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--- a/testdata/recetox-xMSannotator/batch1_neg/NumberOfCorrelationsPerFeature_cor0.7.csv
+++ b/testdata/recetox-xMSannotator/batch1_neg/NumberOfCorrelationsPerFeature_cor0.7.csv
--- a/testdata/recetox-xMSannotator/batch1_neg/Readme.txt
+++ b/testdata/recetox-xMSannotator/batch1_neg/Readme.txt
+[1] "Output files description:"
+[1] "Stage1.csv includes clustering of features based on intensity and retention time without annotations"
+[1] "DBresults/Stage2.csv includes clustering results along with simple m/z based database matching"
+[1] "DBresults/Stage3.csv includes scores for annotations assigned in stage 2 based on multiple criteria"
+[1] "DBresults/Stage4.csv and DBresults/Stage5.csv include the confidence levels before and after redundancy (multiple matches) filtering, respectively"
--- a/testdata/recetox-xMSannotator/batch1_neg/Stage1.csv
+++ b/testdata/recetox-xMSannotator/batch1_neg/Stage1.csv
--- a/testdata/recetox-xMSannotator/batch1_neg/Stage2.csv
+++ b/testdata/recetox-xMSannotator/batch1_neg/Stage2.csv
--- a/testdata/recetox-xMSannotator/batch1_neg/Stage2_withisotopes.txt
+++ b/testdata/recetox-xMSannotator/batch1_neg/Stage2_withisotopes.txt
--- a/testdata/recetox-xMSannotator/batch1_neg/Stage3.csv
+++ b/testdata/recetox-xMSannotator/batch1_neg/Stage3.csv
--- a/testdata/recetox-xMSannotator/batch1_neg/Stage4.csv
+++ b/testdata/recetox-xMSannotator/batch1_neg/Stage4.csv
--- a/testdata/recetox-xMSannotator/batch1_neg/Stage5.csv
+++ b/testdata/recetox-xMSannotator/batch1_neg/Stage5.csv
--- a/testdata/recetox-xMSannotator/batch1_neg/chemCompMZ.Rda
+++ b/testdata/recetox-xMSannotator/batch1_neg/chemCompMZ.Rda
--- a/testdata/recetox-xMSannotator/batch1_neg/chemscoremat.Rds
+++ b/testdata/recetox-xMSannotator/batch1_neg/chemscoremat.Rds
--- a/testdata/recetox-xMSannotator/batch1_neg/global_cor.Rda
+++ b/testdata/recetox-xMSannotator/batch1_neg/global_cor.Rda
--- a/testdata/recetox-xMSannotator/batch1_neg/global_cor_integ.Rda
+++ b/testdata/recetox-xMSannotator/batch1_neg/global_cor_integ.Rda
--- a/testdata/recetox-xMSannotator/batch1_neg/step1_results.Rda
+++ b/testdata/recetox-xMSannotator/batch1_neg/step1_results.Rda
--- a/testdata/recetox-xMSannotator/batch1_neg/tempobjects.Rda
+++ b/testdata/recetox-xMSannotator/batch1_neg/tempobjects.Rda
--- a/testdata/recetox-xMSannotator/compounds.rds
+++ b/testdata/recetox-xMSannotator/compounds.rds
--- a/testdata/recetox-xMSannotator/qc_matrix/NumberOfCorrelationsPerFeature_cor0.7.csv
+++ b/testdata/recetox-xMSannotator/qc_matrix/NumberOfCorrelationsPerFeature_cor0.7.csv
--- a/testdata/recetox-xMSannotator/qc_matrix/Readme.txt
+++ b/testdata/recetox-xMSannotator/qc_matrix/Readme.txt
+[1] "Output files description:"
+[1] "Stage1.csv includes clustering of features based on intensity and retention time without annotations"
+[1] "DBresults/Stage2.csv includes clustering results along with simple m/z based database matching"
+[1] "DBresults/Stage3.csv includes scores for annotations assigned in stage 2 based on multiple criteria"
+[1] "DBresults/Stage4.csv and DBresults/Stage5.csv include the confidence levels before and after redundancy (multiple matches) filtering, respectively"
--- a/testdata/recetox-xMSannotator/qc_matrix/Stage1.csv
+++ b/testdata/recetox-xMSannotator/qc_matrix/Stage1.csv
--- a/testdata/recetox-xMSannotator/qc_matrix/Stage2.csv
+++ b/testdata/recetox-xMSannotator/qc_matrix/Stage2.csv
--- a/testdata/recetox-xMSannotator/qc_matrix/Stage2_withisotopes.txt
+++ b/testdata/recetox-xMSannotator/qc_matrix/Stage2_withisotopes.txt
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