| Next changeset 1:ad4176b336dc (2024-09-16) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit c6e502d8af84750003e4ba001c61817acedd1896 |
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help.xml macros.xml mfassignr_findRecalSeries.xml test-data/QC1_1_POS_500.tabular test-data/findrecalseries/selected_series.tabular test-data/histnoise/plot.png test-data/isofiltr/iso_out.tabular test-data/isofiltr/mono_out.tabular test-data/mfassign/unambig.tabular test-data/mfassigncho/unambig.tabular test-data/recal/recalibrants.tabular test-data/recallist/recal_series.tabular test-data/snplot/plot.png |
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| diff -r 000000000000 -r a26b860d6ce7 help.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/help.xml Fri Sep 13 10:08:49 2024 +0000 |
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| b'@@ -0,0 +1,192 @@\n+<macros>\n+\n+<token name="@GENERAL_HELP@">\n+General Information\n+===================\n+\n+Overview\n+--------\n+ \n+MFAssignR is an R package for the molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements. It contains several functions for the noise assessment, isotope filtering, interal mass recalibration, and MF assignment. \n+\n+The MFAssignR package was originally developed by Simeon Schum et al. (2020), the source code can be found on `GitHub`_.\n+Please submit eventual Galaxy-related bug reports as `issues`_ on the repository.\n+\n+.. _GitHub: https://github.com/skschum/MFAssignR\n+.. _issues: https://github.com/RECETOX/galaxytools/issues\n+\n+\n+Workflow\n+--------\n+ \n+.. image:: https://github.com/RECETOX/MFAssignR/raw/master/overview.png\n+ :width: 1512\n+ :height: 720\n+ :scale: 60\n+ :alt: A picture of a workflow diagram.\n+\n+The recommended workflow how to run the MFAssignR package is as follows:\n+\n+(1) Run KMDNoise() to determine the noise level for the data.\n+(2) Check effectiveness of S/N threshold using SNplot().\n+(3) Use IsoFiltR() to identify potential 13C and 34S isotope masses.\n+(4) Using the S/N threshold, and the two data frames output from IsoFiltR(), run MFAssignCHO() to assign MF with C, H, and O to assess the mass accuracy.\n+(5) Use RecalList() to generate a list of the potential recalibrant series.\n+(6) Choose the most suitable recalibrant series using FindRecalSeries().\n+(7) After choosing recalibrant series, use Recal() to recalibrate the mass lists.\n+(8) Assign MF to the recalibrated mass list using MFAssign().\n+(9) Check the output plots from MFAssign() to evaluate the quality of the assignments.\n+\n+For detailed documentation on the individual steps please see the individual tool wrappers.\n+</token>\n+\n+<token name="@KMDNOISE_HELP@">\n+MFAssignR - KMDNoise\n+=============================\n+\n+This tool is the first step of the MFAssignR workflow (can be substitued by HistNoise or run in paralell).\n+\n+KMDnoise is a Kendrick Mass Defect (KMD) approach for the noise estimation. It selects a subset of the data using the linear equation y=0.1132x + b, where y stands for the KMD value, x for the measured ion mass and b is the y-intercept. The default y-intercepts of 0.05 and 0.2 in KMDNoise are used to isolate the largest analyte free region of noise in most mass spectra. The intensity of the peaks within this \xe2\x80\x9cslice\xe2\x80\x9d are then averaged and that value is defined as the noise level for the mass spectrum. This value is then multiplied with a user-defined signal-to-noise ratio (typically 3-10) to remove low intensity m/z values.\n+\n+Output: \n+\n+- noise estimate - this noise level can then be multiplied by the user chosen value (3, 6, 10) in order to set the signal to noise cut for formula assignment.\n+- KMD plot - bounds of the noise estimation area are highlighted in red.\n+</token>\n+\n+<token name="@HISTNOISE_HELP@">\n+MFAssignR - HistNoise\n+=============================\n+\n+This tool is the first step of the MFAssignR workflow (can be substitued by KMDNoise or run in paralell (-> SNplot)). \n+\n+HistNoise function creates a histogram using natural log of the intensity, which can be then used to determine the noise level for the data analyze, and also the estimated noise level. The noise level can be then multiplied by whatever value in order to reach the value to be used to cut the data.\n+\n+Output:\n+\n+- noise estimate - this noise level can then be multiplied by the user chosen value in order to set the signal to noise cut for formula assignment\n+- Histogram - shows where the cut is being applied\n+\n+</token>\n+\n+<token name="@SNPLOT_HELP@">\n+MFAssignR - SNplot\n+=============================\n+\n+This tool is the second step of the MFAssignR workflow (KMDNoise -> SNplot -> IsoFiltR).\n+\n+SNplot function plots the mass spectrum with the S/N cut denoted by different colors for the mass spectrum peaks (red indicates noise, blue indicates signal). This'..b'dentifies the homologous series that could be used for recalibration. On the input, there is the output from MFAssign() or MFAssignCHO() functions. It returns a dataframe that contains the CH2 homologous series that contain more than 3 members.\n+\n+Output: \n+\n+- Dataframe that contains the CH2 homologous series that contain more than 3 members.\n+</token>\n+\n+<token name="@FINDRECALSERIES_HELP@">\n+MFAssignR - FindRecalSeries\n+=============================\n+\n+This tool is the sixth step of the MFAssignR workflow (RecalList -> FindRecalSeries -> Recal)\n+\n+This function takes on input the CH2 homologous recalibration series, which are provided by the RecalList function and tries to find the most suitable series combination for recalibration based on the following criteria:\n+\n+(1) Series should cover the full mass spectral range,\n+(2) Series should be optimally long and combined have a \xe2\x80\x9cTall Peak\xe2\x80\x9d at least every 100 m/z,\n+(3) Abundance score: the higher, the better,\n+(4) Peak score: the closer to 0, the better,\n+(5) Peak Distance: the closer to 1, the better,\n+(6) Series Score: the closer to this value, the better.\n+\n+Combinations of 5 series are assembled, scores are computed for other metrics (in case of Peak proximity and Peak\n+distance, an inverted score is computed) and these are summed. Finally, either a series of the size of combination or top 10 unique series having the highest score are outputted.\n+\n+Output: \n+\n+- Dataframe of n or 10 most suitable recalibrant series.\n+</token>\n+\n+<token name="@RECAL_HELP@">\n+MFAssignR - Recal\n+=============================\n+\n+This tool is the seventh step of the MFAssignR workflow (FindRecalSeries -> Recal -> MFAssign)\n+\n+Recal() function recalibrates the \'Mono\' and \'Iso\' outputs from the IsoFiltR() function and prepares a dataframe containing chose recalibrants. Also it outputs a plot for the qualitative assessment of recalibrants. The input to the function is output from MFAssign() or MFAssignCHO(). \n+\n+It is important for recalibrant masses to cover the entire mass range of interest, and they should be among the most abundant peaks in their region of the spectrum - by default we take first 10 recalibrant series. We recommend to sort the Recalibration Series table based on the Series Score (largest to smallest). In case that error "Gap in recalibrant coverage, try adding more recalibrant series" would occur, we recommend to provide more diverse series.\n+\n+Output: \n+\n+- Mass spectrum \n+- Recalibrated dataframe of monoisotopic masses \n+- Recalibrated dataframe of isotopic masses\n+- Recalibrants list\n+</token>\n+\n+<token name="@MFASSIGN_HELP@">\n+MFAssignR - MFAssign\n+=============================\n+\n+This tool is the last step of the MFAssignR workflow (Recal -> MFAssign)\n+\n+Recal() function recalibrates the \'Mono\' and \'Iso\' outputs from the IsoFiltR() function and prepares a dataframe containing chose recalibrants. Also it outputs a plot for the qualitative assessment of recalibrants. The input to the function is output from MFAssign() or MFAssignCHO(). \n+\n+It is important for recalibrant masses to cover the entire mass range of interest, and they should be among the most abundant peaks in their region of the spectrum - by default we take first 10 recalibrant series. We recommend to sort the Recalibration Series table based on the Series Score (largest to smallest). In case that error "Gap in recalibrant coverage, try adding more recalibrant series" would occur, we recommend to provide more diverse series.\n+\n+Output: \n+\n+- Unambig - data frame containing unambiguous assignments\n+- Ambig - data frame containing ambiguous assignments\n+- None - data frame containing unassigned masses\n+- MSAssign - ggplot of mass spectrum highlighting assigned/unassigned\n+- Error - ggplot of the Error vs. m/z\n+- MSgroups - ggplot of mass spectrum colored by molecular group\n+- VK - ggplot of van Krevelen plot, colored by molecular group\n+</token>\n+</macros>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r a26b860d6ce7 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 13 10:08:49 2024 +0000 |
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| b'@@ -0,0 +1,161 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">1.1.1</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">r-mfassignr</requirement>\n+ </requirements>\n+ </xml>\n+\n+ <xml name="refs">\n+ <xrefs>\n+ <xref type="bio.tools">mfassignr</xref>\n+ </xrefs>\n+ </xml>\n+\n+ <xml name="creator">\n+ <creator>\n+ <person\n+ givenName="Kristina"\n+ familyName="Gomoryova"\n+ url="https://github.com/KristinaGomoryova"\n+ identifier="0000-0003-4407-3917" />\n+ <person\n+ givenName="Helge"\n+ familyName="Hecht"\n+ url="https://github.com/hechth"\n+ identifier="0000-0001-6744-996X" />\n+ <person\n+ givenName="Zargham"\n+ familyName="Ahmad"\n+ url="https://github.com/zargham-ahmad"\n+ identifier="0000-0002-6096-224X" />\n+ <organization\n+ url="https://www.recetox.muni.cz/"\n+ email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"\n+ name="RECETOX MUNI" />\n+ </creator>\n+ </xml>\n+\n+ <xml name="kmdnoise_param">\n+ <param name="input_file" type="data" format="tabular" label="Input data"\n+ help= "Input data frame, first column is mass, second column is intensity"/>\n+ <param name="upper_y" type="float" label="upper limit for the y intercept" value="0.2"\n+ help= "The upper y-intercept value to isolate noise peaks in the equation for the KMD plot: y = 0.001123*x + b. Default value is set to 0.2, so that it does not interact with any potentially double-charged peaks."/>\n+ <param name="lower_y" type="float" label="lower limit for the y intercept" value="0.05"\n+ help="The lower y-intercept value to isolate noise peaks in the equation for the KMD plot: y = 0.001123*x + b. Default value is set to 0.05 to ensure no analyte peaks are incorporated into the noise estimation."/>\n+ <param name="upper_x" optional="true" type="float" label="upper limit for the x intercept"\n+ help="If not set, it defaults to maximum mass in the mass spectrum."/>\n+ <param name="lower_x" optional="true" type="float" label="lower limit for the x intercept"\n+ help="If not set, it defaults to minimum mass in the mass spectrum."/>\n+ </xml>\n+\n+ <xml name="histnoise_param">\n+ <param name="input_file" type="data" format="tabular" label="Input data"\n+ help= "Input data frame, first column is mass, second column is intensity"/>\n+ <param name="SN" type="float" label="signal-to-noise threshold" value="0"\n+ help= "A numeric value for situations where a predefined noise value is desired, default is 0"/>\n+ <param name="bin" type="float" label="bindwidth of the histogram" value="0.01"\n+ help= "A numeric value determining the binwidth of the histogram, default is 0.01"/>\n+ </xml>\n+\n+ <xml name="noise_threshold_params">\n+ <param name="sn_ratio" type="float" label="SN ratio" value="6"\n+ help= "Noise multiplier. Recommended value is 6."/>\n+ <param name="kmdn" type="float" label="Estimated noise" value="0"\n+ help= "Estimated noise, either from the KMDNoise or HistNoise function."/>\n+ </xml>\n+\n+ <xml name="snplot_param">\n+ <param name="input_file" type="data" format="tabular" label="Input data"\n+ help= "Input data frame, first column is mass, second column is intensity"/>\n+ <param name="cut" type="float" label="cut" value="0"\n+ help= "A numeric value of the intensity cut value being investigated"/>\n+ <param name="mass" type="float" label="mass" value="300"\n+ help= "A numeric value setting a centerpoint to look at the mass spect'..b' help= "Combinations of how many series should be computed." value="5"/>\n+ <param name="abundance_score_threshold" type="float" label="Abundance score threshold" value="100"\n+ help= "A threshold for filtering abundance score parameter. The series with higher values are better."/>\n+ <param name="peak_distance_threshold" type="float" label="Peak distance threshold" value="2"\n+ help= "A threshold for the peak distance parameter. The closer this value is to 1, the better."/>\n+ <param name="coverage_threshold" type="integer" label="How many % of the m/z range should be covered."\n+ help= "How many % of the m/z range should be covered." value="90"/>\n+ <param name="fill_series" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Whether to return top 10 unique series (TRUE) or series only from the best combination."\n+ help= "If TRUE, top 10 unique series will be returned, otherwise only the series from the best\n+ combination will be returned." value="false"/>\n+ </xml>\n+\n+ <xml name="recal_param">\n+ <param name="input_file" type="data" format="tabular" label="Input data (Output from MFAssign)"\n+ help= "Input data frame, the output from MFAssign or MFAssignCHO"/>\n+ <param name="series" type="data" format="tabular" label="Calibration series (Output from RecalList)"\n+ help= "Calibration series (Output from RecalList). At maximum the first 10 rows are used."/>\n+ <param name="peaks" type="data" format="tabular" label="Peaks dataframe (Mono from IsoFiltR)"\n+ help= "Peaks data frame, the Mono output from IsoFiltR"/> \n+ <param name="isopeaks" type="data" format="tabular" label="Isopeaks dataframe (Iso from IsoFiltR)" \n+ help= "Isopeaks data frame, the Mono output from IsoFiltR"/>\n+ <expand macro="ionmode_param" />\n+ <expand macro="noise_threshold_params" />\n+ <param name="mzRange" type="float" label="Mass windows used for the segmented recalibration" value="30"\n+ help= "Mass windows used for the segmented recalibration"/>\n+ <param name="step_O" type="float" label="Number of oxygen steps for formula extension" value="3"\n+ help= "Number of oxygen steps for formula extension"/>\n+ <param name="step_H2" type="float" label="Number of H2 steps for formula extension" value="5"\n+ help= "Number of H2 steps for formula extension"/>\n+ <param name="CalPeak" type="float" label="Maximum allowed recalibrant peaks per mzRange defined segment" value="150" help= "Maximum allowed recalibrant peaks per mzRange defined segment"/> \n+\n+ </xml>\n+\n+ <xml name="isofiltr_param">\n+ <param name="peaks" type="data" format="tabular" label="Input Peak Data"\n+ help="The input data frame containing abundance and peak mass."/>\n+ <param name="SN" type="float" value="0" label="Signal-to-Noise Ratio"\n+ help="Sets the noise cut for the data; peaks below this value will not be evaluated."/>\n+ <param name="Carbrat" type="float" value="60" min="5" label="Maximum 13C/12C Ratio"\n+ help="Sets the maximum allowed ratio for matching 13C isotopes."/>\n+ <param name="Sulfrat" type="float" value="30" label="Maximum 34S/32S Ratio"\n+ help="Sets the maximum allowed ratio for matching 34S isotopes."/>\n+ <param name="Sulferr" type="float" value="5" label="Maximum Error for 34S Matching (ppm)"\n+ help="Sets the maximum allowed error (ppm) for 34S mass matching."/>\n+ <param name="Carberr" type="float" value="5" label="Maximum Error for 13C Matching (ppm)"\n+ help="Sets the maximum allowed error (ppm) for 13C mass matching."/>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1016/j.envres.2020.110114</citation>\n+ </citations> \n+ </xml>\n+\n+</macros>\n' |
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| diff -r 000000000000 -r a26b860d6ce7 mfassignr_findRecalSeries.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mfassignr_findRecalSeries.xml Fri Sep 13 10:08:49 2024 +0000 |
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| @@ -0,0 +1,64 @@ +<tool id="mfassignr_findRecalSeries" name="MFAssignR FindRecalSeries" version="@TOOL_VERSION@+galaxy0" profile="23.0"> + <description>Selects most suitable series for recalibration</description> + <macros> + <import>macros.xml</import> + <import>help.xml</import> + </macros> + <edam_topics> + <edam_topic>topic_3172</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3627</edam_operation> + </edam_operations> + <expand macro="creator" /> + <expand macro="refs" /> + + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + Rscript -e 'packageVersion("MFAssignR")' && + Rscript '${mfassignr_findrecalseries}' + ]]> + </command> + <configfiles> + <configfile name="mfassignr_findrecalseries"><![CDATA[ + library(dplyr) + df <- read.table("$input_file", header=TRUE, sep="\t") + result <- MFAssignR::FindRecalSeries( + df = df, + global_min = $global_min, + global_max = $global_max, + number_of_combinations = $number_of_combinations, + abundance_score_threshold = $abundance_score_threshold, + peak_distance_threshold = $peak_distance_threshold, + coverage_threshold = $coverage_threshold, + fill_series = $fill_series + ) |> dplyr::rename(Series = series) + + write.table(result, file="$final_series", sep="\t", row.names=FALSE) + ]]></configfile> + </configfiles> + <inputs> + <expand macro="findrecalseries_param"/> + </inputs> + <outputs> + <data name="final_series" format="tabular" label="Final recalibration series"/> + </outputs> + <tests> + <test> + <param name="input_file" value="recallist/recal_series.tabular"/> + <param name="global_min" value="100"/> + <param name="global_max" value="500"/> + <param name="abundance_score_threshold" value="50"/> + <param name="number_of_combinations" value="3"/> + <param name="coverage_threshold" value="50"/> + <param name="fill_series" value="TRUE"/> + <output name="final_series" file="findrecalseries/selected_series.tabular"/> + </test> + </tests> + <help> + @FINDRECALSERIES_HELP@ + + @GENERAL_HELP@ + </help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r a26b860d6ce7 test-data/QC1_1_POS_500.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/QC1_1_POS_500.tabular Fri Sep 13 10:08:49 2024 +0000 |
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| b'@@ -0,0 +1,11676 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|
| b |
| diff -r 000000000000 -r a26b860d6ce7 test-data/findrecalseries/selected_series.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/findrecalseries/selected_series.tabular Fri Sep 13 10:08:49 2024 +0000 |
| b |
| @@ -0,0 +1,6 @@ +"Series" "total_abundance" "total_series_length" "peak_proximity" "peak_distance_proximity" "series_id" "sum_score" +"O_H_7" 437.136255030871 504.562 129.612788237483 2723.59808058946 "O_H_7 O2_H_6 O2_H_11" 3794.90912385781 +"O2_H_6" 437.136255030871 504.562 129.612788237483 2723.59808058946 "O_H_7 O2_H_6 O2_H_11" 3794.90912385781 +"O2_H_11" 437.136255030871 504.562 129.612788237483 2723.59808058946 "O_H_7 O2_H_6 O2_H_11" 3794.90912385781 +"O4_H_11" 943.304144088114 392.438 134.36084248065 1826.47532994759 "O2_H_6 O2_H_11 O4_H_11" 3296.57831651636 +"O3_H_12" 330.037060987448 364.407 135.12153276257 1826.47538570915 "O2_H_6 O3_H_12 O2_H_11" 2656.04097945917 |
| b |
| diff -r 000000000000 -r a26b860d6ce7 test-data/histnoise/plot.png |
| b |
| Binary file test-data/histnoise/plot.png has changed |
| b |
| diff -r 000000000000 -r a26b860d6ce7 test-data/isofiltr/iso_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isofiltr/iso_out.tabular Fri Sep 13 10:08:49 2024 +0000 |
| b |
| b'@@ -0,0 +1,2474 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|
| b |
| diff -r 000000000000 -r a26b860d6ce7 test-data/isofiltr/mono_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isofiltr/mono_out.tabular Fri Sep 13 10:08:49 2024 +0000 |
| b |
| b'@@ -0,0 +1,9203 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58483432405\n+496.213108260225\t989758.025889664\t194.942881074892\n+496.216077815534\t10178467.1550318\t362.918314773313\n+496.216078841243\t31275970.6115013\t441.609060225376\n+496.219049276795\t66365848.8074783\t657.407700012858\n+496.227949207539\t9061157.52341216\t650.499020894996\n+496.235368977352\t1510055.23948167\t851.302389453439\n+496.238330854308\t2201560.73527239\t558.638452017084\n+496.240176661019\t3256087.56632304\t200.453283615612\n+496.24426152048\t15065873.1828542\t404.107310889274\n+496.253165080587\t122957804.910435\t488.526090510203\n+496.273935051956\t410511291.027155\t569.228609743317\n+496.309544053542\t28142062.2756453\t669.421267706797\n+496.339223434401\t36218364.1982068\t907.356822372301\n+496.355546095555\t10541523.5607168\t971.371355227529\n+496.36296574308\t256407.515203075\t970.550708382651\n+496.386711682873\t498542.264248119\t1074.22883230875\n+496.417879207857\t5439046.62969312\t1179.11426491687\n+496.419359638752\t20977203.2873171\t940.206287172522\n+496.419359639509\t36874982.4003041\t921.24600068907\n+496.419362494184\t7229369.22280762\t1118.06096321429\n+496.419367075015\t7051063.21370908\t1318.76242748238\n+497.174578280662\t105959355.703291\t518.121628393255\n+497.238159226791\t121944899.124135\t499.248413991038\n+497.238160145162\t871960405.9\t533.297411015051\n+497.273872984588\t41631276.8930532\t697.231700134634\n+497.314055337443\t6422178.27017768\t858.76771236634\n+497.3319153\t373897.677842323\t928.444196999705\n+497.345308316198\t41374848.3598885\t749.724949545562\n+497.394434269742\t512694571.755652\t1080.87242902722\n+497.416761855493\t2638444.15406449\t1075.99643520893\n+498.158939528929\t198722427.709083\t511.8831101\n+498.191763405918\t3088487.53942805\t204.891333374763\n+498.1932595972\t12817425.9649905\t456.8425458\n+498.194750734376\t26679247.68\t350.403258378115\n+498.235045680081\t53562287.4364518\t600.359632017701\n+498.241014194979\t160510725.066736\t534.135846840907\n+498.243993958507\t53852417.8181517\t266.144974377967\n+498.24996356954\t1365478.66953941\t265.899331165661\n+498.267879031912\t207895443.6\t593.426045741132\n+498.269371532917\t555760401.896121\t588.41021906169\n+498.28877372918\t55865448.4324611\t543.92407082832\n+498.303703882262\t64626080.4619776\t745.9582668\n+498.324600750334\t27811603.0095765\t726.008268906568\n+498.360432665793\t351050.216159775\t976.082160964563\n+498.363416657684\t2707135.41959218\t862.186816600895\n+498.424633250144\t1267436.88539191\t921.566472129971\n+498.862429087054\t782439.925428304\t868.465297342923\n+498.878882867119\t148237.483504131\t1297.82872036827\n+498.880378113594\t272474.848211345\t1296.44242520691\n+498.899813275577\t9079966.64643745\t1037.01734650981\n+499.121183404306\t8676636.121\t225.127568017406\n+499.219963055109\t5430892.71966532\t613.1957225\n+499.2708584\t227391268.453864\t600.151891414137\n+499.288822984076\t23128292.5564576\t696.070263572641\n+499.308284714898\t36711228.3855236\t624.011387558514\n+499.311283053321\t1491641.08746936\t859.49855343588\n+499.326253234904\t8518503.07767788\t732.178361134203\n+499.330747083195\t22395964.6126047\t880.44935086572\n+499.335234028285\t102195712.831771\t580.38664357188\n+499.336731327911\t12487513.0395696\t570.10877514211\n+499.3547034\t902287.899589865\t792.051878966504\n+499.369679460285\t383336.906296847\t918.6658438\n+499.813219611989\t1028979.07395053\t859.818484397682\n+499.898704677475\t3803835.37465049\t1318.89095158717\n' |
| b |
| diff -r 000000000000 -r a26b860d6ce7 test-data/mfassign/unambig.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mfassign/unambig.tabular Fri Sep 13 10:08:49 2024 +0000 |
| b |
| b'@@ -0,0 +1,1357 @@\n+"exp_mass"\t"abundance"\t"RT"\t"formula"\t"class"\t"group"\t"C"\t"H"\t"O"\t"N"\t"S"\t"P"\t"E"\t"S34"\t"N15"\t"D"\t"Cl"\t"Fl"\t"Cl37"\t"Br"\t"Br81"\t"I"\t"M"\t"NH4"\t"POE"\t"NOE"\t"Z"\t"neutral_mass"\t"theor_mass"\t"err_ppm"\t"AE_ppm"\t"NM"\t"KM"\t"KMD"\t"DBE"\t"O_C"\t"H_C"\t"DBEO"\t"max_LA"\t"actual_LA"\t"rule_13"\t"max_H"\t"H_test"\t"C13_mass"\t"C13_abund"\t"C13_RT"\t"C13_mass2"\t"C13_abund2"\t"C13_RT2"\t"S34_mass"\t"S34_abund"\t"S34_RT"\t"tag"\n+113.059668300037\t34089624.9593056\t175.588810777774\t"C6H8O2"\t"O2"\t"CHO"\t6\t8\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t112.052391847877\t113.05970595196\t-0.336020698653698\t0.34\t113\t112.933424864385\t0.0665751356149684\t3\t0.333333333333333\t1.33333333333333\t1\t8.61941765383077\t8\t0.9\t14\t0.6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+113.059750299613\t109164662.210703\t129.616524856628\t"C6H8O2"\t"O2"\t"CHO"\t6\t8\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t112.052473847453\t113.05970595196\t0.395775760048756\t0.4\t113\t112.9335067724\t0.0664932276004322\t3\t0.333333333333333\t1.33333333333333\t1\t8.61941765383077\t8\t0.9\t14\t0.6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+115.038996485973\t95204343.6149802\t126.124561596817\t"C5H6O3"\t"O3"\t"CHO"\t5\t6\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t114.031720033813\t115.03897051046\t0.227791995104014\t0.23\t115\t114.910542914786\t0.0894570852138941\t3\t0.6\t1.2\t0\t8.77166877371538\t8\t0.9\t12\t0.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+115.054231533359\t97316198.4500411\t486.860812934674\t"C9H6"\t""\t"CH"\t9\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t114.046955081199\t115.05422664356\t0.0428753139246947\t0.04\t115\t114.925760950582\t0.0742390494179119\t7\t0\t0.666666666666667\t7\t8.77284232241538\t9\t1\t20\t0.3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+115.075265540226\t23920192.6144326\t167.40968733339\t"C6H10O2"\t"O2"\t"CHO"\t6\t10\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t114.067989088066\t115.07535601576\t-0.793171990951019\t0.79\t115\t114.946771470689\t0.0532285293108856\t2\t0.333333333333333\t1.66666666666667\t0\t8.77446765873846\t8\t0.9\t14\t0.7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+115.075431411708\t75254335.0387775\t255.255342064005\t"C6H10O2"\t"O2"\t"CHO"\t6\t10\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t114.068154959548\t115.07535601576\t0.660972801872154\t0.66\t115\t114.946937156958\t0.0530628430424684\t2\t0.333333333333333\t1.66666666666667\t0\t8.77446765873846\t8\t0.9\t14\t0.7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+117.054617173705\t106351841.6822\t604.088170928428\t"C5H8O3"\t"O3"\t"CHO"\t5\t8\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t116.047340721545\t117.05462057426\t-0.0293031702982305\t0.03\t117\t116.923912942451\t0.0760870575485342\t2\t0.6\t1.6\t-1\t8.92671877862308\t8\t0.9\t12\t0.7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+117.069572629504\t63116320.3841112\t386.001176\t"C9H8"\t""\t"CH"\t9\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t116.062296177344\t117.06987670736\t-2.61995381804255\t2.62\t117\t116.938851698855\t0.0611483011450815\t6\t0\t0.888888888888889\t6\t8.92789232732308\t9\t1\t20\t0.4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+117.069742846604\t59916324.7610906\t448.183657284805\t"C9H8"\t""\t"CH"\t9\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t116.062466394444\t117.06987670736\t-1.15335095102569\t1.15\t117\t116.939021725889\t0.0609782741110223\t6\t0\t0.888888888888889\t6\t8.92789232732308\t9\t1\t20\t0.4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+117.070083035453\t65132525.6124874\t525.247553400879\t"C9H8"\t""\t"CH"\t9\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t116.062806583293\t117.06987670736\t1.77772793088697\t1.78\t117\t116.93936153488\t0.0606384651199363\t6\t0\t0.888888888888889\t6\t8.92789232732308\t9\t1\t20\t0.4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+119.049041072813\t31036054.9520427\t745.850153780004\t"C8H6O"\t"O"\t"CHO"\t8\t6\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t118.041764620653\t119.04914126586\t-0.848793198965757\t0.85\t119\t118.916109850016\t0.0838901499836311\t6\t0.125\t0.75\t5\t9.08014344720769\t9\t1\t18\t0.3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+119.085478343665\t331652044.4\t445.799815387253\t"C9H10"\t""\t"CH"\t9\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t118.078201891505\t119.08552677116\t-0.410130694969878\t0.41\t119\t118.952506434686\t0.047493565313772\t5\t0\t1.11111111111111\t5\t9.08294233223077\t9\t1\t20\t0.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+205.049879260367\t25057828.0730095\t441.740553989'..b'1975\t7\t0.391304347826087\t1.47826086956522\t-2\t34.9400217450231\t32\t0.9\t48\t0.7\t456.230946479829\t45289911.11\t434.71332789406\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+471.257627890045\t108101264.075496\t651.72075223684\t"C24H38O9"\t"O9"\t"CHO"\t24\t38\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t470.250351437885\t471.25885926506\t-2.61855203556216\t2.62\t471\t470.731417412723\t0.268582587277081\t6\t0.375\t1.58333333333333\t-3\t36.1731986779154\t33\t0.9\t50\t0.8\t472.261372374224\t55444788.958204\t658.263083511565\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+489.268017849423\t349260974.056504\t637.129135429991\t"C24H40O10"\t"O10"\t"CHO"\t24\t40\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t488.260741397263\t489.26942395116\t-2.87981731428469\t2.88\t489\t488.721696809775\t0.278303190225074\t5\t0.416666666666667\t1.66666666666667\t-5\t37.5586267306923\t34\t0.9\t50\t0.8\t490.270150539605\t52923548.6756728\t619.483627940287\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+211.096070564606\t239294409.157566\t413.48871691023\t"C11H14O4"\t"O4"\t"CHO"\t11\t14\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t210.088794112446\t211.09648538796\t-1.9745144225551\t1.97\t211\t210.860358806369\t0.139641193631121\t5\t0.363636363636364\t1.27272727272727\t1\t16.1607083796769\t15\t0.9\t24\t0.6\t212.100156161221\t116039661.895991\t540.7818394\t213.102241927018\t51757808.2121238\t1169.09736296144\t0\t0\t0\t"Unambiguous"\n+269.137886563028\t1392655532.3658\t518.818451299712\t"C14H20O5"\t"O5"\t"CHO"\t14\t20\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t268.130610110868\t269.13835020166\t-1.72915219108549\t1.73\t269\t268.837364794526\t0.16263520547443\t5\t0.357142857142857\t1.42857142857143\t0\t20.6254672115\t19\t0.9\t30\t0.7\t270.141400334091\t70367267.6481761\t462.325416104228\t271.144546336217\t37715909.6382535\t448.881715830418\t0\t0\t0\t"Unambiguous"\n+269.1378886\t264040468.25271\t751.264342873686\t"C14H20O5"\t"O5"\t"CHO"\t14\t20\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t268.13061214784\t269.13835020166\t-1.72155523867608\t1.72\t269\t268.837366829223\t0.162633170776985\t5\t0.357142857142857\t1.42857142857143\t0\t20.6254672115\t19\t0.9\t30\t0.7\t270.141400334091\t70367267.6481761\t462.325416104228\t271.144546336217\t37715909.6382535\t448.881715830418\t0\t0\t0\t"Unambiguous"\n+387.179885767399\t4584519619.04008\t670.72696114176\t"C22H26O6"\t"O6"\t"CHO"\t22\t26\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t386.172609315239\t387.18021501536\t-0.85259273464097\t0.85\t387\t386.747557248047\t0.252442751953311\t10\t0.272727272727273\t1.18181818181818\t4\t29.7056106587077\t28\t0.9\t46\t0.6\t388.183711100624\t1057206254.9458\t670.779770938928\t389.186293912598\t101515761.666327\t669.1106436\t0\t0\t0\t"Unambiguous"\n+417.210994152317\t285886200.644374\t594.731729053663\t"C20H32O9"\t"O9"\t"CHO"\t20\t32\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t416.203717700157\t417.21190907366\t-2.19825365327157\t2.2\t417\t416.745132629057\t0.254867370943316\t5\t0.45\t1.6\t-4\t32.0157409708846\t29\t0.9\t42\t0.8\t418.214546045893\t167453243.614012\t624.5336148\t419.218266175515\t88561275.320055\t521.022328918228\t0\t0\t0\t"Unambiguous"\n+419.31504119354\t2207096818.21113\t990.344459003458\t"C26H42O4"\t"O4"\t"CHO"\t26\t42\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t418.30776474138\t419.31558628116\t-1.3030779390525\t1.3\t419\t418.846830272557\t0.153169727443242\t6\t0.153846153846154\t1.61538461538462\t2\t32.1775622945385\t30\t0.9\t54\t0.8\t420.318107423668\t392919110.295159\t1191.77766683947\t421.3212894\t58924659.4320049\t991.3030829\t0\t0\t0\t"Unambiguous"\n+419.315042002557\t873591445.130999\t1017.56678703395\t"C26H42O4"\t"O4"\t"CHO"\t26\t42\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t418.307765550397\t419.31558628116\t-1.30114391322741\t1.3\t419\t418.84683108067\t0.15316891932963\t6\t0.153846153846154\t1.61538461538462\t2\t32.1775622945385\t30\t0.9\t54\t0.8\t420.318107423668\t392919110.295159\t1191.77766683947\t421.3212894\t58924659.4320049\t991.3030829\t0\t0\t0\t"Unambiguous"\n+419.31504667458\t842931105.434556\t1319.73410588945\t"C26H42O4"\t"O4"\t"CHO"\t26\t42\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t418.30777022242\t419.31558628116\t-1.28997503370425\t1.29\t419\t418.846835747477\t0.153164252523425\t6\t0.153846153846154\t1.61538461538462\t2\t32.1775622945385\t30\t0.9\t54\t0.8\t420.318107423668\t392919110.295159\t1191.77766683947\t421.3212894\t58924659.4320049\t991.3030829\t0\t0\t0\t"Unambiguous"\n' |
| b |
| diff -r 000000000000 -r a26b860d6ce7 test-data/mfassigncho/unambig.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mfassigncho/unambig.tabular Fri Sep 13 10:08:49 2024 +0000 |
| b |
| b'@@ -0,0 +1,1331 @@\n+"abundance"\t"exp_mass"\t"RT"\t"formula"\t"class"\t"group"\t"C"\t"H"\t"O"\t"N"\t"S"\t"P"\t"E"\t"S34"\t"N15"\t"D"\t"Cl"\t"Fl"\t"Cl37"\t"Br"\t"Br81"\t"I"\t"M"\t"NH4"\t"POE"\t"NOE"\t"Z"\t"neutral_mass"\t"theor_mass"\t"err_ppm"\t"AE_ppm"\t"NM"\t"KM"\t"KMD"\t"DBE"\t"O_C"\t"H_C"\t"DBEO"\t"max_LA"\t"actual_LA"\t"rule_13"\t"max_H"\t"H_test"\t"C13_mass"\t"C13_abund"\t"C13_RT"\t"C13_mass2"\t"C13_abund2"\t"C13_RT2"\t"S34_mass"\t"S34_abund"\t"S34_RT"\t"tag"\n+21010220.7087587\t111.043788975043\t170.235668271814\t"C6H6O2"\t"O2"\t"CHO"\t6\t6\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t110.036512522883\t111.04405588816\t-2.42567772171828\t2.43\t111\t110.919796488254\t0.0802035117456654\t4\t0.333333333333333\t1\t2\t8.46436764892308\t8\t0.9\t14\t0.4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+34089624.9593056\t113.059668300037\t175.588810777774\t"C6H8O2"\t"O2"\t"CHO"\t6\t8\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t112.052391847877\t113.05970595196\t-0.336020698653698\t0.34\t113\t112.933424864385\t0.0665751356149684\t3\t0.333333333333333\t1.33333333333333\t1\t8.61941765383077\t8\t0.9\t14\t0.6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+109164662.210703\t113.059750299613\t129.616524856628\t"C6H8O2"\t"O2"\t"CHO"\t6\t8\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t112.052473847453\t113.05970595196\t0.395775760048756\t0.4\t113\t112.9335067724\t0.0664932276004322\t3\t0.333333333333333\t1.33333333333333\t1\t8.61941765383077\t8\t0.9\t14\t0.6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+95204343.6149802\t115.038996485973\t126.124561596817\t"C5H6O3"\t"O3"\t"CHO"\t5\t6\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t114.031720033813\t115.03897051046\t0.227791995104014\t0.23\t115\t114.910542914786\t0.0894570852138941\t3\t0.6\t1.2\t0\t8.77166877371538\t8\t0.9\t12\t0.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+97316198.4500411\t115.054231533359\t486.860812934674\t"C9H6"\t""\t"CH"\t9\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t114.046955081199\t115.05422664356\t0.0428753139246947\t0.04\t115\t114.925760950582\t0.0742390494179119\t7\t0\t0.666666666666667\t7\t8.77284232241538\t9\t1\t20\t0.3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+23920192.6144326\t115.075265540226\t167.40968733339\t"C6H10O2"\t"O2"\t"CHO"\t6\t10\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t114.067989088066\t115.07535601576\t-0.793171990951019\t0.79\t115\t114.946771470689\t0.0532285293108856\t2\t0.333333333333333\t1.66666666666667\t0\t8.77446765873846\t8\t0.9\t14\t0.7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+75254335.0387775\t115.075431411708\t255.255342064005\t"C6H10O2"\t"O2"\t"CHO"\t6\t10\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t114.068154959548\t115.07535601576\t0.660972801872154\t0.66\t115\t114.946937156958\t0.0530628430424684\t2\t0.333333333333333\t1.66666666666667\t0\t8.77446765873846\t8\t0.9\t14\t0.7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+106351841.6822\t117.054617173705\t604.088170928428\t"C5H8O3"\t"O3"\t"CHO"\t5\t8\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t116.047340721545\t117.05462057426\t-0.0293031702982305\t0.03\t117\t116.923912942451\t0.0760870575485342\t2\t0.6\t1.6\t-1\t8.92671877862308\t8\t0.9\t12\t0.7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+63116320.3841112\t117.069572629504\t386.001176\t"C9H8"\t""\t"CH"\t9\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t116.062296177344\t117.06987670736\t-2.61995381804255\t2.62\t117\t116.938851698855\t0.0611483011450815\t6\t0\t0.888888888888889\t6\t8.92789232732308\t9\t1\t20\t0.4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+59916324.7610906\t117.069742846604\t448.183657284805\t"C9H8"\t""\t"CH"\t9\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t116.062466394444\t117.06987670736\t-1.15335095102569\t1.15\t117\t116.939021725889\t0.0609782741110223\t6\t0\t0.888888888888889\t6\t8.92789232732308\t9\t1\t20\t0.4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+65132525.6124874\t117.070083035453\t525.247553400879\t"C9H8"\t""\t"CH"\t9\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t116.062806583293\t117.06987670736\t1.77772793088697\t1.78\t117\t116.93936153488\t0.0606384651199363\t6\t0\t0.888888888888889\t6\t8.92789232732308\t9\t1\t20\t0.4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+31036054.9520427\t119.049041072813\t745.850153780004\t"C8H6O"\t"O"\t"CHO"\t8\t6\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t118.041764620653\t119.04914126586\t-0.848793198965757\t0.85\t119\t118.916109850016\t0.0838901499836311\t6\t0.125\t0.75\t5\t9.08014344720769\t9\t1\t18\t0.3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+331652044.4\t119.085478343665\t445.799'..b'37885\t471.25885926506\t-2.61855203556216\t2.62\t471\t470.731417412723\t0.268582587277081\t6\t0.375\t1.58333333333333\t-3\t36.1731986779154\t33\t0.9\t50\t0.8\t472.261372374224\t55444788.958204\t658.263083511565\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+123319726.022436\t433.258596293594\t737.378214575481\t"C25H36O6"\t"O6"\t"CHO"\t25\t36\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t432.251319841434\t433.25846533436\t0.302970119470214\t0.3\t433\t432.77481587442\t0.225184125579915\t8\t0.24\t1.44\t2\t33.2500914524769\t31\t0.9\t52\t0.7\t434.261129443117\t64919075.9423223\t737.4600869\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+27737975.3080147\t471.257622276222\t305.970043386351\t"C24H38O9"\t"O9"\t"CHO"\t24\t38\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t470.250345824062\t471.25885926506\t-2.63049001236666\t2.63\t471\t470.731411805168\t0.268588194831693\t6\t0.375\t1.58333333333333\t-3\t36.1731986779154\t33\t0.9\t50\t0.8\t472.261372374224\t55444788.958204\t658.263083511565\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+143763866.17314\t461.077505221709\t217.820933392077\t"C14H20O17"\t"O17"\t"CHO"\t14\t20\t17\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t460.070228769549\t461.07732566926\t0.390271827519897\t0.39\t461\t460.562661960303\t0.43733803969667\t5\t1.21428571428571\t1.42857142857143\t-12\t35.3900037859308\t31\t0.9\t30\t0.7\t462.080871632118\t21662796.869184\t218.428160542263\t0\t0\t0\t0\t0\t0\t"Unambiguous"\n+1392655532.3658\t269.137886563028\t518.818451299712\t"C14H20O5"\t"O5"\t"CHO"\t14\t20\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t268.130610110868\t269.13835020166\t-1.72915219108549\t1.73\t269\t268.837364794526\t0.16263520547443\t5\t0.357142857142857\t1.42857142857143\t0\t20.6254672115\t19\t0.9\t30\t0.7\t270.141400334091\t70367267.6481761\t462.325416104228\t271.144546336217\t37715909.6382535\t448.881715830418\t0\t0\t0\t"Unambiguous"\n+264040468.25271\t269.1378886\t751.264342873686\t"C14H20O5"\t"O5"\t"CHO"\t14\t20\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t268.13061214784\t269.13835020166\t-1.72155523867608\t1.72\t269\t268.837366829223\t0.162633170776985\t5\t0.357142857142857\t1.42857142857143\t0\t20.6254672115\t19\t0.9\t30\t0.7\t270.141400334091\t70367267.6481761\t462.325416104228\t271.144546336217\t37715909.6382535\t448.881715830418\t0\t0\t0\t"Unambiguous"\n+4584519619.04008\t387.179885767399\t670.72696114176\t"C22H26O6"\t"O6"\t"CHO"\t22\t26\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t386.172609315239\t387.18021501536\t-0.85259273464097\t0.85\t387\t386.747557248047\t0.252442751953311\t10\t0.272727272727273\t1.18181818181818\t4\t29.7056106587077\t28\t0.9\t46\t0.6\t388.183711100624\t1057206254.9458\t670.779770938928\t389.186293912598\t101515761.666327\t669.1106436\t0\t0\t0\t"Unambiguous"\n+285886200.644374\t417.210994152317\t594.731729053663\t"C20H32O9"\t"O9"\t"CHO"\t20\t32\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t416.203717700157\t417.21190907366\t-2.19825365327157\t2.2\t417\t416.745132629057\t0.254867370943316\t5\t0.45\t1.6\t-4\t32.0157409708846\t29\t0.9\t42\t0.8\t418.214546045893\t167453243.614012\t624.5336148\t419.218266175515\t88561275.320055\t521.022328918228\t0\t0\t0\t"Unambiguous"\n+873591445.130999\t419.315042002557\t1017.56678703395\t"C26H42O4"\t"O4"\t"CHO"\t26\t42\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t418.307765550397\t419.31558628116\t-1.30114391322741\t1.3\t419\t418.84683108067\t0.15316891932963\t6\t0.153846153846154\t1.61538461538462\t2\t32.1775622945385\t30\t0.9\t54\t0.8\t420.318107423668\t392919110.295159\t1191.77766683947\t421.3212894\t58924659.4320049\t991.3030829\t0\t0\t0\t"Unambiguous"\n+2207096818.21113\t419.31504119354\t990.344459003458\t"C26H42O4"\t"O4"\t"CHO"\t26\t42\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t418.30776474138\t419.31558628116\t-1.3030779390525\t1.3\t419\t418.846830272557\t0.153169727443242\t6\t0.153846153846154\t1.61538461538462\t2\t32.1775622945385\t30\t0.9\t54\t0.8\t420.318107423668\t392919110.295159\t1191.77766683947\t421.3212894\t58924659.4320049\t991.3030829\t0\t0\t0\t"Unambiguous"\n+842931105.434556\t419.31504667458\t1319.73410588945\t"C26H42O4"\t"O4"\t"CHO"\t26\t42\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t418.30777022242\t419.31558628116\t-1.28997503370425\t1.29\t419\t418.846835747477\t0.153164252523425\t6\t0.153846153846154\t1.61538461538462\t2\t32.1775622945385\t30\t0.9\t54\t0.8\t420.318107423668\t392919110.295159\t1191.77766683947\t421.3212894\t58924659.4320049\t991.3030829\t0\t0\t0\t"Unambiguous"\n' |
| b |
| diff -r 000000000000 -r a26b860d6ce7 test-data/recal/recalibrants.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/recal/recalibrants.tabular Fri Sep 13 10:08:49 2024 +0000 |
| b |
| b'@@ -0,0 +1,677 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\t279.12270013786\t0.732437693741977\t0.939357873357113\n+279.23135454172\t"C18H30O2"\t279.23185665376\t0.126396254553331\t1.79819038567926\n+279.231355640483\t"C18H30O2"\t279.23185665376\t0.122461299271082\t1.79425543711485\n+281.13761021831\t"C15H20O5"\t281.13835020166\t0.960304056142152\t2.63209679316573\n+281.137610738539\t"C15H20O5"\t281.13835020166\t0.958453615084006\t2.63024635534263\n+281.138243293062\t"C15H20O5"\t281.13835020166\t1.29152608336664\t0.380270418236245\n+281.174303000536\t"C16H24O4"\t281.17473570696\t0.132871009079202\t1.53892355560869\n+283.190032092455\t"C16H26O4"\t283.19038577076\t0.422888579725451\t1.24890646980384\n+283.190033711306\t"C16H26O4"\t283.19038577076\t0.428605065011239\t1.24318999395213\n+283.190034825775\t"C16H26O4"\t283.19038577076\t0.432540477131393\t1.2392545884559\n+283.262312527003\t"C18H34O2"\t283.26315678136\t1.3086673113547\t2.98045946597623\n+287.200184358761\t"C19H26O2"\t287.20055652616\t0.375949992525095\t1.2958449785359\n+289.179529598855\t"C18H24O3"\t289.17982108466\t0.663821231031105\t1.0079742212214\n+291.231420762583\t"C19H30O2"\t291.23185665376\t0.175079330688238\t1.4967153044789\n+266.14610143058\t"C15H20O4"\t266.14679057936\t0.917563157300656\t2.58935596592176\n+266.14610143058\t"C15H20O4"\t266.14679057936\t0.917563157300656\t2.58935596592176\n+266.182811998121\t"C16H24O3"\t266.18317608466\t0.303990377331071\t1.36780447335256\n+266.182811998121\t"C16H24O3"\t266.18317608466\t0.303990377331071\t1.36780447335256\n+278.21853290475\t"C18H28O2"\t278.21956158996\t2.02559539609604\t3.69738635232981\n+284.194143062649\t"C16H26O4"\t284.19374077076\t3.08735456836633\t1.41555506444424\n+284.194143062649\t"C16H26O4"\t284.19374077076\t3.08735456836633\t1.41555506444424\n+284.194143062649\t"C16H26O4"\t284.19374077076\t3.08735456836633\t1.41555506444424\n+299.236443896427\t"C21H30O"\t299.23694203146\t0.651756068302325\t1.66468427872214\n+303.194973778509\t"C19H26O3"\t303.19547114846\t0.62749848102663\t1.64042671588087\n+303.194974339572\t"C19H26O3"\t303.19547114846\t0.625647979815064\t1.63857621654412\n+303.194974912944\t"C19H26O3"\t303.19547114846\t0.623756880884793\t1.63668511967614\n+303.194976080426\t"C19H26O3"\t303.19547114846\t0.619906285233851\t1.6328345279623\n+307.189946735382\t"C18H26O4"\t307.19038577076\t0.416267900630724\t1.42919634952033\n+307.189947923199\t"C18H26O4"\t307.19038577076\t0.41240118405448\t1.42532963682999\n+307.18994792349\t"C18H26O4"\t307.19038577076\t0.412400236634515\t1.42532868941003\n+319.189936569937\t"C19H26O4"\t319.19038577076\t0.394384665565221\t1.40731313659619\n+321.205872158847\t"C19H28O4"\t321.20603583456\t0.503363261639355\t0.509566118743638\n+321.205872765715\t"C19H28O4"\t321.20603583456\t0.505252605459811\t0.507676776869838\n+323.184827444901\t"C18H26O5"\t323.18530039306\t0.450467843125308\t1.4633962573597\n+323.184828083672\t"C18H26O5"\t323.18530039306\t0.448491355572382\t1.46141977191739\n+300.2405905\t"C21H30O"\t300.24029703146\t1.99037642915533\t0.977445542485022\n+308.1930418\t"C18H26O4"\t308.19374077076\t1.25503137428853\t2.26795897354048\n+308.1930418\t"C18H26O4"\t308.19374077076\t1.25503137428853\t2.26795897354048\n+308.1930418\t"C18H26O4"\t308.19374077076\t1.25503137428853\t2.26795897354048\n+320.193218960245\t"C19H26O4"\t320.19374077076\t0.616742945498346\t1.62967119125355\n+324.188220066161\t"C18H26O5"\t324.18865539306\t0.329891120366754\t1.34281965682138\n+324.188220066161\t"C18H26O5"\t324.18865539306\t0.329891120366754\t1.34281965682138\n' |
| b |
| diff -r 000000000000 -r a26b860d6ce7 test-data/recallist/recal_series.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/recallist/recal_series.tabular Fri Sep 13 10:08:49 2024 +0000 |
| b |
| b'@@ -0,0 +1,82 @@\n+"Series"\t"Number.Observed"\t"Series.Index"\t"Mass.Range"\t"Tall.Peak"\t"Abundance.Score"\t"Peak.Score"\t"Peak.Distance"\t"Series.Score"\n+"_H_4"\t8\t54\t"121.101-177.164"\t121.101133005817\t-40.744548219864\t0.513008460106113\t2.0022239614575\t0.6255625\n+"_H_5"\t7\t60\t"119.085-203.179"\t119.085478343665\t0\t0.00189700255432302\t2.002230609633\t1.00095918367347\n+"_H_6"\t9\t49\t"117.07-173.133"\t145.101380561463\t-56.0021549559649\t0.13569292865165\t2.00220483719043\t0.556055555555556\n+"O_H_3"\t12\t37\t"125.096-265.253"\t153.127570993099\t-31.622351105407\t0.0015695541785917\t4.0916000492481e-08\t0.91760119047619\n+"O_H_4"\t24\t18\t"123.08-235.205"\t151.111735640747\t-28.2884966922516\t0.623476031387814\t1.00110604074271\t0.375372023809524\n+"O_H_5"\t18\t27\t"121.064-233.19"\t149.096105311228\t21.4305154780686\t0.352916430267584\t2.00223805817479\t0.5005\n+"O_H_6"\t17\t28\t"119.049-273.221"\t175.111612481644\t-9.97452232152313\t0.0274294484213061\t1.00111137429357\t0.706605042016807\n+"O_H_7"\t12\t39\t"131.049-299.236"\t131.049175570564\t172.333212266955\t0.840925082711506\t1.00111591861886\t1.08444642857143\n+"O2_H_6"\t26\t15\t"121.028-275.2"\t135.044203360548\t132.070890535917\t0.00790053195276584\t1.00111745248393\t0.462010989010989\n+"O2_H_7"\t14\t32\t"147.044-287.2"\t189.091144991185\t8.83386407948655\t0.147303531551518\t2.00219708641086\t0.786510204081633\n+"O2_H_3"\t23\t19\t"113.06-253.216"\t169.122270213149\t4.76056043166079\t0.0701292750649239\t8.28695842106494e-12\t0.478745341614907\n+"O2_H_4"\t33\t6\t"111.044-279.231"\t167.106692449667\t82.4236049322032\t0.286865201338275\t4.00445257623936\t0.394344155844156\n+"O3_H_2"\t19\t24\t"117.055-299.257"\t145.085900628212\t6.27902654417553\t0.802218975083\t3.00336379805057\t0.737601503759398\n+"O3_H_3"\t31\t8\t"115.039-297.242"\t185.117196150203\t47.4227725825158\t0.778828196734631\t1.00111893363993\t0.45208064516129\n+"O3_H_7"\t33\t7\t"149.023-415.32"\t177.05459583337\t-10.9317163240029\t0.195437412108535\t4.0044736834895\t0.606703463203463\n+"O4_H_1"\t8\t53\t"177.112-359.316"\t177.112147092172\t-26.2941074418532\t0.151915356730647\t2.00222462284679\t1.75182142857143\n+"O2_H_2"\t27\t13\t"115.075-283.262"\t171.137877553161\t-69.1344724131683\t0.207568470854973\t1.00110628326907\t0.481976190476191\n+"O3_H_12"\t14\t34\t"251.07-279.102"\t279.101165261479\t65.2340182235317\t0.149300279614808\t0\t0.214448979591837\n+"O2_H_8"\t5\t74\t"187.076-355.262"\t229.122456513599\t-51.6968737595267\t0.273206935258389\t5.00556212952736\t2.60265714285714\n+"O3_H_5"\t36\t4\t"125.023-419.351"\t237.148279500834\t43.9267963624442\t0.0746045081170269\t4.00447726198\t0.611761904761905\n+"O2_H_11"\t5\t78\t"209.06-391.263"\t223.074691790747\t132.732152227999\t0.540579659159889\t1.00107229090536\t2.8029\n+"O_H_8"\t5\t73\t"171.081-269.19"\t269.190034324818\t-84.1542998489119\t0.062211091207672\t4.23693827867412e-05\t1.60155714285714\n+"O3_H_4"\t36\t3\t"127.039-323.257"\t239.16391307677\t37.1217086846939\t0.117558310016219\t4.00445515003443\t0.417099206349206\n+"O4_H_3"\t30\t10\t"145.049-341.268"\t229.143400253236\t23.742221018427\t0.0948022540425468\t2.00221116860679\t0.500521428571428\n+"O2_H_5"\t37\t2\t"123.044-431.389"\t221.153498294039\t30.1182563966444\t0.265731820127386\t2.00224719208636\t0.622287644787645\n+"O4_H_5"\t30\t11\t"141.018-337.236"\t253.143063541297\t45.0295848929684\t0.329810765327225\t2.00223138994564\t0.500519047619048\n+"O4_H_2"\t21\t21\t"161.081-371.315"\t203.127702568166\t14.8126016290571\t0.216169485485103\t1.00111575924557\t0.762700680272109\n+"O4_H_7"\t25\t17\t"193.049-431.317"\t277.143094912085\t-39.7124352799229\t0.0207206865928199\t6.00667325540743\t0.720765714285714\n+"O4_H_4"\t34\t5\t"143.034-339.252"\t227.127382267807\t51.3580490610349\t0.116192915928226\t2.00222457351421\t0.441634453781513\n+"O3_H_6"\t27\t14\t"151.039-319.227"\t221.116873599366\t8.32628083030641\t0.0284160198840399\t5.00556424587978\t0.481978835978836\n+"O5_H_6"\t28\t12\t"211.06-407.278"\t267.122418171045\t-8.32628083030643\t0.079441195728107\t3.82635832149195e-05\t0.536270408163265\n+"O5_H_3"\t22\t20\t"189.076-357.264"\t245.138110912711\t20.2587245791274\t0.00524719019601846\t2.00224152631921\t0.591519480519481\n+"O5_H_8"\t14\t33\t"221.044-361.2"\t249.075478055657\t-52.2755612'..b'45\t0.16259969783224\t4.00439854372114\t1.16777380952381\n+"O10_H_2"\t4\t79\t"285.082-425.238"\t355.160039122111\t-62.6454758053799\t0.150072989997034\t5.00556513080393\t2.75278571428571\n+"O7_H_6"\t8\t55\t"299.113-495.33"\t313.128264107885\t2.22863472776223\t0.124302182854094\t13.0144285819602\t1.8769375\n+"O6_H_2"\t12\t36\t"249.134-375.274"\t347.242588877017\t-31.515656260483\t0.0710777260539349\t6.00671922576264\t0.834166666666667\n+"O8_H_1"\t5\t69\t"213.061-311.169"\t311.16936123622\t27.8251864824375\t0.198145538844287\t1.00111011193714\t1.60154285714286\n+"O6_H_7"\t9\t50\t"253.071-407.242"\t351.1796217\t11.6976374801684\t0.213201464774084\t2.00233308426821\t1.33469047619048\n+"O6_H_4"\t21\t22\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