Repository 'mspurity_averagefragspectra'
hg clone https://toolshed.g2.bx.psu.edu/repos/computational-metabolomics/mspurity_averagefragspectra

Changeset 2:96fba93b4c8a (2020-04-01)
Previous changeset 1:4207233ead9c (2019-12-05) Next changeset 3:ccda730c6cf7 (2020-04-09)
Commit message:
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8"
modified:
combineAnnotations.R
createDatabase.R
macros.xml
test-data/averageFragSpectra_output_all.RData
test-data/averageFragSpectra_output_all_only.RData
test-data/averageFragSpectra_output_inter.RData
test-data/averageFragSpectra_output_intra.RData
test-data/combineAnnotations_combined_annotations.sqlite
test-data/combineAnnotations_combined_annotations.tsv
test-data/createDatabase_output.sqlite
test-data/createDatabase_output_eic.sqlite
test-data/createMSP_output_av_all_metadata.msp
test-data/filterFragSpectra_output.RData
test-data/flagRemove_output.tsv
test-data/frag4feature_output.RData
test-data/purityA_output.RData
test-data/spectralMatching_db_with_spectral_matching.sqlite
test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite
b
diff -r 4207233ead9c -r 96fba93b4c8a combineAnnotations.R
--- a/combineAnnotations.R Thu Dec 05 07:37:41 2019 -0500
+++ b/combineAnnotations.R Wed Apr 01 11:05:00 2020 -0400
b
@@ -20,7 +20,9 @@
   make_option("--probmetab_weight", type="numeric"),
   make_option("--ms1_lookup_weight", type="numeric"),
   make_option("--biosim_weight", type="numeric"),
-
+  
+  make_option("--summaryOutput", action="store_true"),
+  
   make_option("--create_new_database", action="store_true"),
   make_option("--outdir", type="character", default="."),
 
@@ -56,11 +58,21 @@
                'biosim'=opt$biosim_weight
                )
 print(weights)
-if (round(!sum(unlist(weights),0)==1)){
+
+if (is.null(opt$probmetab_resultPth)){
+  opt$probmetab_resultPth = NA
+}
 
+if (round(!sum(unlist(weights),0)==1)){
   stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
 }
 
+if (is.null(opt$summaryOutput)){
+  summaryOutput = FALSE
+}else{
+ summaryOutput = TRUE
+}
+
 if (opt$compoundDbType=='local_config'){
   # load in compound config
   # Soure local function taken from workflow4metabolomics
@@ -76,8 +88,6 @@
   compoundDbPass = NA
 }
 
-
-
 summary_output <- msPurity::combineAnnotations(
                             sm_resultPth = sm_resultPth,
                             compoundDbPth = compoundDbPth,
@@ -94,7 +104,12 @@
                             compoundDbPort = compoundDbPort,
                             compoundDbUser = compoundDbUser,
                             compoundDbPass = compoundDbPass,
-                            weights = weights)
+                            weights = weights,
+                            summaryOutput = summaryOutput)
+if (summaryOutput){
+  write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
+}
+
 
 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
 
b
diff -r 4207233ead9c -r 96fba93b4c8a createDatabase.R
--- a/createDatabase.R Thu Dec 05 07:37:41 2019 -0500
+++ b/createDatabase.R Wed Apr 01 11:05:00 2020 -0400
b
@@ -115,10 +115,10 @@
 
 
 
-if(is.null(opt$grp_peaklist)){
+if(is.null(opt$grpPeaklist)){
   grpPeaklist = NA
 }else{
-  grpPeaklist = opt$grp_peaklist
+  grpPeaklist = opt$grpPeaklist
 }
 
 
b
diff -r 4207233ead9c -r 96fba93b4c8a macros.xml
--- a/macros.xml Thu Dec 05 07:37:41 2019 -0500
+++ b/macros.xml Wed Apr 01 11:05:00 2020 -0400
b
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.12.0</token>
-    <token name="@GALAXY_TOOL_VERSION@">1</token>
+    <token name="@TOOL_VERSION@">1.12.2</token>
+    <token name="@GALAXY_TOOL_VERSION@">0</token>
 
     <xml name="requirements">
         <requirements>
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/averageFragSpectra_output_all.RData
b
Binary file test-data/averageFragSpectra_output_all.RData has changed
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/averageFragSpectra_output_all_only.RData
b
Binary file test-data/averageFragSpectra_output_all_only.RData has changed
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/averageFragSpectra_output_inter.RData
b
Binary file test-data/averageFragSpectra_output_inter.RData has changed
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/averageFragSpectra_output_intra.RData
b
Binary file test-data/averageFragSpectra_output_intra.RData has changed
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/combineAnnotations_combined_annotations.sqlite
b
Binary file test-data/combineAnnotations_combined_annotations.sqlite has changed
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/combineAnnotations_combined_annotations.tsv
--- a/test-data/combineAnnotations_combined_annotations.tsv Thu Dec 05 07:37:41 2019 -0500
+++ b/test-data/combineAnnotations_combined_annotations.tsv Wed Apr 01 11:05:00 2020 -0400
[
b'@@ -1,107 +1,102 @@\n-"grpid"\t"grp_name"\t"mz"\t"rt"\t"inchikey"\t"inchi"\t"inchikey..7"\t"inchikey1"\t"inchikey2"\t"inchikey3"\t"name"\t"exact_mass"\t"molecular_formula"\t"pubchem_cids"\t"kegg_cids"\t"kegg_brite"\t"kegg_drugs"\t"hmdb_ids"\t"hmdb_bio_custom_flag"\t"hmdb_drug_flag"\t"biosim_max_count"\t"biosim_hmdb_ids"\t"fragmentation_acquistion_num"\t"mean_precursor_ion_purity"\t"accession"\t"sirius_score"\t"sirius_wscore"\t"metfrag_score"\t"metfrag_wscore"\t"sm_score"\t"sm_wscore"\t"probmetab_score"\t"probmetab_wscore"\t"ms1_lookup_score"\t"ms1_lookup_wscore"\t"biosim_max_score"\t"biosim_wscore"\t"wscore"\t"rank"\t"adduct_overall"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-UHFFFAOYSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)"\t"ONIBWKKTOPOVIA-UHFFFAOYSA-N"\t"ONIBWKKTOPOVIA"\t"UHFFFAOYSA"\t"N"\t"DL-Proline"\t115.063328534\t"C5H9NO2"\t"614,25246272"\t"C16435"\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\t"CCMSLIB00000577898"\t"1.0"\t0.2\t0.9\t0.18\t0.87867085623127\t0.263601256869381\t"0"\t0\t0\t0\t1\t0.25\t0.893601256869381\t1\t"[M+H]+,M+H"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-AZXPZELESA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i4+1"\t"ONIBWKKTOPOVIA-AZXPZELESA-N"\t"ONIBWKKTOPOVIA"\t"AZXPZELESA"\t"N"\t""\t116.066683369\t"C5H9NO2"\t"10290769"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-BYPYZUCNSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1"\t"ONIBWKKTOPOVIA-BYPYZUCNSA-N"\t"ONIBWKKTOPOVIA"\t"BYPYZUCNSA"\t"N"\t"L-Pro"\t115.063328534\t"C5H9NO2"\t"145742,6971047"\t"C00148"\t"Compounds with biological roles [BR:br08001]"\t"D00035"\t"HMDB0000162"\t"True"\t"False"\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-GIZBTRSZSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i1+2,2+2,3+2,4+2,5+2"\t"ONIBWKKTOPOVIA-GIZBTRSZSA-N"\t"ONIBWKKTOPOVIA"\t"GIZBTRSZSA"\t"N"\t"L-PROLINE, [U-14C]"\t125.0795385\t"C5H9NO2"\t"12210869"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-GTTLGWSSSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i1+1D,4+1,6+1/t1?,4-"\t"ONIBWKKTOPOVIA-GTTLGWSSSA-N"\t"ONIBWKKTOPOVIA"\t"GTTLGWSSSA"\t"N"\t"SCHEMBL16945363"\t119.07334984\t"C5H9NO2"\t"118264374"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-HOSYLAQJSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i5+1"\t"ONIBWKKTOPOVIA-HOSYLAQJSA-N"\t"ONIBWKKTOPOVIA"\t"HOSYLAQJSA"\t"N"\t"DL-Proline-1-13C"\t116.066683369\t"C5H9NO2"\t"59340910"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-IDEBNGHGSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i1+1,2+1,3+1,4+1,5+1,6+1"\t"ONIBWKKTOPOVIA-IDEBNGHGSA-N"\t"ONIBWKKTOPOVIA"\t"IDEBNGHGSA"\t"N"\t"SCHEMBL18875607"\t121.0771376\t"C5H9NO2"\t"129148531"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-IXBOUXNVSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i4+1"\t"ONIBWKKTOPOVIA-IXBOUXNVSA-N"\t"ONIBWKKTOPOVIA"\t"IXBOUXNVSA"\t"N"\t""\t116.066683369\t"C5H9NO2"\t"100915807"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-JGTYJTGKSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i6+1"\t"ONIBWKKTOPOVIA-JGTYJTGKSA-N"\t"ONIBWKKTOPOVIA"\t"JGTYJTGKSA"\t"N"\t"L-Proline-15N"\t116.'..b'/i3D2,4D2"\t"RWRDLPDLKQPQOW-KHORGVISSA-N"\t"RWRDLPDLKQPQOW"\t"KHORGVISSA"\t"N"\t"ACM42403258"\t75.098606278\t"C4H9N"\t"12196049"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8696\t0.2174\t0.2174\t14\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-MNYXATJNSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i/hT"\t"RWRDLPDLKQPQOW-MNYXATJNSA-N"\t"RWRDLPDLKQPQOW"\t"MNYXATJNSA"\t"N"\t""\t73.081723544\t"C4H9N"\t"57750053"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8696\t0.2174\t0.2174\t14\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-SMZGMGDZSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i3D2"\t"RWRDLPDLKQPQOW-SMZGMGDZSA-N"\t"RWRDLPDLKQPQOW"\t"SMZGMGDZSA"\t"N"\t""\t73.086052786\t"C4H9N"\t"57608710"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8696\t0.2174\t0.2174\t14\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-LNLMKGTHSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2"\t"RWRDLPDLKQPQOW-LNLMKGTHSA-N"\t"RWRDLPDLKQPQOW"\t"LNLMKGTHSA"\t"N"\t""\t75.098606278\t"C4H9N"\t"57608709"\t""\t""\t""\t""\t""\t""\t2\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8333\t0.208325\t0.208325\t15\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-QAOQSSEZSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D,3D2"\t"RWRDLPDLKQPQOW-QAOQSSEZSA-N"\t"RWRDLPDLKQPQOW"\t"QAOQSSEZSA"\t"N"\t""\t74.092329532\t"C4H9N"\t"90927493"\t""\t""\t""\t""\t""\t""\t2\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8\t0.2\t0.2\t16\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-SVYQBANQSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D2,4D2"\t"RWRDLPDLKQPQOW-SVYQBANQSA-N"\t"RWRDLPDLKQPQOW"\t"SVYQBANQSA"\t"N"\t"Pyrrolidine-2,2,3,3,4,4,5,5-d8"\t79.123713262\t"C4H9N"\t"12196044"\t""\t""\t""\t""\t""\t""\t2\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8\t0.2\t0.2\t16\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-HJOWPTDZSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D,4D2/hD"\t"RWRDLPDLKQPQOW-HJOWPTDZSA-N"\t"RWRDLPDLKQPQOW"\t"HJOWPTDZSA"\t"N"\t"pyrrolidine-d8"\t79.123713262\t"C4H9N"\t"129715569"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.7143\t0.178575\t0.178575\t17\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-KLRAWXKOSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D2,4D2/hD"\t"RWRDLPDLKQPQOW-KLRAWXKOSA-N"\t"RWRDLPDLKQPQOW"\t"KLRAWXKOSA"\t"N"\t""\t80.12999001\t"C4H9N"\t"60135501"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.7143\t0.178575\t0.178575\t17\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"MWFMGBPGAXYFAR-UHFFFAOYSA-N"\t"InChI=1S/C4H7NO/c1-4(2,6)3-5/h6H,1-2H3"\t"MWFMGBPGAXYFAR-UHFFFAOYSA-N"\t"MWFMGBPGAXYFAR"\t"UHFFFAOYSA"\t"N"\t"ACETONE CYANOHYDRIN"\t85.05276385\t"C4H7NO"\t"6406"\t"C02659"\t""\t""\t"HMDB0060427"\t"False"\t"False"\t0\t"HMDB0031456"\t"277,343,409,410"\t0.99\tNA\t"0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.6923\t0.173075\t0.173075\t18\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RRUDCFGSUDOHDG-UHFFFAOYSA-N"\t"InChI=1S/C2H5NO2/c1-2(4)3-5/h5H,1H3,(H,3,4)"\t"RRUDCFGSUDOHDG-UHFFFAOYSA-N"\t"RRUDCFGSUDOHDG"\t"UHFFFAOYSA"\t"N"\t"acetohydroxamic acid"\t75.032028405\t"C2H5NO2"\t"1990"\t"C06808"\t"Anatomical Therapeutic Chemical (ATC) classification [BR:br08303]"\t"D00220"\t"HMDB0014691"\t"False"\t"True"\t0\t"HMDB0003338"\t"277,343,409,410"\t0.99\tNA\t"0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.5455\t0.136375\t0.136375\t19\t"[M+H]+"\n+27\t"M132T74"\t132.101827517612\t73.554846736017\t"AGPKZVBTJJNPAG-UHFFFAOYSA-N"\t"InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)"\t"AGPKZVBTJJNPAG-UHFFFAOYSA-N"\t"AGPKZVBTJJNPAG"\t"UHFFFAOYSA"\t"N"\t"2-ammonio-3-methylpentanoate"\t131.09462866\t"C6H13NO2"\t"791,57397079"\t"C16434"\t""\t""\t"HMDB0033923"\t"True"\t"False"\t18\t"HMDB0000172"\t"478,547,616,475,541,607"\t1\t"CE000616"\t"0"\t0\t0\t0\t0.940890528192141\t0.282267158457642\t0\t0\t0\t0\t1\t0.25\t0.532267158457642\t1\t"[M+H]+"\n'
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/createDatabase_output.sqlite
b
Binary file test-data/createDatabase_output.sqlite has changed
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/createDatabase_output_eic.sqlite
b
Binary file test-data/createDatabase_output_eic.sqlite has changed
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/createMSP_output_av_all_metadata.msp
--- a/test-data/createMSP_output_av_all_metadata.msp Thu Dec 05 07:37:41 2019 -0500
+++ b/test-data/createMSP_output_av_all_metadata.msp Wed Apr 01 11:05:00 2020 -0400
b
@@ -10,7 +10,7 @@
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826 502873.46875 100
@@ -28,7 +28,7 @@
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826 502873.46875 100
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/filterFragSpectra_output.RData
b
Binary file test-data/filterFragSpectra_output.RData has changed
b
diff -r 4207233ead9c -r 96fba93b4c8a test-data/flagRemove_output.tsv
--- a/test-data/flagRemove_output.tsv Thu Dec 05 07:37:41 2019 -0500
+++ b/test-data/flagRemove_output.tsv Wed Apr 01 11:05:00 2020 -0400
b
@@ -1,7 +1,7 @@
-"grpid" "ID" "mzmed" "mzmin" "mzmax" "rtmed" "rtmin" "rtmax" "npeaks" "KO" "WT" "ko15" "ko16" "ko18" "wt19" "wt21" "wt22" "KO_median_I" "WT_median_I" "KO_RSD_I" "WT_RSD_I" "KO_coverage" "WT_coverage" "KO_RSD_RT" "WT_RSD_RT" "rsd_all_RT" "grpid.1" "KO_valid" "WT_valid" "all_sample_valid" "mzmin_full" "mzmax_full" "rtmin_full" "rtmax_full"
-"1" "1" 205 205 205 2794.024 2793.436 2803.044 3 0 3 NA NA NA 1507943.06947222 1533767.074875 1354004.93486208 NA 1507943.06947222 NA 6.63321894286696 0 1 NA 0.19255594131829 0.19255594131829 1 0 1 1 205 205 2767.512 2816.3
-"2" "2" 231 231 231 2519.839 2504.508 2535.473 6 1 3 NA NA 30766.3350000011 45103.2999999989 104989.362833335 49776.3899999999 30766.3350000011 49776.3899999999 NA 49.9951594827002 0.333333333333333 1 NA 0.360049078987311 0.432545161192324 2 0 1 1 231 231 2507.963 2514.738
-"3" "3" 402.200012207031 402.200012207031 402.200012207031 3598.551 3592.212 3610.036 4 1 3 NA NA 14554.4999999997 37458.7453333329 91785.7281052629 142007.379692308 14554.4999999997 91785.7281052629 NA 57.8293736085665 0.333333333333333 1 NA 0.251337522585405 0.206331444617903 3 0 1 1 402.200012207031 402.200012207031 3563.503 3597.137
-"4" "4" 449.100006103516 449.100006103516 449.100006103516 2667.26 2664.638 2676.652 3 0 3 NA NA NA 6663.76999999991 11221.0499999998 6830.35200000006 NA 6830.35200000006 NA 31.3702198972974 0 1 NA 0.236631537850627 0.236631537850627 4 0 1 1 449.100006103516 449.100006103516 2659.233 2670.393
-"5" "5" 564.200012207031 564.200012207031 564.200012207031 3498.002 3491.993 3507.349 4 0 3 NA NA NA 149980.21 87237.7950000002 160589.344999999 NA 149980.21 NA 29.896461605479 0 1 NA 0.135256683436928 0.135256683436928 5 0 1 1 564.200012207031 564.200012207031 3473.214 3501.034
-"6" "6" 586.299987792969 586.299987792969 586.299987792969 3308.894 3308.249 3310.396 3 0 3 NA NA NA 10504.2799999998 7491.65500000026 12363.4999999997 NA 10504.2799999998 NA 24.294650028749 0 1 NA 0.0332903660058522 0.0332903660058522 6 0 1 1 586.299987792969 586.299987792969 3304.199 3312.024
+"grpid" "ID" "mzmed" "mzmin" "mzmax" "rtmed" "rtmin" "rtmax" "npeaks" "KO" "WT" "ko15" "ko16" "ko18" "wt19" "wt21" "wt22" "KO_median_I" "WT_median_I" "KO_RSD_I" "WT_RSD_I" "KO_coverage" "WT_coverage" "KO_RSD_RT" "WT_RSD_RT" "rsd_all_RT" "grpid.1" "KO_valid" "WT_valid" "all_sample_valid" "mzmin_full" "mzmax_full" "rtmin_full" "rtmax_full" "grp_names"
+"1" "1" "205" "205" "205" "2794.024" "2793.436" "2803.044" "3" "0" "3" NA NA NA "1507943.06947222" "1533767.074875" "1354004.93486208" NA "1507943.06947222" NA "6.63321894286696" "0" "1" NA "0.19255594131829" "0.19255594131829" "1" "0" "1" "1" "205" "205" "2767.512" "2816.3" "M205T2794"
+"2" "2" "231" "231" "231" "2519.839" "2504.508" "2535.473" "6" "1" "3" NA NA "30766.3350000011" "45103.2999999989" "104989.362833335" "49776.3899999999" "30766.3350000011" "49776.3899999999" NA "49.9951594827002" "0.333333333333333" "1" NA "0.360049078987311" "0.432545161192324" "2" "0" "1" "1" "231" "231" "2507.963" "2514.738" "M231T2520"
+"3" "3" "402.200012207031" "402.200012207031" "402.200012207031" "3598.551" "3592.212" "3610.036" "4" "1" "3" NA NA "14554.4999999997" "37458.7453333329" "91785.7281052629" "142007.379692308" "14554.4999999997" "91785.7281052629" NA "57.8293736085665" "0.333333333333333" "1" NA "0.251337522585405" "0.206331444617903" "3" "0" "1" "1" "402.200012207031" "402.200012207031" "3563.503" "3597.137" "M402T3599"
+"4" "4" "449.100006103516" "449.100006103516" "449.100006103516" "2667.26" "2664.638" "2676.652" "3" "0" "3" NA NA NA "6663.76999999991" "11221.0499999998" "6830.35200000006" NA "6830.35200000006" NA "31.3702198972974" "0" "1" NA "0.236631537850627" "0.236631537850627" "4" "0" "1" "1" "449.100006103516" "449.100006103516" "2659.233" "2670.393" "M449T2667"
+"5" "5" "564.200012207031" "564.200012207031" "564.200012207031" "3498.002" "3491.993" "3507.349" "4" "0" "3" NA NA NA "149980.21" "87237.7950000002" "160589.344999999" NA "149980.21" NA "29.896461605479" "0" "1" NA "0.135256683436928" "0.135256683436928" "5" "0" "1" "1" "564.200012207031" "564.200012207031" "3473.214" "3501.034" "M564T3498"
+"6" "6" "586.299987792969" "586.299987792969" "586.299987792969" "3308.894" "3308.249" "3310.396" "3" "0" "3" NA NA NA "10504.2799999998" "7491.65500000026" "12363.4999999997" NA "10504.2799999998" NA "24.294650028749" "0" "1" NA "0.0332903660058522" "0.0332903660058522" "6" "0" "1" "1" "586.299987792969" "586.299987792969" "3304.199" "3312.024" "M586T3309"
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