Skip to content

Commit

Permalink
add correct test files in test-data folder (#5810)
Browse files Browse the repository at this point in the history 
* add correct test files in test-data folder

* upgrade version from 0.2.1 to 0.2.2

* add correct test files in test-data folder

* add new parameter "disfit_tail_option" for metabologram, differential analysis and timecourse analysis
  • Loading branch information
@bdartigues
bdartigues authored Mar 4, 2024
1 parent 3a3b40c commit 0e7c185
Show file tree
Hide file tree
Showing 12 changed files with 176 additions and 173 deletions.
1 change: 1 addition & 0 deletions tools/dimet/dimet_differential_analysis.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@
'++analysis.method.statistical_test=${statistical_test}'
'++analysis.method.grouping=${groups}'
'++analysis.method.correction_method=${correction_method}'
'++analysis.method.disfit_tail_option="auto"'
'++analysis.method.impute_values=${impute_values}'
'++analysis.statistical_test=${statistical_test}'
'++analysis.dataset.subfolder='
Expand Down
1 change: 1 addition & 0 deletions tools/dimet/dimet_metabologram.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@
'++analysis.method.correction_method=${correction_method}'
'++analysis.method.impute_values=${impute_values}'
'++analysis.statistical_test=${statistical_test}'
'++analysis.method.disfit_tail_option="auto"'
'++analysis.dataset.subfolder='
'++analysis.dataset.conditions=${$conditions}'
'++analysis.dataset.pathways=${pathways}'
Expand Down
1 change: 1 addition & 0 deletions tools/dimet/dimet_timecourse_analysis.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@
'++analysis.method.statistical_test=${statistical_test}'
'++analysis.method.grouping=${groups}'
'++analysis.method.correction_method=${correction_method}'
'++analysis.method.disfit_tail_option="auto"'
'++analysis.method.impute_values=${impute_values}'
'++analysis.dataset.subfolder='
'++analysis.dataset.label='
Expand Down
2 changes: 1 addition & 1 deletion tools/dimet/macros.xml
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">0.2.1</token>
<token name="@TOOL_VERSION@">0.2.2</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@EXECUTABLE@">pca</token>
<xml name="requirements">
Expand Down
48 changes: 24 additions & 24 deletions tools/dimet/test-data/abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv
View file
Original file line number Diff line number Diff line change
@@ -1,25 +1,25 @@
metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_cell_T0-1 Ctrl_cell_T0-2 L-Cyc_cell_T0-1 L-Cyc_cell_T0-2 gmean_1 gmean_2
L-Tyrosine 0.659969 0.044578 1.0 0.544 1.580048 0 0 1.346502 2.475187 cell 5.059224 5.449813 3.712722 2.974626 5.250888 3.323245
L-Methionine 0.564183 0.075348 1.0 0.488153 1.47855 0 0 1.21324 2.485367 cell 5.928871 5.711734 4.498494 3.443504 5.81929 3.935808
L-Aspartic_acid 1.159351 0.071437 1.0 0.435311 2.23357 0 0 1.126485 2.587769 cell 3.824739 2.962785 1.8363 1.23697 3.366286 1.507132
Ile_Leu 0.693524 0.078103 1.0 0.414254 1.617229 0 0 1.080144 2.607445 cell 4.393714 5.288745 3.31357 2.6813 4.820501 2.980717
L-Tryptophan 0.837035 0.077877 1.0 0.411565 1.786375 0 0 1.07544 2.613053 cell 3.918551 4.59966 2.843111 1.986607 4.245468 2.376582
L-Phenylalanine 0.676734 0.082439 1.0 0.397203 1.598517 0 0 1.043392 2.62685 cell 4.492276 5.358136 3.448884 2.731286 4.906142 3.069184
L-Histidine 0.662413 0.124722 1.0 0.342512 1.582728 0 0 0.893231 2.607882 cell 5.135867 4.726362 3.833131 2.527985 4.926862 3.112892
L-Lysine 0.700054 0.108484 1.0 0.32716 1.624566 0 0 0.879075 2.68699 cell 4.289814 5.133306 3.410739 2.446316 4.692646 2.888554
L-Valine 0.48785 0.113542 1.0 0.317079 1.402354 0 0 0.853637 2.692194 cell 6.655174 5.844043 4.990406 3.96298 6.236435 4.44712
L-Glutamic_acid 0.830004 0.137338 1.0 0.265185 1.777691 0 0 0.723262 2.727386 cell 4.556485 3.416118 2.692856 1.829099 3.945312 2.219347
L-Serine 0.556596 0.152386 1.0 0.23191 1.470794 0 0 0.638261 2.752194 cell 5.905558 4.753595 4.115334 3.153364 5.298361 3.602381
Hexose-phosphate 0.76747 0.157597 1.0 0.22649 1.702282 0 0 0.62225 2.747362 cell 4.735898 3.493336 2.871086 1.988536 4.067442 2.389405
L-Proline 0.519615 0.177905 1.0 0.223644 1.433572 0 0 0.601013 2.687365 cell 6.102914 4.603201 4.002188 3.415549 5.300277 3.697252
L-Lactic_acid 0.766316 0.216319 1.0 0.194497 1.70092 0 0 0.51042 2.624306 cell 2.828561 4.538379 2.318141 1.914073 3.582887 2.10644
Hexose 0.648059 0.202852 1.0 0.1683 1.567058 0 0 0.459334 2.729259 cell 5.122919 3.575551 3.116217 2.39366 4.279867 2.731147
Fumaric_acid 0.623283 0.19388 1.0 0.156841 1.540376 0 0 0.437164 2.787315 cell 3.977834 5.293909 2.506594 3.54067 4.588931 2.979098
L-Malic_acid 0.276766 0.295582 1.0 0.151833 1.211476 0 0 0.371422 2.446251 cell 8.445961 8.514381 8.074539 6.06813 8.480102 6.999811
L-Arginine 0.574794 0.200943 1.0 0.144438 1.489464 0 0 0.403393 2.792837 cell 4.234461 5.565819 3.831068 2.772982 4.854714 3.259368
L-Threonine 0.540842 0.220629 1.0 0.113082 1.454821 0 0 0.316715 2.800767 cell 5.715582 4.30713 3.990415 2.914815 4.961628 3.410472
L-Glutamine 0.98619 0.263749 1.0 0.087801 1.980946 0 0 0.237703 2.707301 cell 3.806965 2.018081 1.780378 1.099664 2.77178 1.39922
Glycine 0.567169 0.318145 1.0 -0.012773 1.481613 0 0 -0.035287 2.762706 cell 5.028385 3.20148 3.236767 2.265679 4.012265 2.708039
Pyruvic_acid 0.472738 0.490805 1.0 -0.131405 1.387741 0 0 -0.317152 2.413541 cell 1.811325 4.224866 2.158282 1.84113 2.766334 1.993409
L-Alanine 0.440859 0.494601 1.0 -0.237912 1.357412 0 0 -0.631111 2.652708 cell 4.684396 2.511054 3.142165 2.031688 3.42969 2.526638
Fructose_1,6-bisphosphate 2.638184 1 1 2.0 cell 3.220864 1.220864 3.220864 1.220864
L-Tyrosine 0.659969 0.044578 1.0 0.544 1.580048 0.0 0.0 1.346502 2.475187 cell 5.059224 5.449813 3.712722 2.974626 5.250888 3.323245
L-Aspartic_acid 1.159351 0.071437 1.0 0.435311 2.23357 0.0 0.0 1.126485 2.587769 cell 3.824739 2.962785 1.8363 1.23697 3.366286 1.507132
L-Methionine 0.564183 0.075348 1.0 0.488153 1.47855 0.0 0.0 1.21324 2.485367 cell 5.928871 5.711734 4.498494 3.443504 5.81929 3.935808
L-Tryptophan 0.837035 0.077877 1.0 0.411565 1.786375 0.0 0.0 1.07544 2.613053 cell 3.918551 4.59966 2.843111 1.986607 4.245468 2.376582
Ile_Leu 0.693524 0.078103 1.0 0.414254 1.617229 0.0 0.0 1.080144 2.607445 cell 4.393714 5.288745 3.31357 2.6813 4.820501 2.980717
L-Phenylalanine 0.676734 0.082439 1.0 0.397203 1.598517 0.0 0.0 1.043392 2.62685 cell 4.492276 5.358136 3.448884 2.731286 4.906142 3.069184
L-Lysine 0.700054 0.108484 1.0 0.32716 1.624566 0.0 0.0 0.879075 2.68699 cell 4.289814 5.133306 3.410739 2.446316 4.692646 2.888554
L-Valine 0.48785 0.113542 1.0 0.317079 1.402354 0.0 0.0 0.853637 2.692194 cell 6.655174 5.844043 4.990406 3.96298 6.236435 4.44712
L-Histidine 0.662413 0.124722 1.0 0.342512 1.582728 0.0 0.0 0.893231 2.607882 cell 5.135867 4.726362 3.833131 2.527985 4.926862 3.112892
L-Glutamic_acid 0.830004 0.137338 1.0 0.265185 1.777691 0.0 0.0 0.723262 2.727386 cell 4.556485 3.416118 2.692856 1.829099 3.945312 2.219347
L-Serine 0.556596 0.152386 1.0 0.23191 1.470794 0.0 0.0 0.638261 2.752194 cell 5.905558 4.753595 4.115334 3.153364 5.298361 3.602381
Hexose-phosphate 0.76747 0.157597 1.0 0.22649 1.702282 0.0 0.0 0.62225 2.747362 cell 4.735898 3.493336 2.871086 1.988536 4.067442 2.389405
L-Proline 0.519615 0.177905 1.0 0.223644 1.433572 0.0 0.0 0.601013 2.687365 cell 6.102914 4.603201 4.002188 3.415549 5.300277 3.697252
Fumaric_acid 0.623283 0.19388 1.0 0.156841 1.540376 0.0 0.0 0.437164 2.787315 cell 3.977834 5.293909 2.506594 3.54067 4.588931 2.979098
L-Arginine 0.574794 0.200943 1.0 0.144438 1.489464 0.0 0.0 0.403393 2.792837 cell 4.234461 5.565819 3.831068 2.772982 4.854714 3.259368
Hexose 0.648059 0.202852 1.0 0.1683 1.567058 0.0 0.0 0.459334 2.729259 cell 5.122919 3.575551 3.116217 2.39366 4.279867 2.731147
L-Lactic_acid 0.766316 0.216319 1.0 0.194497 1.70092 0.0 0.0 0.51042 2.624306 cell 2.828561 4.538379 2.318141 1.914073 3.582887 2.10644
L-Threonine 0.540842 0.220629 1.0 0.113082 1.454821 0.0 0.0 0.316715 2.800767 cell 5.715582 4.30713 3.990415 2.914815 4.961628 3.410472
L-Glutamine 0.98619 0.263749 1.0 0.087801 1.980946 0.0 0.0 0.237703 2.707301 cell 3.806965 2.018081 1.780378 1.099664 2.77178 1.39922
L-Malic_acid 0.276766 0.295582 1.0 0.151833 1.211476 0.0 0.0 0.371422 2.446251 cell 8.445961 8.514381 8.074539 6.06813 8.480102 6.999811
Glycine 0.567169 0.318145 1.0 -0.012773 1.481613 0.0 0.0 -0.035287 2.762706 cell 5.028385 3.20148 3.236767 2.265679 4.012265 2.708039
Pyruvic_acid 0.472738 0.490805 1.0 -0.131405 1.387741 0.0 0.0 -0.317152 2.413541 cell 1.811325 4.224866 2.158282 1.84113 2.766334 1.993409
L-Alanine 0.440859 0.494601 1.0 -0.237912 1.357412 0.0 0.0 -0.631111 2.652708 cell 4.684396 2.511054 3.142165 2.031688 3.42969 2.526638
Fructose_1,6-bisphosphate 2.638184 1.0 1.0 2.0 cell 3.220864 1.220864 3.220864 1.220864
48 changes: 24 additions & 24 deletions tools/dimet/test-data/abundance--cell-Control-T2h-Control-T0-Tt.tsv
View file
Original file line number Diff line number Diff line change
@@ -1,25 +1,25 @@
metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_cell_T2h-1 Ctrl_cell_T2h-2 Ctrl_cell_T0-1 Ctrl_cell_T0-2 gmean_1 gmean_2
L-Tryptophan -0.777998 0.034692 0.69385 0.664552 0.583176 0 0 1.541549 2.319681 cell 2.660282 2.70099 4.242539 4.979963 2.680559 4.596486
L-Aspartic_acid -2.274085 0.039066 0.781312 0.556683 0.206744 0 0 1.374553 2.469185 cell 0.327076 0.791534 2.796261 2.166087 0.508814 2.461086
L-Lysine -0.558396 0.071556 1.0 0.497716 0.679057 0 0 1.23415 2.479625 cell 3.776027 3.993588 5.227738 6.255652 3.883284 5.718646
L-Arginine -0.658636 0.111701 1.0 0.440969 0.633477 0 0 1.087359 2.465839 cell 3.035924 2.953846 4.123283 5.419685 2.994604 4.72725
L-Histidine -0.68301 0.090057 1.0 0.413676 0.622865 0 0 1.065086 2.574685 cell 2.578187 3.676926 5.152872 4.742012 3.078929 4.943175
L-Tyrosine -0.589456 0.191484 1.0 0.235832 0.664593 0 0 0.617152 2.616914 cell 2.671781 4.292502 4.909654 5.288695 3.386536 5.095651
L-Methionine -0.489868 0.261207 1.0 0.168943 0.71209 0 0 0.427099 2.528072 cell 3.0957 4.99071 5.623772 5.417809 3.930616 5.51983
L-Phenylalanine -0.608451 0.19931 1.0 0.160334 0.655901 0 0 0.442554 2.760207 cell 2.526754 3.990049 4.432603 5.286961 3.175196 4.840971
L-Malic_acid -0.842519 0.323037 1.0 0.123892 0.557669 0 0 0.2985 2.409353 cell 1.235551 3.317115 3.615615 3.644904 2.024467 3.63023
Ile_Leu -0.554218 0.227774 1.0 0.111354 0.681026 0 0 0.309498 2.779406 cell 2.749607 4.283823 4.593321 5.529013 3.43203 5.039497
L-Lactic_acid -0.468969 0.32893 1.0 0.109159 0.722481 0 0 0.264176 2.420103 cell 3.143658 3.203459 3.467635 5.563761 3.173418 4.39239
Fumaric_acid -1.082458 0.257085 1.0 0.072691 0.472224 0 0 0.201376 2.770286 cell 0.878066 2.539989 2.741365 3.648352 1.493412 3.162509
L-Glutamine -1.091499 0.265783 1.0 0.064303 0.469274 0 0 0.177439 2.759429 cell 0.883383 1.753625 3.642812 1.931064 1.244638 2.652264
L-Glutamic_acid -0.765842 0.325511 1.0 -0.028187 0.58811 0 0 -0.078254 2.776208 cell 1.414087 3.21983 4.190295 3.141576 2.133804 3.628241
L-Valine -0.345997 0.35338 1.0 -0.044413 0.786764 0 0 -0.120212 2.706693 cell 4.179372 6.167004 6.886065 6.046792 5.07683 6.452798
L-Threonine -0.463814 0.368868 1.0 -0.099423 0.725067 0 0 -0.278707 2.803234 cell 2.723045 4.443183 5.526279 4.164476 3.47836 4.797297
Pyruvic_acid 0.905946 0.398774 1.0 -0.124124 1.873772 0 0 -0.34081 2.745715 cell 1.633721 3.592255 0.84654 1.974531 2.422549 1.292873
Hexose-phosphate -0.60704 0.407318 1.0 -0.137592 0.656542 0 0 -0.378236 2.748963 cell 1.734049 3.685036 4.483012 3.3068 2.527851 3.85025
Hexose -0.403635 0.446592 1.0 -0.201612 0.755951 0 0 -0.558993 2.772623 cell 2.764282 4.423486 5.536905 3.864493 3.496822 4.625725
L-Serine -0.31232 0.458611 1.0 -0.2056 0.805345 0 0 -0.560471 2.726026 cell 3.868814 5.868893 6.59484 5.308422 4.765045 5.916772
Fructose_1,6-bisphosphate 0.0 1.526778 0 1 0.0 2.23249 cell 0.154691 2.387181 0.398015 0.60768 0.398015
Glycine -0.316365 0.624652 -0.423447 0.803091 0 0 -1.102692 2.604084 cell 2.393939 4.284841 4.998023 3.182149 3.202756 3.988039
L-Proline -0.168249 0.862102 -0.454948 0.889922 0 0 -1.160081 2.549919 cell 2.590021 5.13994 4.720818 3.560737 3.648637 4.09995
L-Alanine -0.07162 0.950212 -0.89366 0.951569 0 0 -1.882381 2.106373 cell 1.96331 4.069683 4.057263 2.174882 2.826668 2.970533
L-Tryptophan -0.777998 0.034692 0.69385 0.664552 0.583176 0.0 0.0 1.541549 2.319681 cell 2.660282 2.70099 4.242539 4.979963 2.680559 4.596486
L-Aspartic_acid -2.274085 0.039066 0.781312 0.556683 0.206744 0.0 0.0 1.374553 2.469185 cell 0.327076 0.791534 2.796261 2.166087 0.508814 2.461086
L-Lysine -0.558396 0.071556 1.0 0.497716 0.679057 0.0 0.0 1.23415 2.479625 cell 3.776027 3.993588 5.227738 6.255652 3.883284 5.718646
L-Histidine -0.68301 0.090057 1.0 0.413676 0.622865 0.0 0.0 1.065086 2.574685 cell 2.578187 3.676926 5.152872 4.742012 3.078929 4.943175
L-Arginine -0.658636 0.111701 1.0 0.440969 0.633477 0.0 0.0 1.087359 2.465839 cell 3.035924 2.953846 4.123283 5.419685 2.994604 4.72725
L-Tyrosine -0.589456 0.191484 1.0 0.235832 0.664593 0.0 0.0 0.617152 2.616914 cell 2.671781 4.292502 4.909654 5.288695 3.386536 5.095651
L-Phenylalanine -0.608451 0.19931 1.0 0.160334 0.655901 0.0 0.0 0.442554 2.760207 cell 2.526754 3.990049 4.432603 5.286961 3.175196 4.840971
Ile_Leu -0.554218 0.227774 1.0 0.111354 0.681026 0.0 0.0 0.309498 2.779406 cell 2.749607 4.283823 4.593321 5.529013 3.43203 5.039497
Fumaric_acid -1.082458 0.257085 1.0 0.072691 0.472224 0.0 0.0 0.201376 2.770286 cell 0.878066 2.539989 2.741365 3.648352 1.493412 3.162509
L-Methionine -0.489868 0.261207 1.0 0.168943 0.71209 0.0 0.0 0.427099 2.528072 cell 3.0957 4.99071 5.623772 5.417809 3.930616 5.51983
L-Glutamine -1.091499 0.265783 1.0 0.064303 0.469274 0.0 0.0 0.177439 2.759429 cell 0.883383 1.753625 3.642812 1.931064 1.244638 2.652264
L-Malic_acid -0.842519 0.323037 1.0 0.123892 0.557669 0.0 0.0 0.2985 2.409353 cell 1.235551 3.317115 3.615615 3.644904 2.024467 3.63023
L-Glutamic_acid -0.765842 0.325511 1.0 -0.028187 0.58811 0.0 0.0 -0.078254 2.776208 cell 1.414087 3.21983 4.190295 3.141576 2.133804 3.628241
L-Lactic_acid -0.468969 0.32893 1.0 0.109159 0.722481 0.0 0.0 0.264176 2.420103 cell 3.143658 3.203459 3.467635 5.563761 3.173418 4.39239
L-Valine -0.345997 0.35338 1.0 -0.044413 0.786764 0.0 0.0 -0.120212 2.706693 cell 4.179372 6.167004 6.886065 6.046792 5.07683 6.452798
L-Threonine -0.463814 0.368868 1.0 -0.099423 0.725067 0.0 0.0 -0.278707 2.803234 cell 2.723045 4.443183 5.526279 4.164476 3.47836 4.797297
Pyruvic_acid 0.905946 0.398774 1.0 -0.124124 1.873772 0.0 0.0 -0.34081 2.745715 cell 1.633721 3.592255 0.84654 1.974531 2.422549 1.292873
Hexose-phosphate -0.60704 0.407318 1.0 -0.137592 0.656542 0.0 0.0 -0.378236 2.748963 cell 1.734049 3.685036 4.483012 3.3068 2.527851 3.85025
Hexose -0.403635 0.446592 1.0 -0.201612 0.755951 0.0 0.0 -0.558993 2.772623 cell 2.764282 4.423486 5.536905 3.864493 3.496822 4.625725
L-Serine -0.31232 0.458611 1.0 -0.2056 0.805345 0.0 0.0 -0.560471 2.726026 cell 3.868814 5.868893 6.59484 5.308422 4.765045 5.916772
Glycine -0.316365 0.624652 -0.423447 0.803091 0.0 0.0 -1.102692 2.604084 cell 2.393939 4.284841 4.998023 3.182149 3.202756 3.988039
L-Proline -0.168249 0.862102 -0.454948 0.889922 0.0 0.0 -1.160081 2.549919 cell 2.590021 5.13994 4.720818 3.560737 3.648637 4.09995
L-Alanine -0.07162 0.950212 -0.89366 0.951569 0.0 0.0 -1.882381 2.106373 cell 1.96331 4.069683 4.057263 2.174882 2.826668 2.970533
Fructose_1,6-bisphosphate 0.0 1.526778 0.0 1.0 0.0 2.23249 cell 0.154691 2.387181 0.398015 0.60768 0.398015
Loading

0 comments on commit 0e7c185

Please sign in to comment.