changeset 14:b20a4121a436 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
author tomnl
date Fri, 11 May 2018 06:01:21 -0400
parents eea94e398c26
children faea3f40e305
files anticipated_purity_dims.R create_sqlite_db.R spectral_matching.R test-data/anticipated_purity_dims.tsv test-data/dimspy_peakmatrix.tsv
diffstat 5 files changed, 136 insertions(+), 122 deletions(-) [+]
line wrap: on
line diff
--- a/anticipated_purity_dims.R	Tue May 08 05:30:13 2018 -0400
+++ b/anticipated_purity_dims.R	Fri May 11 06:01:21 2018 -0400
@@ -29,31 +29,41 @@
 
   df <- read.table(opt$peaks_file, header = TRUE, sep='\t')
   filename = NA
+  mzml_file <- opt$mzML_file
 }else{
   indf <- read.table(opt$peaks_file,
                      header = TRUE, sep='\t', stringsAsFactors = FALSE)
-	
-  filename = colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
-  print(filename)
-  # check if the data file is mzML or RAW (can only use mzML currently) so
-  # we expect an mzML file of the same name in the same folder
-  indf$i <- indf[,colnames(indf)==filename]
-  indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])
+  
 
-  filename = sub("raw", "mzML", filename, ignore.case = TRUE)
-  print(filename)
+  if (file.exists(opt$mzML_file)){
+     mzml_file <- opt$mzML_file
+  }else{
+     
+     filename = colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
+     print(filename)
+     # check if the data file is mzML or RAW (can only use mzML currently) so
+     # we expect an mzML file of the same name in the same folder
+     indf$i <- indf[,colnames(indf)==filename]
+     indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])
+
+     filename = sub("raw", "mzML", filename, ignore.case = TRUE)
+     print(filename)
+
+     mzml_file <- file.path(opt$mzML_file, filename)
+
+  }	
+  
   df <- indf[4:nrow(indf),]
   if ('blank_flag' %in% colnames(df)){
-    df <- df[df$blank_flag==1,]
+      df <- df[df$blank_flag==1,]
   }
-
   colnames(df)[colnames(df)=='m.z'] <- 'mz'
 
   if ('nan' %in% df$mz){
     df[df$mz=='nan',]$mz <- NA
   }
   df$mz <- as.numeric(df$mz)
-  mzml_file <- file.path(opt$mzML_file, filename)	
+	
 
 
 
--- a/create_sqlite_db.R	Tue May 08 05:30:13 2018 -0400
+++ b/create_sqlite_db.R	Fri May 11 06:01:21 2018 -0400
@@ -46,6 +46,7 @@
 
 
 
+
 option_list <- list(
   make_option(c("-o", "--out_dir"), type="character"),
   make_option("--pa", type="character"),
@@ -109,13 +110,13 @@
 }
 
 
-print(pa@fileList)
-print(xset@filepaths)
+
 
 
 db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
                           grp_peaklist=grp_peaklist, db_name=opt$db_name)
 
+print(db_pth)
 
 if (!is.null(opt$eic)){
   if (is.null(opt$raw_rt_columns)){
@@ -123,6 +124,8 @@
   }else{
     rtrawColumns <- TRUE
   }
+  # previous check should have matched filelists together
+  xset@filepaths <- unname(pa@fileList)
 
   # Saves the EICS into the previously created database
   px <- msPurity::purityX(xset, saveEIC = TRUE,
--- a/spectral_matching.R	Tue May 08 05:30:13 2018 -0400
+++ b/spectral_matching.R	Fri May 11 06:01:21 2018 -0400
@@ -1,4 +1,5 @@
 library(msPurity)
+library(msPurityData)
 library(optparse)
 print(sessionInfo())
 
@@ -6,7 +7,7 @@
 option_list <- list(
   make_option(c("-o", "--out_dir"), type="character"),
   make_option("--target_db_pth", type="character"),
-  make_option("--library_db_pth", type="character"),
+  make_option("--library_db_pth", type="character", default=NA),
   make_option("--ra_thres_l", default=0),
   make_option("--ra_thres_t", default=2),
   make_option("--cores", default=1),
--- a/test-data/anticipated_purity_dims.tsv	Tue May 08 05:30:13 2018 -0400
+++ b/test-data/anticipated_purity_dims.tsv	Fri May 11 06:01:21 2018 -0400
@@ -1,105 +1,105 @@
-"mz"	"present"	"occurrence"	"purity"	"rsd_all"	"blank_flag"	"flags"	"A02_Polar_Daph_WAX1_Phenyl_LCMS_Pos_DIMS.mzML"	"i"	"medianPurity"	"meanPurity"	"sdPurity"	"cvPurity"	"sdePurity"	"medianPeakNum"
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-72.0804488318	1	1	1	NA	1	1	"282356.694196"	NA	0.476393449015639	0.491371797539656	0.0959939418911048	19.5359079157077	0.00899065639730063	3
-72.0807946804	1	1	1	NA	1	1	"242795.036574"	NA	0.408868285818401	0.413678708258705	0.0963729445058641	23.2965687094523	0.00902615324445423	4
-75.0913582568	1	1	1	NA	1	1	"195736.137751"	NA	0.459383030656064	0.474810934372905	0.132551039182737	27.916593655915	0.0124145422608961	4
-75.0916836387	1	1	1	NA	1	1	"204270.938871"	NA	0.476040133259869	0.487345328966681	0.132269392840645	27.1407942128215	0.0123881636641073	4
-84.0805289745	1	1	1	NA	1	1	"132563.310059"	NA	0.538722764069125	0.556981810892634	0.209884767937749	37.682517423932	0.0196575095717612	5
-84.0807820515	1	1	1	NA	1	1	"140127.582831"	NA	0.5505876981432	0.572987236535537	0.193308605470024	33.7369828059049	0.0181050097139868	5
-84.9112399606	1	1	1	NA	1	1	"122855.946347"	NA	0.32276675677724	0.327703846067696	0.0947526802174731	28.9141190603846	0.00887440159010228	6
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+255.135716622	1	1	1	NA	1	1	"217409.046327"	0.722742628240063	0.722620903503393	0.0771306433791256	10.6737354268584	0.00722394662270566	2
+258.11005415	1	1	1	NA	1	1	"1115782.48355"	1	0.998989650412204	0.00759802222211233	0.760570664468569	0.000711619980931282	1
+259.113428484	1	1	1	NA	1	1	"116684.024123"	0.40943839312185	0.414664220914468	0.111090050920774	26.7903632186508	0.0104504729170969	4
+260.026986373	1	1	1	NA	1	1	"114329.273026"	0.834789069821472	0.847982448683166	0.142597975529527	16.8161470500914	0.0133555240641229	1
+262.139666583	1	1	1	NA	1	1	"112895.448374"	1	0.873757428844562	0.143619940675396	16.4370494526514	0.0134512398696781	4
+263.013036178	1	1	1	NA	1	1	"109641.587791"	0.341354546076094	0.345083410338949	0.0702030543390681	20.3437929021604	0.00657511846236699	5
+265.069706061	1	1	1	NA	1	1	"117335.705028"	0.535835841158933	0.552604088184114	0.13111179807168	23.7261722949825	0.0122797449804899	3
+271.077737641	1	1	1	NA	1	1	"450346.351974"	0.890554482567277	0.890000125563021	0.0491961434495172	5.52765578750849	0.00460764099393555	2
+276.155374087	1	1	1	NA	1	1	"136931.070613"	0.647990474549476	0.647778048196749	0.0884741270155522	13.6580928084615	0.00828636120548428	3
+280.092071266	1	1	1	NA	1	1	"4695554.13158"	1	1	0	0	0	1
+281.095366093	1	1	1	NA	1	1	"340729.456277"	1	0.962121343327033	0.0537481189998876	5.5864179058772	0.00503397256544992	1
+287.051676968	1	1	1	NA	1	1	"242733.36705"	0.771021230917071	0.768797501339101	0.0846791903309667	11.0144986402104	0.00793093282002092	2
+290.145887292	1	1	1	NA	1	1	"113405.155344"	1	0.912976640198171	0.122323676132966	13.3983358113537	0.011456661948665	4
+292.197944568	1	1	1	NA	1	1	"284733.869866"	1	0.946299361732444	0.0830140830525254	8.77249699297554	0.00777498123484596	1
+295.035845285	1	1	1	NA	1	1	"165469.133189"	1	0.946438667823634	0.120155782220767	12.6955698563193	0.0113033051792031	1
+296.065981413	1	1	1	NA	1	1	"2118414.36513"	1	1	0	0	0	1
+297.069291673	1	1	1	NA	1	1	"164842.79237"	0.640424674805916	0.652908708298409	0.128668878850103	19.7070244606533	0.012050944632313	3
+298.064070296	1	1	1	NA	1	1	"138663.554301"	0.487445588689514	0.499865711270908	0.102282113256446	20.4619182612855	0.00962189184027137	4
+304.161525258	1	1	1	NA	1	1	"419869.29057"	1	0.972356491662697	0.0385307174146733	3.96261224613074	0.00360873232406467	1
+312.166592178	1	1	1	NA	1	1	"148686.24328"	1	0.924022031662414	0.10845341092504	11.7371022777369	0.0102024386904567	1
+326.143410047	1	1	1	NA	1	1	"125171.338949"	1	0.935622006691498	0.104469097443653	11.1657375196925	0.00978442744144706	3
+348.079411021	1	1	1	NA	1	1	"224606.194901"	0.763842231385576	0.7670558334405	0.0752246033459717	9.80692670161498	0.00704542961756979	3
+364.053454491	1	1	1	NA	1	1	"111448.034526"	1	0.869279361784151	0.156249338921548	17.9745828315599	0.0146340913902941	1
--- a/test-data/dimspy_peakmatrix.tsv	Tue May 08 05:30:13 2018 -0400
+++ b/test-data/dimspy_peakmatrix.tsv	Fri May 11 06:01:21 2018 -0400
@@ -1,4 +1,4 @@
-m/z	present	occurrence	purity	rsd_all	blank_flag	flags	A02_Polar_Daph_WAX1_Phenyl_LCMS_Pos_DIMS.mzML
+m/z	present	occurrence	purity	rsd_all	blank_flag	flags	FULL_SCAN.mzML
 missing values							0
 tags_class_label							sample
 tags_untyped							
@@ -283,4 +283,4 @@
 nan	0	0.0	nan	nan	0	0	0.0
 nan	0	0.0	nan	nan	0	0	0.0
 nan	0	0.0	nan	nan	0	0	0.0
-nan	0	0.0	nan	nan	0	0	0.0
\ No newline at end of file
+nan	0	0.0	nan	nan	0	0	0.0