine_m+5\t759078.910255353\t2524045.07333924\t4885691.13888485\t3165983.42813674\n+Glycine_m+0\t351385748.144003\t288508872.183558\t539990286.990539\t434522921.675196\n+Glycine_m+1\t0.0\t0.0\t0.0\t1037743.83817362\n+Glycine_m+2\t3379536.20780698\t4260751.30313178\t34318845.5323041\t32711304.0440702\n+Serine_m+0\t767551134.703101\t1401631648.95252\t1755940589.92104\t1586811859.18687\n+Serine_m+1\t0.0\t5656551.64155338\t100669598.509621\t77667337.6864193\n+Serine_m+2\t2601803.97703171\t6980913.62083828\t60096361.4698284\t49045099.5083873\n+Serine_m+3\t3560033.88821059\t9251135.34864081\t48679171.1326257\t40470373.2459848\n'

diff -r 000000000000 -r 3cb0128a59a6 test-data/IsotopologuesProp.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/IsotopologuesProp.tsv Thu Mar 28 13:19:21 2024 +0000

b'@@ -0,0 +1,273 @@\n+ID\tT0_A_1\tT0_A_2\tT24_A_1\tT24_A_2\n+2_3-PG_m+0\t0.023701408\t0.026667837\t0.003395407\t0.003205955\n+2_3-PG_m+1\t0.0\t0.0\t0.0\t0.0\n+2_3-PG_m+2\t0.015379329\t0.015064063\t0.017029723\t0.015483229\n+2_3-PG_m+3\t0.960919263\t0.958268099\t0.97957487\t0.981310816\n+2-OHGLu_m+0\t0.972778716\t0.960016157\t0.238843937\t0.234383527\n+2-OHGLu_m+1\t0.0\t0.0\t0.0\t0.0\n+2-OHGLu_m+2\t0.010895035\t0.017205705\t0.192964526\t0.196160619\n+2-OHGLu_m+3\t0.005950244\t0.009013212\t0.059767469\t0.058659647\n+2-OHGLu_m+4\t0.005523145\t0.006877621\t0.336822772\t0.343016204\n+2-OHGLu_m+5\t0.00485286\t0.006887305\t0.171601296\t0.167780003\n+6-PG_m+0\t0.037457355\t0.036781579\t0.005718111\t0.005878683\n+6-PG_m+1\t0.0\t0.0\t0.0\t0.0\n+6-PG_m+2\t0.0\t0.0\t0.0\t0.0\n+6-PG_m+3\t0.000926261\t0.000956358\t0.0\t0.0\n+6-PG_m+4\t0.001444237\t0.001253565\t0.002551898\t0.002514724\n+6-PG_m+5\t0.062954742\t0.065300112\t0.134539624\t0.124734868\n+6-PG_m+6\t0.897217405\t0.895708386\t0.857190367\t0.866871725\n+a-KG_m+0\t0.785385761\t0.757293314\t0.162727984\t0.144179503\n+a-KG_m+1\t0.011699044\t0.01539635\t0.008560292\t0.006390832\n+a-KG_m+2\t0.12582041\t0.146649941\t0.210189793\t0.217916761\n+a-KG_m+3\t0.039363536\t0.039765125\t0.068696446\t0.065942692\n+a-KG_m+4\t0.037731249\t0.04089527\t0.360114754\t0.377021366\n+a-KG_m+5\t0.0\t0.0\t0.189710731\t0.188548847\n+Cit_m+0\t0.596189136\t0.579140099\t0.192981167\t0.184131935\n+Cit_m+1\t0.0\t0.000852019\t0.01186688\t0.011125925\n+Cit_m+2\t0.136767531\t0.139618898\t0.191021176\t0.200807853\n+Cit_m+3\t0.145771913\t0.153110891\t0.087115002\t0.086741024\n+Cit_m+4\t0.035309851\t0.035061942\t0.253476286\t0.259950196\n+Cit_m+5\t0.085255321\t0.091494467\t0.247588862\t0.248052219\n+Cit_m+6\t0.000706248\t0.000721684\t0.015950627\t0.009190849\n+Fru6P_m+0\t0.035534282\t0.036850885\t0.0\t0.0\n+Fru6P_m+1\t0.0\t0.0\t0.0\t0.0\n+Fru6P_m+2\t0.0\t0.0\t0.0\t0.0\n+Fru6P_m+3\t0.005400689\t0.005198568\t7.38e-18\t2.76e-18\n+Fru6P_m+4\t0.0\t0.0\t0.0\t0.0\n+Fru6P_m+5\t0.02720244\t0.031225743\t0.030969121\t0.020891211\n+Fru6P_m+6\t0.931862589\t0.926724803\t0.969030879\t0.979108789\n+FruBP_m+0\t0.004852356\t0.005055942\t0.000771831\t0.000667182\n+FruBP_m+1\t0.0\t0.0\t0.0\t0.0\n+FruBP_m+2\t0.0\t2.41e-05\t0.0\t0.0\n+FruBP_m+3\t0.022343466\t0.021903636\t0.001152829\t0.001221804\n+FruBP_m+4\t0.000385173\t0.000411286\t0.00070927\t0.000640891\n+FruBP_m+5\t0.056528555\t0.055902759\t0.051191518\t0.048283811\n+FruBP_m+6\t0.91589045\t0.91670229\t0.946174552\t0.949186312\n+Fru1P_m+0\t0.377951916\t0.388533234\t0.0\t0.0\n+Fru1P_m+1\t0.0\t0.0\t0.010907608\t0.009540546\n+Fru1P_m+2\t0.0\t0.0\t0.0\t0.0\n+Fru1P_m+3\t0.00838139\t0.008538834\t0.0\t0.0\n+Fru1P_m+4\t0.0\t0.0\t0.0\t0.0\n+Fru1P_m+5\t0.020823235\t0.020885002\t0.036106205\t0.034096734\n+Fru1P_m+6\t0.592843459\t0.582042931\t0.952986187\t0.95636272\n+Fum_m+0\t0.714960723\t0.770061029\t0.42101459\t0.492302496\n+Fum_m+1\t0.006844463\t0.022654129\t0.008448858\t0.037105574\n+Fum_m+2\t0.032512911\t0.043974063\t0.170459943\t0.170649142\n+Fum_m+3\t0.245681903\t0.163310778\t0.382715156\t0.279657123\n+Fum_m+4\t0.0\t0.0\t0.017361453\t0.020285666\n+Glc6P_m+0\t0.0\t0.0\t0.0\t0.0\n+Glc6P_m+1\t0.0\t0.0\t0.0\t0.0\n+Glc6P_m+2\t0.0\t0.0\t0.0\t0.0\n+Glc6P_m+3\t6.01e-18\t5.7e-18\t2.48e-18\t4.45e-18\n+Glc6P_m+4\t0.0\t0.0\t0.0\t0.0\n+Glc6P_m+5\t0.030655226\t0.030582719\t0.029968485\t0.030982854\n+Glc6P_m+6\t0.969344774\t0.969417281\t0.970031515\t0.969017146\n+Gly3P_m+0\t0.968864238\t0.939989929\t0.740122176\t0.540986832\n+Gly3P_m+1\t0.0\t0.0\t0.0\t0.0\n+Gly3P_m+2\t0.031135762\t0.060010071\t0.259877824\t0.459013168\n+Gly3P_m+3\t0.0\t0.0\t0.0\t0.0\n+IsoCit_m+0\t0.896475392\t0.907649949\t0.304047291\t0.24972057\n+IsoCit_m+1\t0.0\t0.0\t0.0\t0.001349168\n+IsoCit_m+2\t0.04042087\t0.026503508\t0.168140637\t0.173977242\n+IsoCit_m+3\t0.032203579\t0.035717664\t0.048137309\t0.056861265\n+IsoCit_m+4\t0.015434801\t0.008755359\t0.282277629\t0.301438517\n+IsoCit_m+5\t0.015465359\t0.02137352\t0.197397134\t0.216653238\n+IsoCit_m+6\t0.0\t0.0\t0.0\t0.0\n+Mal_m+0\t0.59477915\t0.654803527\t0.329978064\t0.386390531\n+Mal_m+1\t0.037381956\t0.0585494\t0.016934898\t0.046274316\n+Mal_m+2\t0.057097997\t0.060755708\t0.199148228\t0.195001652\n+Mal_m+3\t0.302082397\t0.219829224\t0.418461309\t0.345168703\n+Mal_m+4\t0.008658501\t0.006062141\t0.035477501\t0.027164798\n+P5P_m+0\t0.134431323\t0.129158388\t0.023798472\t0.014294427\n+P5P_m'..b'49\t0.538369139\n+GMP_m+6\t0.0\t0.0\t0.031774118\t0.040177237\n+GMP_m+7\t0.0\t0.0\t0.0\t0.0\n+GMP_m+8\t0.0\t0.0\t0.0\t0.0\n+GMP_m+9\t0.0\t0.0\t0.0\t0.0\n+GTP_m+0\t0.965200586\t0.966846912\t0.354909212\t0.355681707\n+GTP_m+1\t0.0\t0.0\t0.0\t0.0\n+GTP_m+10\t0.0\t0.0\t0.0\t0.0\n+GTP_m+2\t0.0\t0.0\t0.0\t0.0\n+GTP_m+3\t0.0\t0.0\t0.0\t0.0\n+GTP_m+4\t0.001083762\t0.001037347\t0.014280944\t0.014544886\n+GTP_m+5\t0.033125378\t0.031555867\t0.553194521\t0.572137322\n+GTP_m+6\t0.000590274\t0.000559875\t0.057773908\t0.038960249\n+GTP_m+7\t0.0\t0.0\t0.014520741\t0.012307724\n+GTP_m+8\t0.0\t0.0\t0.005320675\t0.006368112\n+GTP_m+9\t0.0\t0.0\t0.0\t0.0\n+UDP_m+0\t0.92896738\t0.91907719\t0.324841076\t0.317346168\n+UDP_m+1\t0.0\t0.0\t0.0\t0.0\n+UDP_m+2\t0.0\t0.0\t0.0\t0.0\n+UDP_m+3\t0.001075896\t0.001563053\t0.001604487\t0.001633097\n+UDP_m+4\t0.001178341\t0.001139977\t0.004645542\t0.004913791\n+UDP_m+5\t0.030045813\t0.03316117\t0.172740469\t0.172717985\n+UDP_m+6\t0.002064183\t0.002027979\t0.028765349\t0.030755332\n+UDP_m+7\t0.025141777\t0.029332632\t0.32079859\t0.324853603\n+UDP_m+8\t0.011526609\t0.013697999\t0.146604487\t0.147780023\n+UDP_m+9\t0.0\t0.0\t0.0\t0.0\n+UMP_m+0\t0.984878917\t0.983728827\t0.324827298\t0.321063727\n+UMP_m+1\t0.0\t0.0\t0.0\t0.0\n+UMP_m+2\t0.0\t0.0\t0.0\t0.0\n+UMP_m+3\t0.0\t0.0\t0.001457679\t0.001467481\n+UMP_m+4\t0.00027951\t0.000287395\t0.004792156\t0.004889211\n+UMP_m+5\t0.006054599\t0.006707019\t0.167056735\t0.167244082\n+UMP_m+6\t0.000728557\t0.000747516\t0.030210559\t0.027883325\n+UMP_m+7\t0.005526997\t0.005857368\t0.321585302\t0.329006202\n+UMP_m+8\t0.002531421\t0.002671875\t0.150070272\t0.148445972\n+UMP_m+9\t0.0\t0.0\t0.0\t0.0\n+UTP_m+0\t0.921608286\t0.920255739\t0.330908955\t0.327019999\n+UTP_m+1\t0.0\t0.0\t0.0\t0.0\n+UTP_m+2\t0.0\t0.0\t0.0\t0.0\n+UTP_m+3\t0.001443989\t0.001252246\t0.00121139\t0.001268544\n+UTP_m+4\t0.001089172\t0.001163637\t0.004678507\t0.004837464\n+UTP_m+5\t0.030319648\t0.03045817\t0.169583902\t0.170870617\n+UTP_m+6\t0.002231841\t0.002438458\t0.030655478\t0.02904109\n+UTP_m+7\t0.029929978\t0.030587534\t0.316261529\t0.322253016\n+UTP_m+8\t0.013377086\t0.013844215\t0.146700237\t0.144709268\n+UTP_m+9\t0.0\t0.0\t0.0\t0.0\n+Glutamate_m+0\t0.50610349\t0.558608108\t0.181397966\t0.190024556\n+Glutamate_m+1\t0.011835192\t0.007700798\t0.010979457\t0.002963137\n+Glutamate_m+2\t0.346780152\t0.281138017\t0.239068728\t0.241851215\n+Glutamate_m+3\t0.0\t0.0\t0.0\t0.0\n+Glutamate_m+4\t0.100563273\t0.112022227\t0.369632776\t0.36651633\n+Glutamate_m+5\t0.034717893\t0.04053085\t0.198921073\t0.198644762\n+Alanine_m+0\t0.797827810843437\t0.663531441011596\t0.213422524358863\t0.210272876993444\n+Alanine_m+1\t0.0\t0.0\t0.0\t0.0011881439434148\n+Alanine_m+2\t0.0\t0.0042716381468342\t0.0247402818753038\t0.0261639005314399\n+Alanine_m+3\t0.202172189156562\t0.332196920841569\t0.761837193765833\t0.7623750785317\n+Aspartate_m+0\t0.603890677581362\t0.689710607871533\t0.613234481244536\t0.755852129441776\n+Aspartate_m+1\t0.0\t0.0\t0.0\t0.0120725651067026\n+Aspartate_m+2\t0.0707571372193389\t0.0368351589082373\t0.119935014266428\t0.0840992872607313\n+Aspartate_m+3\t0.325352185199299\t0.266347741146907\t0.231677626948993\t0.136326427920786\n+Aspartate_m+4\t0.0\t0.0071064920733223\t0.0351528775400419\t0.0116495902700031\n+Glutamine_m+0\t0.558224379431548\t0.534970515077528\t0.357686765967965\t0.394346261334926\n+Glutamine_m+1\t0.0\t0.0\t0.0\t0.0\n+Glutamine_m+2\t0.218870663945394\t0.23193249511345\t0.178015723103887\t0.163630599046039\n+Glutamine_m+3\t0.0916599661008154\t0.0901476617423574\t0.0653089102980375\t0.0629680495782074\n+Glutamine_m+4\t0.0819263531851077\t0.0915573753735872\t0.262191212778537\t0.257719514292717\n+Glutamine_m+5\t0.0493186373371339\t0.0513919526930764\t0.136797387851571\t0.121335575748108\n+Glycine_m+0\t0.990473881304418\t0.98544674391971\t0.940243252999395\t0.927928532826468\n+Glycine_m+1\t0.0\t0.0\t0.0\t0.0022161135101774\n+Glycine_m+2\t0.0095261186955812\t0.0145532560802896\t0.0597567470006043\t0.0698553536633538\n+Serine_m+0\t0.992036015830537\t0.984623611348174\t0.893433065646788\t0.904684539049209\n+Serine_m+1\t0.0\t0.0039736362326335\t0.0512212933228717\t0.044280258675419\n+Serine_m+2\t0.0033627508769757\t0.0049039791481565\t0.0305773878514993\t0.027961943304422\n+Serine_m+3\t0.004601233292487\t0.006498773271035\t0.0247682531788402\t0.0230732589709498\n'

diff -r 000000000000 -r 3cb0128a59a6 test-data/MeanEnrichment13C.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MeanEnrichment13C.tsv Thu Mar 28 13:19:21 2024 +0000

@@ -0,0 +1,39 @@
+ID T0_A_1 T0_A_2 T24_A_1 T24_A_2
+2-OHGLu 0.017199536 0.024679611 0.554105805 0.555853002
+2_3-PG 0.971172149 0.968310808 0.990928018 0.991632969
+6-PG 0.951105645 0.951439035 0.971007986 0.972493931
+ADP 0.003738982 0.004008507 0.271460511 0.27088157
+AMP 0.0 0.0 0.228237637 0.22612141
+ATP 0.003436966 0.003086443 0.265350794 0.262665128
+Alanine 0.202172189156562 0.335044679606125 0.778330715016035 0.780213726867131
+Aspartate 0.279392707509143 0.225284877387621 0.268878604885001 0.158962196117634
+CDP 0.0 0.0 0.146289689 0.144598702
+CMP 0.0 0.0 0.113220385 0.133502934
+CTP 0.0 0.0 0.183202864 0.172278526
+Cit 0.213767383 0.223578782 0.500467909 0.501361946
+Fru1P 0.61438685 0.603716516 0.984892626 0.986366756
+Fru6P 0.957231633 0.95534554 0.99483848 0.996518132
+FruBP 0.974426094 0.97452196 0.989883411 0.990460984
+Fum 0.202228999 0.150133648 0.391740006 0.324629472
+GDP 0.017703928 0.019574621 0.33238682 0.328737224
+GMP 0.007532149 0.010311189 0.297106267 0.298957488
+GTP 0.017350358 0.016528797 0.331395041 0.328972661
+Glc6P 0.994890796 0.99490288 0.995005253 0.994836191
+Glutamate 0.256247611 0.244143998 0.592450676 0.589190939
+Glutamine 0.257403965123867 0.271499448082741 0.456941993494779 0.430744256547623
+Gly3P 0.020757175 0.040006714 0.173251883 0.306008778
+Glycine 0.0095261186955812 0.0145532560802896 0.0597567470006043 0.0709634104184425
+IsoCit 0.052753079 0.050341507 0.432798231 0.468151284
+Mal 0.273114785 0.215949263 0.453131321 0.39511073
+P5P 0.849407517 0.854019392 0.971418047 0.981187602
+PEP 0.9444266 0.941640672 0.988260882 0.977861953
+PRPP 0.907420259 0.913331631 0.989872714 0.989877877
+Pyr 0.27997276 0.339111202 0.735022864 0.688262843
+Rib1P 0.135582454 0.107900708 0.639810746 0.646721355
+Sed7P 0.447321347 0.423149937 0.976468478 0.98203847
+Serine 0.0068430672104708 0.0110926381140172 0.0622269428541303 0.0564746407323709
+Suc 0.098491758 0.128662761 0.270779617 0.288237022
+UDP 0.04875117 0.055792801 0.497568455 0.503210198
+UMP 0.010522524 0.011282928 0.499083109 0.502010093
+UTP 0.054467164 0.055577705 0.493514798 0.496133375
+a-KG 0.106471093 0.118314537 0.604808378 0.618176425

diff -r 000000000000 -r 3cb0128a59a6 test-data/Mean_enrichment_data.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mean_enrichment_data.tsv Thu Mar 28 13:19:21 2024 +0000

diff -r 000000000000 -r 3cb0128a59a6 test-data/TRACER_IsoCor_out_example.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TRACER_IsoCor_out_example.tsv Thu Mar 28 13:19:21 2024 +0000

b'@@ -0,0 +1,1089 @@\n+sample\tmetabolite\tderivative\tisotopologue\tarea\tcorrected_area\tisotopologue_fraction\tresiduum\tmean_enrichment\n+T0_A_1\t2_3-PG\t\t0\t196369\t206171.4626\t0.023701408\t2.94E-05\t0.971172149\n+T0_A_1\t2_3-PG\t\t1\t0\t0\t0\t-0.000821912\t0.971172149\n+T0_A_1\t2_3-PG\t\t2\t132936\t133780.182\t0.015379329\t1.70E-17\t0.971172149\n+T0_A_1\t2_3-PG\t\t3\t8213874\t8358749.348\t0.960919263\t0\t0.971172149\n+T0_A_1\t2-OHGLu\t\t0\t5197470\t5550339.322\t0.972778716\t0.000992369\t0.017199536\n+T0_A_1\t2-OHGLu\t\t1\t191280\t0\t0\t-0.017726177\t0.017199536\n+T0_A_1\t2-OHGLu\t\t2\t119376\t62163.30727\t0.010895035\t-1.83E-11\t0.017199536\n+T0_A_1\t2-OHGLu\t\t3\t37927\t33950.03875\t0.005950244\t5.28E-12\t0.017199536\n+T0_A_1\t2-OHGLu\t\t4\t32251\t31513.15643\t0.005523145\t2.20E-11\t0.017199536\n+T0_A_1\t2-OHGLu\t\t5\t28088\t27688.74195\t0.00485286\t-4.18E-11\t0.017199536\n+T0_A_1\t6-PG\t\t0\t283827\t309932.3475\t0.037457355\t7.97E-05\t0.951105645\n+T0_A_1\t6-PG\t\t1\t12752\t0\t0\t-0.000879972\t0.951105645\n+T0_A_1\t6-PG\t\t2\t0\t0\t0\t-0.000795708\t0.951105645\n+T0_A_1\t6-PG\t\t3\t7648\t7664.136895\t0.000926261\t-4.09E-13\t0.951105645\n+T0_A_1\t6-PG\t\t4\t11737\t11950.01113\t0.001444237\t-6.71E-13\t0.951105645\n+T0_A_1\t6-PG\t\t5\t502713\t520904.6672\t0.062954742\t9.25E-13\t0.951105645\n+T0_A_1\t6-PG\t\t6\t7243671\t7423820.948\t0.897217405\t-6.24E-14\t0.951105645\n+T0_A_1\ta-KG\t\t0\t413371\t441807.2042\t0.785385761\t1.34E-11\t0.106471093\n+T0_A_1\ta-KG\t\t1\t29366\t6581.125045\t0.011699044\t-1.52E-10\t0.106471093\n+T0_A_1\ta-KG\t\t2\t68471\t70778.42058\t0.12582041\t1.12E-08\t0.106471093\n+T0_A_1\ta-KG\t\t3\t23742\t22143.37798\t0.039363536\t-6.75E-08\t0.106471093\n+T0_A_1\ta-KG\t\t4\t21268\t21225.1587\t0.037731249\t6.15E-06\t0.106471093\n+T0_A_1\ta-KG\t\t5\t0\t0\t0\t-0.000483187\t0.106471093\n+T0_A_1\tCit\t\t0\t3351409\t3639184.111\t0.596189136\t1.67E-06\t0.213767383\n+T0_A_1\tCit\t\t1\t228973\t0\t0\t-2.44E-05\t0.213767383\n+T0_A_1\tCit\t\t2\t840397\t834839.4782\t0.136767531\t6.75E-14\t0.213767383\n+T0_A_1\tCit\t\t3\t886410\t889802.9149\t0.145771913\t1.59E-14\t0.213767383\n+T0_A_1\tCit\t\t4\t249683\t215534.0325\t0.035309851\t-2.54E-14\t0.213767383\n+T0_A_1\tCit\t\t5\t524038\t520405.0021\t0.085255321\t1.91E-14\t0.213767383\n+T0_A_1\tCit\t\t6\t14926\t4310.989009\t0.000706248\t1.62E-14\t0.213767383\n+T0_A_1\tFru6P\t\t0\t157009\t170520.7743\t0.035534282\t0.000176319\t0.957231633\n+T0_A_1\tFru6P\t\t1\t0\t0\t0\t-0.002326517\t0.957231633\n+T0_A_1\tFru6P\t\t2\t0\t0\t0\t-0.000686633\t0.957231633\n+T0_A_1\tFru6P\t\t3\t24757\t25916.65274\t0.005400689\t7.51E-06\t0.957231633\n+T0_A_1\tFru6P\t\t4\t0\t0\t0\t-0.000201546\t0.957231633\n+T0_A_1\tFru6P\t\t5\t126638\t130538.1956\t0.02720244\t3.38E-14\t0.957231633\n+T0_A_1\tFru6P\t\t6\t4370894\t4471792.31\t0.931862589\t3.58E-15\t0.957231633\n+T0_A_1\tFruBP\t\t0\t171439\t187489.9969\t0.004852356\t2.62E-05\t0.974426094\n+T0_A_1\tFruBP\t\t1\t0\t0\t0\t-0.000322554\t0.974426094\n+T0_A_1\tFruBP\t\t2\t0\t0\t0\t-0.000121937\t0.974426094\n+T0_A_1\tFruBP\t\t3\t810949\t863328.265\t0.022343466\t-3.21E-13\t0.974426094\n+T0_A_1\tFruBP\t\t4\t45403\t14882.67759\t0.000385173\t-5.22E-13\t0.974426094\n+T0_A_1\tFruBP\t\t5\t2116367\t2184204.485\t0.056528555\t7.82E-13\t0.974426094\n+T0_A_1\tFruBP\t\t6\t34355935\t35389053.16\t0.91589045\t-3.50E-14\t0.974426094\n+T0_A_1\tFru1P\t\t0\t3004149\t3269098.651\t0.377951916\t0.001186326\t0.61438685\n+T0_A_1\tFru1P\t\t1\t84785\t0\t0\t-0.014841739\t0.61438685\n+T0_A_1\tFru1P\t\t2\t0\t0\t0\t-0.007377195\t0.61438685\n+T0_A_1\tFru1P\t\t3\t72636\t72494.90812\t0.00838139\t1.39E-05\t0.61438685\n+T0_A_1\tFru1P\t\t4\t0\t0\t0\t-0.000374239\t0.61438685\n+T0_A_1\tFru1P\t\t5\t175421\t180110.7695\t0.020823235\t-5.22E-12\t0.61438685\n+T0_A_1\tFru1P\t\t6\t5012593\t5127805.073\t0.592843459\t2.35E-13\t0.61438685\n+T0_A_1\tFum\t\t0\t576240\t607669.8452\t0.714960723\t-5.41E-10\t0.202228999\n+T0_A_1\tFum\t\t1\t31384\t5817.345549\t0.006844463\t4.12E-08\t0.202228999\n+T0_A_1\tFum\t\t2\t27406\t27633.8473\t0.032512911\t-4.09E-07\t0.202228999\n+T0_A_1\tFum\t\t3\t205172\t208813.5466\t0.245681903\t3.71E-05\t0.202228999\n+T0_A_1\tFum\t\t4\t0\t0\t0\t-0.003008713\t0.202228999\n+T0_A_1\tGlc6P\t\t0\t0\t0\t0\t0\t0.994890796\n+T0_A_1\tGlc6P\t\t1\t0\t0\t0\t0\t0.994890796\n+T0_A_1\tGlc6P\t\t2\t0\t0\t0\t0\t0.994890796\n+T0_A_1\tGlc6P\t\t3\t0\t8.24E-12\t6.01E-18\t-5.82E-18\t0.994890796\n+T0_A_1\tGlc6P\t\t4\t0\t0\t0\t-2.17E-19\t0.994890796\n+T0_A_1\tGlc6P\t\t5\t40636\t42042.82428\t0.030655226\t0\t0.994890796\n+T0_A_1\tGlc6P\t\t6\t1299478\t1329430.474\t0.969344774\t0\t0.99489'..b'6.094\t0.004913791\t5.25E-08\t0.503210198\n+T24_A_2\tUDP\t\t5\t4021559\t4351388.195\t0.172717985\t-2.77E-06\t0.503210198\n+T24_A_2\tUDP\t\t6\t952509\t774837.5878\t0.030755332\t-5.21E-06\t0.503210198\n+T24_A_2\tUDP\t\t7\t7854283\t8184232.418\t0.324853603\t0.000210392\t0.503210198\n+T24_A_2\tUDP\t\t8\t3845167\t3723111.105\t0.147780023\t0.000209589\t0.503210198\n+T24_A_2\tUDP\t\t9\t69005\t0\t0\t-0.008664799\t0.503210198\n+T24_A_2\tUMP\t\t0\t6612779\t7472639.169\t0.321063727\t0.001494751\t0.502010093\n+T24_A_2\tUMP\t\t1\t428557\t0\t0\t-0.012842425\t0.502010093\n+T24_A_2\tUMP\t\t2\t72957\t0\t0\t-0.003721553\t0.502010093\n+T24_A_2\tUMP\t\t3\t44504\t34155.08191\t0.001467481\t8.82E-09\t0.502010093\n+T24_A_2\tUMP\t\t4\t108573\t113794.5688\t0.004889211\t6.01E-08\t0.502010093\n+T24_A_2\tUMP\t\t5\t3624005\t3892543.973\t0.167244082\t-1.31E-06\t0.502010093\n+T24_A_2\tUMP\t\t6\t811799\t648974.0373\t0.027883325\t-4.11E-06\t0.502010093\n+T24_A_2\tUMP\t\t7\t7370645\t7657497.326\t0.329006202\t0.000132889\t0.502010093\n+T24_A_2\tUMP\t\t8\t3579277\t3455024.933\t0.148445972\t0.000167928\t0.502010093\n+T24_A_2\tUMP\t\t9\t48331\t0\t0\t-0.007323251\t0.502010093\n+T24_A_2\tUTP\t\t0\t8569698\t9822895.553\t0.327019999\t0.001680748\t0.496133375\n+T24_A_2\tUTP\t\t1\t564083\t0\t0\t-0.013379774\t0.496133375\n+T24_A_2\tUTP\t\t2\t165857\t0\t0\t-0.004995094\t0.496133375\n+T24_A_2\tUTP\t\t3\t64958\t38104.0243\t0.001268544\t5.28E-08\t0.496133375\n+T24_A_2\tUTP\t\t4\t139603\t145305.8033\t0.004837464\t1.21E-07\t0.496133375\n+T24_A_2\tUTP\t\t5\t4708691\t5132543.055\t0.170870617\t-4.57E-06\t0.496133375\n+T24_A_2\tUTP\t\t6\t1083383\t872324.617\t0.02904109\t-7.32E-06\t0.496133375\n+T24_A_2\tUTP\t\t7\t9251233\t9679706.825\t0.322253016\t0.000281371\t0.496133375\n+T24_A_2\tUTP\t\t8\t4478612\t4346718.954\t0.144709268\t0.000235305\t0.496133375\n+T24_A_2\tUTP\t\t9\t122316\t0\t0\t-0.00924707\t0.496133375\n+T24_A_2\tGlutamate\t\t0\t7507502\t8038304.389\t0.190024556\t2.61E-07\t0.589190939\n+T24_A_2\tGlutamate\t\t1\t535518\t125344.8429\t0.002963137\t-6.03E-06\t0.589190939\n+T24_A_2\tGlutamate\t\t2\t9788852\t10230644.51\t0.241851215\t0.000272279\t0.589190939\n+T24_A_2\tGlutamate\t\t3\t0\t0\t0\t-0.008015062\t0.589190939\n+T24_A_2\tGlutamate\t\t4\t15120956\t15504153.16\t0.36651633\t1.18E-11\t0.589190939\n+T24_A_2\tGlutamate\t\t5\t8468489\t8402951.134\t0.198644762\t-6.51E-13\t0.589190939\n+T24_A_2\tAlanine\t\t0\t21238142\t22142620.8021233\t0.210272876993444\t0\t0.780213726867131\n+T24_A_2\tAlanine\t\t1\t826602\t125116.568401705\t0.00118814394341481\t0\t0.780213726867131\n+T24_A_2\tAlanine\t\t2\t2710794\t2755169.07580148\t0.0261639005314399\t0\t0.780213726867131\n+T24_A_2\tAlanine\t\t3\t79558999\t80281311.1908994\t0.7623750785317\t0\t0.780213726867131\n+T24_A_2\tAspartate\t\t0\t20443386\t21649634.1645916\t0.755852129441776\t0\t0.158962196117634\n+T24_A_2\tAspartate\t\t1\t1245646\t345790.674931823\t0.0120725651067026\t0\t0.158962196117634\n+T24_A_2\tAspartate\t\t2\t2351013\t2408829.36195787\t0.0840992872607313\t0\t0.158962196117634\n+T24_A_2\tAspartate\t\t3\t3862552\t3904754.8806012\t0.136326427920786\t0\t0.158962196117634\n+T24_A_2\tAspartate\t\t4\t376301\t333675.540081126\t0.0116495902700031\t0\t0.158962196117634\n+T24_A_2\tGlutamine\t\t0\t9626621\t10289593.3087746\t0.394346261334926\t0.00116101386257697\t0.430744256547623\n+T24_A_2\tGlutamine\t\t1\t0\t0\t0\t-0.0210247019567943\t0.430744256547623\n+T24_A_2\tGlutamine\t\t2\t4080774\t4269578.49519186\t0.163630599046039\t-1.84E-12\t0.430744256547623\n+T24_A_2\tGlutamine\t\t3\t1719672\t1643011.95455286\t0.0629680495782074\t-7.45E-13\t0.430744256547623\n+T24_A_2\tGlutamine\t\t4\t6585640\t6724620.59315617\t0.257719514292717\t1.10E-12\t0.430744256547623\n+T24_A_2\tGlutamine\t\t5\t3194763\t3165983.42813674\t0.121335575748108\t4.13E-14\t0.430744256547623\n+T24_A_2\tGlycine\t\t0\t421378209\t434522921.675196\t0.927928532826468\t0\t0.0709634104184425\n+T24_A_2\tGlycine\t\t1\t10132260\t1037743.83817362\t0.0022161135101774\t0\t0.0709634104184425\n+T24_A_2\tGlycine\t\t2\t32471951\t32711304.0440702\t0.0698553536633538\t0\t0.0709634104184425\n+T24_A_2\tSerine\t\t0\t1518295536\t1586811859.18687\t0.904684539049209\t0\t0.0564746407323709\n+T24_A_2\tSerine\t\t1\t126117017\t77667337.6864193\t0.044280258675419\t0\t0.0564746407323709\n+T24_A_2\tSerine\t\t2\t50247871\t49045099.5083873\t0.027961943304422\t-4.29E-18\t0.0564746407323709\n+T24_A_2\tSerine\t\t3\t40588182\t40470373.2459848\t0.0230732589709498\t0\t0.0564746407323709\n'

diff -r 000000000000 -r 3cb0128a59a6 test-data/TRACER_dataMatrix.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TRACER_dataMatrix.tsv Thu Mar 28 13:19:21 2024 +0000

@@ -0,0 +1,24 @@
+ID A_T0_endo-1 A_T0_endo-2 Cont_T0_endo-1 Cont_T0_endo-2 A_T24_endo-1 A_T24_endo-2 Cont_T24_endo-1 Cont_T24_endo-2 A_T0_exo-1 A_T0_exo-2 Cont_T0_exo-1 Cont_T0_exo-2 A_T24_exo-1 A_T24_exo-2 Cont_T24_exo-1 Cont_T24_exo-2
+Peak1 206171.4626 285834.0353 298441.8262 268050.3636 36413.27637 27367.17784 26381.30429 23698.7623 206171.4626 285834.0353 298441.8262 268050.3636 36413.27637 27367.17784 26381.30429 23698.7623
+Peak2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Peak3 133780.182 161461.2364 200778.0533 197229.6694 182631.3947 132170.3807 146120.9923 89966.23931 133780.182 161461.2364 200778.0533 197229.6694 182631.3947 132170.3807 146120.9923 89966.23931
+Peak4 8358749.348 10271010.45 11787744.65 11554464.86 10505228.3 8376820.028 9033424.374 6122480.462 8358749.348 10271010.45 11787744.65 11554464.86 10505228.3 8376820.028 9033424.374 6122480.462
+Peak5 5550339.322 6072872.833 5893256.269 7454336.274 3855047.791 3216178.72 4066632.965 5550339.322 6072872.833 5893256.269 7454336.274 3855047.791 3216178.72 3102049.195 4066632.965
+Peak6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Peak7 62163.30727 108839.8963 9976.217534 53035.94662 3114533.603 2691689.195 1611494.416 62163.30727 108839.8963 9976.217534 53035.94662 3114533.603 2691689.195 1845577.773 1611494.416
+Peak8 33950.03875 57015.80123 16218.60873 34068.8323 964673.6406 804919.6602 479959.6627 33950.03875 57015.80123 16218.60873 34068.8323 964673.6406 804919.6602 474922.8927 479959.6627
+Peak9 31513.15643 43506.47502 18965.84568 23046.25122 5436469.924 4706821.45 2732129.436 31513.15643 43506.47502 18965.84568 23046.25122 5436469.924 4706821.45 3200529.756 2732129.436
+Peak10 27688.74195 43567.73063 0 17896.32501 2769721.539 2302254.26 1298081.886 27688.74195 43567.73063 0 17896.32501 2769721.539 2302254.26 1488534.123 1298081.886
+Peak11 309932.3475 342540.1698 253560.3827 242260.6594 101608.1805 84940.35902 85240.79781 67359.24717 309932.3475 342540.1698 253560.3827 242260.6594 101608.1805 84940.35902 85240.79781 67359.24717
+Peak12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Peak13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+Peak14 7664.136895 8906.391308 0 0 0 0 0 0 7664.136895 8906.391308 0 0 0 0 0 0
+Peak15 11950.01113 11674.22491 9922.705217 15475.23458 45346.04708 36334.93958 34524.35854 26037.70094 11950.01113 11674.22491 9922.705217 15475.23458 45346.04708 36334.93958 34524.35854 26037.70094
+Peak16 520904.6672 608128.1002 405342.3913 815587.5165 2390706.721 1802278.633 1807036.326 1207909.718 520904.6672 608128.1002 405342.3913 815587.5165 2390706.721 1802278.633 1807036.326 1207909.718
+Peak17 7423820.948 8341569.748 5394323.444 7384800.665 15231875.3 12525321.98 11279297.92 8040213.605 7423820.948 8341569.748 5394323.444 7384800.665 15231875.3 12525321.98 11279297.92 8040213.605
+Peak18 441807.2042 612669.4773 552526.6043 482434.0877 1476617.063 1056307.521 572619.741 546375.578 441807.2042 612669.4773 552526.6043 482434.0877 1476617.063 1056307.521 572619.741 546375.578
+Peak19 6581.125045 12456.03716 0 2085.213699 77677.31383 46821.38405 28170.23998 32113.8241 6581.125045 12456.03716 0 2085.213699 77677.31383 46821.38405 28170.23998 32113.8241
+Peak20 70778.42058 118643.5176 46309.55877 54983.84668 1907292.33 1596531.466 636158.2851 415566.8382 70778.42058 118643.5176 46309.55877 54983.84668 1907292.33 1596531.466 636158.2851 415566.8382
+Peak21 22143.37798 32170.99354 13728.65106 12489.92256 623361.4049 483118.3355 149649.632 103268.9093 22143.37798 32170.99354 13728.65106 12489.92256 623361.4049 483118.3355 149649.632 103268.9093
+Peak22 21225.1587 33085.30969 9561.259531 10809.82522 3267732.931 2762185.304 1099424.672 647876.2431 21225.1587 33085.30969 9561.259531 10809.82522 3267732.931 2762185.304 1099424.672 647876.2431
+Peak23 0 0 0 0 1721462.381 1381372.254 489385.3877 299919.5187 0 0 0 0 1721462.381 1381372.254 489385.3877 299919.5187

diff -r 000000000000 -r 3cb0128a59a6 test-data/TRACER_generic_sheet.xlsx

Binary file test-data/TRACER_generic_sheet.xlsx has changed

diff -r 000000000000 -r 3cb0128a59a6 test-data/TRACER_metabo_4.xlsx

Binary file test-data/TRACER_metabo_4.xlsx has changed

diff -r 000000000000 -r 3cb0128a59a6 test-data/isotopologuesCorrValues.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/isotopologuesCorrValues.tsv Thu Mar 28 13:19:21 2024 +0000

diff -r 000000000000 -r 3cb0128a59a6 test-data/rawAbundances.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rawAbundances.tsv Thu Mar 28 13:19:21 2024 +0000

diff -r 000000000000 -r 3cb0128a59a6 test-data/sampleMetadata_1.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleMetadata_1.csv Thu Mar 28 13:19:21 2024 +0000

@@ -0,0 +1,5 @@
+"name_to_plot" "condition" "timepoint" "timenum" "compartment" "original_name"
+"sgLDHA_T0-1" "sgLDHA" "T0" 0 "endo" "T0_A_1"
+"sgLDHA_T0-2" "sgLDHA" "T0" 0 "endo" "T0_A_2"
+"sgLDHA_T24-1" "sgLDHA" "T24" 24 "endo" "T24_A_1"
+"sgLDHA_T24-2" "sgLDHA" "T24" 24 "endo" "T24_A_2"

diff -r 000000000000 -r 3cb0128a59a6 test-data/sampleMetadata_2.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleMetadata_2.tsv Thu Mar 28 13:19:21 2024 +0000

@@ -0,0 +1,17 @@
+"name_to_plot" "condition" "timepoint" "timenum" "compartment" "original_name"
+"sgLDHA_T0_endo-1" "sgLDHA" "T0" 0 "endo" "A_T0_endo-1"
+"sgLDHA_T0_endo-2" "sgLDHA" "T0" 0 "endo" "A_T0_endo-2"
+"Cont_T0_endo-1" "sgCont" "T0" 0 "endo" "Cont_T0_endo-1"
+"Cont_T0_cell_endo-2" "sgCont" "T0" 0 "endo" "Cont_T0_endo-2"
+"A_T24_cell_endo-1" "sgLDHA" "T24" 24 "endo" "A_T24_endo-1"
+"A_T24_cell_endo-2" "sgLDHA" "T24" 24 "endo" "A_T24_endo-2"
+"Cont_T24_cell_endo-1" "sgCont" "T24" 24 "endo" "Cont_T24_endo-1"
+"Cont_T24_cell_endo-2" "sgCont" "T24" 24 "endo" "Cont_T24_endo-2"
+"sgLDHA_T0_exo-1" "sgLDHA" "T0" 0 "exo" "A_T0_exo-1"
+"sgLDHA_T0_exo-2" "sgLDHA" "T0" 0 "exo" "A_T0_exo-2"
+"Cont_T0_exo-1" "sgCont" "T0" 0 "exo" "Cont_T0_exo-1"
+"Cont_T0_cell_exo-2" "sgCont" "T0" 0 "exo" "Cont_T0_exo-2"
+"A_T24_cell_exo-1" "sgLDHA" "T24" 24 "exo" "A_T24_exo-1"
+"A_T24_cell_exo-2" "sgLDHA" "T24" 24 "exo" "A_T24_exo-2"
+"Cont_T24_cell_exo-1" "sgCont" "T24" 24 "exo" "Cont_T24_exo-1"
+"Cont_T24_cell_exo-2" "sgCont" "T24" 24 "exo" "Cont_T24_exo-2"

diff -r 000000000000 -r 3cb0128a59a6 test-data/sampleMetadata_3.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleMetadata_3.csv Thu Mar 28 13:19:21 2024 +0000

diff -r 000000000000 -r 3cb0128a59a6 test-data/sampleMetadata_4.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleMetadata_4.csv Thu Mar 28 13:19:21 2024 +0000

@@ -0,0 +1,17 @@
+"name_to_plot" "condition" "timepoint" "timenum" "compartment" "original_name"
+"Cont_c_T0-1" "Control" "T0" 0 "cell" "MCF001089_TD01"
+"Cont_c_T0-2" "Control" "T0" 0 "cell" "MCF001089_TD02"
+"Cont_c_T2h-1" "Control" "T2h" 2 "cell" "MCF001089_TD07"
+"Cont_c_T2h-2" "Control" "T2h" 2 "cell" "MCF001089_TD08"
+"L-Cycl_c_T0-1" "L-Cycloserine" "T0" 0 "cell" "MCF001089_TD19"
+"L-Cycl_c_T0-2" "L-Cycloserine" "T0" 0 "cell" "MCF001089_TD20"
+"L-Cycl_c_T2h-1" "L-Cycloserine" "T2h" 2 "cell" "MCF001089_TD25"
+"L-Cycl_c_T2h-2" "L-Cycloserine" "T2h" 2 "cell" "MCF001089_TD26"
+"Cont_md_T0-1" "Control" "T0" 0 "med" "MCF001089_TD37"
+"Cont_md_T0-2" "Control" "T0" 0 "med" "MCF001089_TD38"
+"Cont_md_T2h-1" "Control" "T2h" 2 "med" "MCF001089_TD43"
+"Cont_md_T2h-2" "Control" "T2h" 2 "med" "MCF001089_TD44"
+"L-Cycl_md_T0-1" "L-Cycloserine" "T0" 0 "med" "MCF001089_TD55"
+"L-Cycl_md_T0-2" "L-Cycloserine" "T0" 0 "med" "MCF001089_TD56"
+"L-Cycl_md_T2h-1" "L-Cycloserine" "T2h" 2 "med" "MCF001089_TD61"
+"L-Cycl_md_T2h-2" "L-Cycloserine" "T2h" 2 "med" "MCF001089_TD62"

diff -r 000000000000 -r 3cb0128a59a6 test-data/variableMetadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/variableMetadata.tsv Thu Mar 28 13:19:21 2024 +0000

@@ -0,0 +1,24 @@
+ID metabolite_name isotope_numeric
+Peak1 2_3-PG 0
+Peak2 2_3-PG 1
+Peak3 2_3-PG 2
+Peak4 2_3-PG 3
+Peak5 2-OHGLu 0
+Peak6 2-OHGLu 1
+Peak7 2-OHGLu 2
+Peak8 2-OHGLu 3
+Peak9 2-OHGLu 4
+Peak10 2-OHGLu 5
+Peak11 6-PG 0
+Peak12 6-PG 1
+Peak13 6-PG 2
+Peak14 6-PG 3
+Peak15 6-PG 4
+Peak16 6-PG 5
+Peak17 6-PG 6
+Peak18 a-KG 0
+Peak19 a-KG 1
+Peak20 a-KG 2
+Peak21 a-KG 3
+Peak22 a-KG 4
+Peak23 a-KG 5

diff -r 000000000000 -r 3cb0128a59a6 tracegroomer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tracegroomer.xml Thu Mar 28 13:19:21 2024 +0000

[

b'@@ -0,0 +1,333 @@\n+<tool id="tracegroomer" name="tracegroomer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">\n+ <description>\n+ TraceGroomer is a solution to format and normalize files for DIMet tool\n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ mkdir -p config &&\n+ #if $sample_metadata_path:\n+ ln -s \'$sample_metadata_path\' ./sample_metadata.csv &&\n+ #end if\n+ #if $type_of_file.type_of_file_selector == "rule_tsv":\n+ #if $variable_metadata_path:\n+ ln -s \'$variable_metadata_path\' ./variableMetadata.tsv &&\n+ #end if\n+ #end if\n+ ln -s \'$param_file\' config/config.yaml &&\n+ python3 -m tracegroomer\n+ -cf \'config/config.yaml\'\n+ -lm \'${labeled_metabo_file}\'\n+ -tf \'${type_of_file_selector}\'\n+ --isosprop_min_admitted ${isosprop_min_admitted}\n+ #if $amount_material:\n+ --amountMaterial_path \'${amount_material}\'\n+ #end if\n+ #if $remove_these_metabolites:\n+ --remove_these_metabolites \'${remove_these_metabolites}\'\n+ #end if\n+ #if $advanced_options.use_internal_standard:\n+ --use_internal_standard ${use_internal_standard}\n+ #end if\n+ $alternative_div_amount_material\n+ $div_isotopologues_by_amount_material\n+ $isotopologues_preview\n+ $fractions_stomp_values\n+ $subtract_blankavg\n+ $under_detection_limit_set_nan\n+ -ox \'tsv\' &&\n+ #if $type_of_file.type_of_file_selector == "IsoCor_out_tsv":\n+ cp -rf \'${AbundanceCorrected}.tsv\' \'${AbundanceCorrected}\' &&\n+ cp -rf \'${MeanEnrichment13C}.tsv\' \'${MeanEnrichment13C}\' &&\n+ cp -rf \'${IsotopologuesProp}.tsv\' \'${IsotopologuesProp}\' &&\n+ cp -rf \'${IsotopologuesAbs}.tsv\' \'${IsotopologuesAbs}\'\n+ #else if $type_of_file.type_of_file_selector == "rule_tsv":\n+ cp -rf \'${Absolute_isotopologue_abundances}.tsv\' \'${Absolute_isotopologue_abundances}\'\n+ #else if $type_of_file.type_of_file_selector == "generic_xlsx":\n+ cp -rf \'${sheetname}.tsv\' \'${isotopologuesCorrValues}\'\n+ #else:\n+ cp -rf \'${raw_abundance_sheet_name}.tsv\' \'${rawAbundances}\' &&\n+ cp -rf \'${frac_contribution_sheet_name}.tsv\' \'${FracContribution_C}\' &&\n+ cp -rf \'${corrected_isotopologues_sheet_name}.tsv\' \'${CorrectedIsotopologues}\'\n+ #end if\n+\n+ ]]></command>\n+\n+ <configfiles>\n+ <configfile name="param_file"><![CDATA[\n+ groom_out_path: \'.\'\n+ metadata: sample_metadata\n+ #if $type_of_file.type_of_file_selector == "IsoCor_out_tsv":\n+ abundances: \'${AbundanceCorrected}\'\n+ mean_enrichment: \'${MeanEnrichment13C}\'\n+ isotopologue_proportions: \'${IsotopologuesProp}\'\n+ isotopologues: \'${IsotopologuesAbs}\'\n+ #end if\n+\n+ #if $type_of_file.type_of_file_selector == "VIBMEC_xlsx":\n+ abundances: \'${raw_abundance_sheet_name}\'\n+ mean_enrichment: \'${frac_contribution_sheet_name}\'\n+ isotopologue_proportions: \'${corrected_isotopologues_sheet_name}\'\n+ isotopologues: null\n+ #end if\n+\n+ #if $type_of_file.type_of_file_selector == "generic_xlsx":\n+ abundances: null\n+ mean_enrichment: null\n+ isotopologue_proportions: null\n+ isotopologues: \'${sheetname}\'\n+ #end if\n+\n+ #if $type_of_file.type_of_file_selector == "rule_tsv":\n+ abundances: null\n+ mean_enrichment: null\n+ isotopologue_proportions: null\n+ isotopologues: \'${Absolute_isotopologue_ab'..b'otopologue proportions, total abundances).\n+\n+\n+**Other input formats**\n+\n+\n+Please visit https://github.com/cbib/TraceGroomer/wiki/3-Supported-input-formats to get information about:\n+ - A \'generic\' .xlsx measurements file, manually set by the user.\n+ - Results provided by the VIB Metabolomics Expertise Center (El-Maven results are shaped by VIB MEC team into a multi-sheet .xlsx file).\n+\n+\n+\n+For any type of input formats mentioned above, a samples\' metadata file must be provided (section "Metadata File Information").\n+\n+\n+**Metadata File Information**\n+\n+Provide a tab-separated file that has the names of the samples in the first column and one header row.\n+Column names must be exactly in this order:\n+\n+ name_to_plot\n+ condition\n+ timepoint\n+ timenum\n+ compartment\n+ original_name\n+\n+Example **Metadata File**:\n+\n+\n+ ==================== =============== ============= ============ ================ =================\n+ **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name**\n+ -------------------- --------------- ------------- ------------ ---------------- -----------------\n+ Control_cell_T0-1 Control T0 0 cell MCF001089_TD01\n+ Control_cell_T0-2 Control T0 0 cell MCF001089_TD02\n+ Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04\n+ Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05\n+ Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07\n+ Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08\n+ Control_med_T24-1 Control T24 24 med MCF001090_TD02\n+ Control_med_T24-2 Control T24 24 med MCF001090_TD03\n+ Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04\n+ Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05\n+ Control_med_T0-1 Control T0 0 med MCF001090_TD06\n+ Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07\n+ ==================== =============== ============= ============ ================ =================\n+\n+\n+The column **original_name** must have the names of the samples as given in your data.\n+\n+The column **name_to_plot** must have the names as you want them to be (or set identical to original_name if you prefer). To set names that\n+are meaningful is a better choice, as we will take them to display the results.\n+\n+The column **timenum** must contain only the numeric part of the timepoint, for example 2,0, 10, 100 (this means, without letters ("T", "t", "s", "h" etc)\n+nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!).\n+\n+The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results\' files names: the longer the\n+compartments names are, the longer the output files\' names! Please pick short and clear abbreviations to fill this column.\n+\n+\n+**Advanced options**\n+\n+These options allow the user to:\n+\n+ - Normalize by the amount of material (number of cells, tissue weight): the user must provide a tab delimited file, with a header, having the first column with the same names as in metadata \'original_name\', and the second column the quantitative information, without zeroes nor negative numbers.\n+ - Normalize by an internal standard (present in your data) at choice.\n+ - Print a preview of isotopologues values.\n+\n+Please visit our Wiki page (https://github.com/cbib/TraceGroomer/wiki) for more information, and how to get help.\n+\n+ ]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n'