# HG changeset patch # User lecorguille # Date 1450886840 18000 # Node ID 2cb13028206005cf865260be6e7181083941ee12 # Parent e18100ba8c100509043ff9c237f4518be2cbe1dc Uploaded diff -r e18100ba8c10 -r 2cb130282060 abims_xcms_report.xml --- a/abims_xcms_report.xml Wed Dec 23 09:30:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,69 +0,0 @@ - - - Create a report of XCMS analysis - - - R - Rscript - xcms - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10.1093/bioinformatics/btu813 - - - diff -r e18100ba8c10 -r 2cb130282060 abims_xcms_retcor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_retcor.xml Wed Dec 23 11:07:20 2015 -0500 @@ -0,0 +1,301 @@ + + + Retention Time Correction using retcor function from xcms R package + + + R + Rscript + xcms + xcms_w4m_script + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (methods['method'] == 'peakgroups') + (options['option'] == 'show') + (family == 'symmetric') + (plottype != 'none') + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **xset.group.RData** + +Parameters +---------- + + | Method: -> **peakgroups** + | smooth: -> **loess** + | extra: -> **1** + | missing -> **1** + | Advanced options: -> **show** + | span -> **0.2** + | family -> **gaussian** + | plottype -> **deviation** + + +Output files +------------ + + | **1) xset.group.retcor.RData: RData file** + + | **2) Example of an xset.group.retcor.TICs_corrected pdf file** + +.. image:: xcms_retcor.png + + ]]> + + + 10.1021/ac051437y + 10.1093/bioinformatics/btu813 + + + diff -r e18100ba8c10 -r 2cb130282060 planemo.sh --- a/planemo.sh Wed Dec 23 09:30:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -planemo shed_init -f --name=xcms_report --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - HTML Report for XCMS analysis" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nThis tool create a HTML report of XCMS analysis" --category="Metabolomics" diff -r e18100ba8c10 -r 2cb130282060 repository_dependencies.xml --- a/repository_dependencies.xml Wed Dec 23 09:30:57 2015 -0500 +++ b/repository_dependencies.xml Wed Dec 23 11:07:20 2015 -0500 @@ -1,4 +1,5 @@ - + + diff -r e18100ba8c10 -r 2cb130282060 static/images/xcms_retcor.png Binary file static/images/xcms_retcor.png has changed diff -r e18100ba8c10 -r 2cb130282060 static/images/xcms_retcor_workflow.png Binary file static/images/xcms_retcor_workflow.png has changed diff -r e18100ba8c10 -r 2cb130282060 test-data/.svn/entries --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/entries Wed Dec 23 11:07:20 2015 -0500 @@ -0,0 +1,49 @@ +10 + +dir +0 +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_report/test-data +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo +add + + + + + + + + + + + + + + + + + + + +87d02074-be8c-4456-a071-04b64888326c + +fillpeaks.RData +file + + + +add + + + + + +has-props +has-prop-mods + +report.html +file + + + +add + diff -r e18100ba8c10 -r 2cb130282060 test-data/.svn/props/fillpeaks.RData.svn-work --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/props/fillpeaks.RData.svn-work Wed Dec 23 11:07:20 2015 -0500 @@ -0,0 +1,5 @@ +K 13 +svn:mime-type +V 24 +application/octet-stream +END diff -r e18100ba8c10 -r 2cb130282060 test-data/fillpeaks.RData Binary file test-data/fillpeaks.RData has changed diff -r e18100ba8c10 -r 2cb130282060 test-data/log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log.txt Wed Dec 23 11:07:20 2015 -0500 @@ -0,0 +1,52 @@ + PACKAGE INFO +parallel 3.1.2 +BiocGenerics 0.14.0 +Biobase 2.28.0 +Rcpp 0.12.0 +mzR 2.2.2 +xcms 1.44.0 +snow 0.3.13 +batch 1.1.4 + + + ARGUMENTS INFO +image test-data/xset.group.RData +xfunction retcor +xsetRdataOutput test-data/xset.group.retcor.RData +ticspdf xset.group.retcor.TICs_corrected.pdf +bicspdf xset.group.retcor.BPCs_corrected.pdf +rplotspdf xset.group.retcor.Rplots.pdf +method obiwarp +profStep 1 +zipfile test-data/sacuri.zip + + + INFILE PROCESSING INFO + + + ARGUMENTS PROCESSING INFO + + + MAIN PROCESSING INFO +center sample: HU_neg_060 +Processing: HU_neg_028 HU_neg_051 HU_neg_017 HU_neg_034 Blanc09 Blanc06 Blanc12 Blanc04 +null device + 1 + + + XSET OBJECT INFO +An "xcmsSet" object with 9 samples + +Time range: 0.7-1139.9 seconds (0-19 minutes) +Mass range: 50.0019-999.9863 m/z +Peaks: 135846 (about 15094 per sample) +Peak Groups: 0 +Sample classes: bio, blank + +Profile settings: method = bin + step = 0.01 + +Memory usage: 13.8 MB + + + DONE diff -r e18100ba8c10 -r 2cb130282060 test-data/report.html --- a/test-data/report.html Wed Dec 23 09:30:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ - - - - -[W4M] XCMS analysis report - - - -

___ XCMS analysis report using Workflow4Metabolomics ___

-

Samples used:

- - -
samplefilename
HU_neg_051 sacuri//bio2/HU_neg_051.mzXML
HU_neg_060 sacuri//bio2/HU_neg_060.mzXML
HU_neg_017 sacuri//bio/HU_neg_017.mzXML
HU_neg_028 sacuri//bio/HU_neg_028.mzXML
Blanc04 sacuri//blank/Blanc04.mzXML
Blanc06 sacuri//blank/Blanc06.mzXML
-

Function launched:

- - - - - - - - - - - - - - - -
timestamp
(ymd-h:m:s)		functionargumentvalue
151221-16:20:54xcmsSetnSlaves1
methodmatchedFilter
step0.01
fwhm30
151221-16:37:00groupmethoddensity
sleep0.001
minfrac0.5
bw30
mzwid0.25
151221-16:37:20fillPeaksmethodchrom
-

Information about the xcmsSet object:

-
-An "xcmsSet" object with 6 samples
-
-Time range: 16.3-1138.9 seconds (0.3-19 minutes)
-Mass range: 61.9883-481.2446 m/z
-Peaks: 1799 (about 300 per sample)
-Peak Groups: 289 
-Sample classes: bio, bio2, blank 
-
-Profile settings: method = bin
-                  step = 0.01
-
-Memory usage: 0.421 MB
-
-

Citations:

- - - diff -r e18100ba8c10 -r 2cb130282060 test-data/sacuri.zip Binary file test-data/sacuri.zip has changed diff -r e18100ba8c10 -r 2cb130282060 test-data/xset.group.RData Binary file test-data/xset.group.RData has changed diff -r e18100ba8c10 -r 2cb130282060 test-data/xset.group.retcor.BPCs_corrected.pdf Binary file test-data/xset.group.retcor.BPCs_corrected.pdf has changed diff -r e18100ba8c10 -r 2cb130282060 test-data/xset.group.retcor.RData Binary file test-data/xset.group.retcor.RData has changed diff -r e18100ba8c10 -r 2cb130282060 test-data/xset.group.retcor.Rplots.pdf Binary file test-data/xset.group.retcor.Rplots.pdf has changed diff -r e18100ba8c10 -r 2cb130282060 test-data/xset.group.retcor.TICs_corrected.pdf Binary file test-data/xset.group.retcor.TICs_corrected.pdf has changed diff -r e18100ba8c10 -r 2cb130282060 tool_dependencies.xml --- a/tool_dependencies.xml Wed Dec 23 09:30:57 2015 -0500 +++ b/tool_dependencies.xml Wed Dec 23 11:07:20 2015 -0500 @@ -6,4 +6,7 @@ + + + diff -r e18100ba8c10 -r 2cb130282060 xcms_report.r --- a/xcms_report.r Wed Dec 23 09:30:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,132 +0,0 @@ -#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file -# version="0.1.0" -#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM - - - -# ----- ARGUMENTS BLACKLIST ----- -#xcms.r -argBlacklist=c("zipfile","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf") -#CAMERA.r -argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path") - -# ----- PACKAGE ----- - -pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch") -for(pkg in pkgs) { - suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) -} - - -# ----- FUNCTION ----- -writehtml = function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") } - - -# ----- ARGUMENTS ----- - -listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects - - -# ----- ARGUMENTS PROCESSING ----- - -#image is an .RData file necessary to use xset variable given by previous tools -load(listArguments[["image"]]); - -htmlOutput = "report.html" -if (!is.null(listArguments[["htmlOutput"]])){ - htmlOutput = listArguments[["htmlOutput"]]; -} - -user_email = NULL -if (!is.null(listArguments[["user_email"]])){ - user_email = listArguments[["user_email"]]; -} - - -# ----- MAIN PROCESSING INFO ----- -writehtml("") -writehtml("") - -writehtml("") - writehtml("") - - writehtml("[W4M] XCMS analysis report") - - writehtml("") -writehtml("") - -writehtml("") - writehtml("

___ XCMS analysis report using Workflow4Metabolomics ___

") - # to pass the planemo shed_test - if (user_email != "test@bx.psu.edu") { - if (!is.null(user_email)) writehtml("By: ",user_email," - ") - writehtml("Date: ",format(Sys.time(), "%y%m%d-%H:%M:%S")) - } - - - writehtml("

Samples used:

") - writehtml("samplefilename") - writehtml(paste("",sampnames(xset),"",xset@filepaths,"")) - writehtml("") - - writehtml("

Function launched:

") - writehtml("") - writehtml("") - for(tool in names(listOFlistArguments)) { - listOFlistArgumentsDisplay=listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)] - - timestamp = strsplit(tool,"_")[[1]][1] - xcmsFunction = strsplit(tool,"_")[[1]][2] - writehtml("") - line_begin="" - for (arg in names(listOFlistArgumentsDisplay)) { - writehtml(line_begin,"") - line_begin="" - } - } - writehtml("
timestamp
(ymd-h:m:s)		functionargumentvalue
",timestamp,"",xcmsFunction,"",arg,"",unlist(listOFlistArgumentsDisplay[arg][1]),"
") - - writehtml("

Information about the xcmsSet object:

") - - log_file=file(htmlOutput, open = "at") - writehtml("
")
-        sink(log_file)
-        sink(log_file, type = "output")
-            xset
-        sink()
-    writehtml("
") - - writehtml("

Citations:

") - writehtml("") - -writehtml("") - -writehtml("") -