| Previous changeset 2:908e1345d7ca (2017-03-31) Next changeset 4:265ee538e120 (2017-08-09) |
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Commit message:
Uploaded |
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modified:
nmr_alignement/NmrAlignment_wrapper.R nmr_alignement/NmrAlignment_xml.xml nmr_alignement/test-data/MTBLS1.zip |
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added:
nmr_alignement/test-data/MTBLS1_alignedSpectra.tabular |
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removed:
nmr_alignement/.Rhistory nmr_alignement/test-data/MTBLS1_bucketedData.tabular nmr_alignement/test-data/MTBLS1_sampleMetadata.tabular nmr_alignement/test-data/MTBLS1_variableMetadata.tabular |
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| diff -r 908e1345d7ca -r f3ec6799c435 nmr_alignement/NmrAlignment_wrapper.R --- a/nmr_alignement/NmrAlignment_wrapper.R Fri Mar 31 09:56:39 2017 -0400 +++ b/nmr_alignement/NmrAlignment_wrapper.R Wed Apr 12 04:32:23 2017 -0400 |
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| @@ -17,7 +17,7 @@ ## Libraries loading ##------------------------------ # ParseCommandArgs function -library(batch) +library(batch) # Alignment library(speaq) @@ -51,7 +51,7 @@ if(!runExampleL) argLs <- parseCommandArgs(evaluate=FALSE) - + ## Parameters Loading ##------------------- # Inputs @@ -61,14 +61,6 @@ zipfile= argLs[["zipfile"]] directory=unzip(zipfile, list=F) directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/") -} else if (!is.null(argLs[["library"]])){ - fileType="zip" - directory=argLs[["library"]] - if(!file.exists(directory)){ - error_message=paste("Cannot access the directory :",directory,".Please verify if the directory exists or not.") - print(error_message) - stop(error_message) - } } else if (!is.null(argLs[["tsvfile"]])){ fileType="tsv" directory <- read.table(argLs[["tsvfile"]],check.names=FALSE,header=TRUE,sep="\t") @@ -78,7 +70,7 @@ ## Spectral width leftBorder <- argLs[["left_border"]] rightBorder <- argLs[["right_border"]] - + ##Exclusion zone(s) exclusionZones <- argLs[["zone_exclusion_choices.choice"]] exclusionZonesBorders <- NULL @@ -89,13 +81,13 @@ exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]]))) } } - + ## Reference spectrum reference <- argLs[["reference"]] ## Size of a small nDivRange nDivRange <- argLs[["nDivRange"]] - + ## Intensity threshold for peak removal baselineThresh <- argLs[["baselineThresh"]] @@ -111,12 +103,12 @@ error.stock <- "\n" if(length(error.stock) > 1) stop(error.stock) - - + + ## Computation ##------------ directory.alignement <- nmr.alignment(fileType=fileType,directory=directory,leftBorder=leftBorder,rightBorder=rightBorder,exclusionZones=exclusionZones, - exclusionZonesBorders=exclusionZonesBorders, reference=reference, nDivRange=nDivRange, + exclusionZonesBorders=exclusionZonesBorders, reference=reference, nDivRange=nDivRange, baselineThresh=baselineThresh, maxshift=50, verbose=FALSE) directory.raw <- directory.alignement[[1]] directory.aligned <- directory.alignement[[2]] @@ -127,7 +119,7 @@ t.directory.aligned <- t(directory.aligned) rownames(t.directory.aligned) <- colnames(directory.aligned) # colnames(t.directory.aligned) <- c("Bucket",colnames(t.directory.aligned)) -write.table(t.directory.aligned,file=alignedSpectra,row.names=TRUE,quote=FALSE,sep="\t") +write.table(t.directory.aligned,file=alignedSpectra,row.names=TRUE,quote=FALSE,sep="\t") excludedZone <- NULL @@ -164,7 +156,7 @@ drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n])[1]):(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n-1])[1])],xlab="", ylab="Aligned spectra", main="") n <- n - 2 } - + drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[1])[1]):ncol(raw.spectra)],xlab="", ylab="Raw spectra", main="") drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[1])[1]):ncol(aligned.spectra)],xlab="", ylab="Aligned spectra", main="") } |
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| diff -r 908e1345d7ca -r f3ec6799c435 nmr_alignement/NmrAlignment_xml.xml --- a/nmr_alignement/NmrAlignment_xml.xml Fri Mar 31 09:56:39 2017 -0400 +++ b/nmr_alignement/NmrAlignment_xml.xml Wed Apr 12 04:32:23 2017 -0400 |
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| b'@@ -1,59 +1,55 @@\n-<tool id="NmrAlignment" name="NMR spectra alignment" version="2.0.2">\r\n-\t<description>based on the Cluster-based Peak Alignment (CluPA) algorithm</description>\r\n-\t <requirements>\r\n- <requirement type="package" version="3.1.2">R</requirement>\r\n-\t <requirement type="package" version="1.1_4">r-batch</requirement>\r\n-\t <requirement type="package" version="1.2.1">r-speaq</requirement>\r\n- \t</requirements>\r\n+<tool id="NmrAlignment" name="NMR spectra alignment" version="2.0.3">\r\n+ <description>based on the Cluster-based Peak Alignment (CluPA) algorithm</description>\r\n+ <requirements>\r\n+ <requirement type="package" version="1.1_4">r-batch</requirement>\r\n+ <requirement type="package" version="1.2.1">r-speaq</requirement>\r\n+ </requirements>\r\n <stdio>\r\n <exit_code range="1:" level="fatal" />\r\n </stdio>\r\n- \t<command>\r\n-\t\t## Wrapper\r\n+ <command>\r\n+ ## Wrapper\r\n Rscript \'$__tool_directory__/NmrAlignment_wrapper.R\'\r\n \r\n-\t\t## File input\r\n- #if $inputs.input == "lib":\r\n- library \'$__app__.config.user_library_import_dir/$__user_email__/$inputs.library\'\r\n-\t\t#elif $inputs.input == "tsv_file":\r\n+ ## File input\r\n+ #if $inputs.input == "tsv_file":\r\n tsvfile $inputs.tsv_file\r\n #elif $inputs.input == "zip_file":\r\n zipfile \'$inputs.zip_file\'\r\n #end if\r\n \r\n-\t\t## Spectra borders\r\n-\t\tleft_border $left_border\r\n-\t\tright_border $right_border\r\n+ ## Spectra borders\r\n+ left_border $left_border\r\n+ right_border $right_border\r\n \r\n-\t\t## Exclusion zone\r\n-\t\tzone_exclusion_choices.choice ${zone_exclusion_choices.choice}\r\n-\t\t#if str($zone_exclusion_choices.choice) == \'yes\':\r\n-\t\t\t#for $i in $zone_exclusion_choices.conditions:\r\n-\t\t\t\tzone_exclusion_left ${i.zone_exclusion_left}\r\n-\t\t\t\tzone_exclusion_right ${i.zone_exclusion_right}\r\n-\t\t\t#end for\r\n-\t\t#end if\r\n+ ## Exclusion zone\r\n+ zone_exclusion_choices.choice ${zone_exclusion_choices.choice}\r\n+ #if str($zone_exclusion_choices.choice) == \'yes\':\r\n+ #for $i in $zone_exclusion_choices.conditions:\r\n+ zone_exclusion_left ${i.zone_exclusion_left}\r\n+ zone_exclusion_right ${i.zone_exclusion_right}\r\n+ #end for\r\n+ #end if\r\n \r\n-\t\t## Reference spectrum\r\n-\t\treference $reference\r\n+ ## Reference spectrum\r\n+ reference $reference\r\n \r\n-\t\t## Segment size\r\n-\t\tnDivRange $nDivRange\r\n+ ## Segment size\r\n+ nDivRange $nDivRange\r\n \r\n-\t\t## Intensity threshold\r\n-\t\tbaselineThresh $baselineThresh\r\n+ ## Intensity threshold\r\n+ baselineThresh $baselineThresh\r\n \r\n-\t\t## Outputs\r\n-\t\tlogOut \'$logOut\'\r\n-\t\talignedSpectra \'$alignedSpectra\'\r\n-\t\tgraphOut \'$graphOut\'\r\n-\t</command>\r\n- \t<inputs>\r\n+ ## Outputs\r\n+ logOut \'$logOut\'\r\n+ alignedSpectra \'$alignedSpectra\'\r\n+ graphOut \'$graphOut\'\r\n+ </command>\r\n+ <inputs>\r\n <conditional name="inputs">\r\n <param name="input" type="select" label="Choose your inputs method" >\r\n <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option>\r\n <option value="tsv_file">Tsv file containing preprocessed spectra (from your history)</option>\r\n- <option value="lib" >Library directory name</option>\r\n </param>\r\n <when value="zip_file">\r\n <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />\r\n@@ -61,41 +57,58 @@\n <when value="tsv_file">\r\n <param name="tsv_file" type="data" format="tabular" label="Tsv file" />\r\n </when>\r\n- <when value="lib">\r\n- <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >\r\n- <validator type="empty_field"/>\r\n- </param>\r\n- '..b'p" />\r\n+ </conditional>\r\n+ <param name="left_border" value="9.3" />\r\n+ <param name="right_border" value="0.2" />\r\n+ <conditional name="zone_exclusion_choices">\r\n+ <param name="choice" value="yes" />\r\n+ <param name="conditions_0|zone_exclusion_left" value="6.0" />\r\n+ <param name="conditions_0|zone_exclusion_right" value="4.24" />\r\n+ <param name="conditions_1|zone_exclusion_left" value="4.0" />\r\n+ <param name="conditions_1|zone_exclusion_right" value="3.2" />\r\n+ </conditional>\r\n+ <param name="reference" value="0" />\r\n+ <param name="nDivRange" value="64" />\r\n+ <param name="baselineThresh" value="0" />\r\n+ <output name="alignedSpectra" value="MTBLS1_alignedSpectra.tabular" />\r\n+ </test>\r\n+ </tests>\r\n \r\n-\t<help>\r\n+ <help>\r\n \r\n .. class:: infomark\r\n \r\n@@ -177,49 +190,49 @@\n ----------\r\n \r\n Bucket width\r\n-\t| size of windows\r\n-\t|\r\n+ | size of windows\r\n+ |\r\n \r\n Left limit\r\n-\t| Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm\r\n-\t|\r\n+ | Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm\r\n+ |\r\n \r\n Right limit\r\n-\t| Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm\r\n-\t|\r\n+ | Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm\r\n+ |\r\n \r\n Exclusion zone(s)\r\n-\t| Spectral regions to exclude, water, solvents, ... resonance\r\n-\t| If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,\r\n-\t| If NO: no zone to exclude\r\n-\t| Default value is NO\r\n-\t|\r\n+ | Spectral regions to exclude, water, solvents, ... resonance\r\n+ | If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,\r\n+ | If NO: no zone to exclude\r\n+ | Default value is NO\r\n+ |\r\n \r\n Left exclusion zone\r\n-\t| Upper boundary of exclusion zone\r\n-\t|\r\n+ | Upper boundary of exclusion zone\r\n+ |\r\n \r\n Right exclusion zone\r\n-\t| Lower boundary of exclusion zone\r\n+ | Lower boundary of exclusion zone\r\n \r\n | *Notes:*\r\n | - these parameters can be used several times using the "Add new exclusion zones" button\r\n |\r\n \r\n Reference spectrum\r\n-\t| spectrum to which other spectra are aligned\r\n-\t| Default value is 0: heuristic strategy to find the optimal template developped in the speaq package\r\n-\t|\r\n+ | spectrum to which other spectra are aligned\r\n+ | Default value is 0: heuristic strategy to find the optimal template developped in the speaq package\r\n+ |\r\n \r\n Segment size\r\n-\t| Size of a single small segment after division of spectra\r\n-\t| Default value: 64 (minimal value adviced)\r\n-\t|\r\n+ | Size of a single small segment after division of spectra\r\n+ | Default value: 64 (minimal value adviced)\r\n+ |\r\n \r\n Intensity threshold\r\n-\t| All peaks with an intensity below this threshold are removed\r\n-\t| Default value: 1\r\n-\t|\r\n+ | All peaks with an intensity below this threshold are removed\r\n+ | Default value: 1\r\n+ |\r\n \r\n \r\n ------------\r\n@@ -227,13 +240,13 @@\n ------------\r\n \r\n alignedSpectra.tsv\r\n-\t| tabular output\r\n-\t| Data matrix with p rows (ppm) and n columns (samples) containing the aligned intensities\r\n-\t|\r\n+ | tabular output\r\n+ | Data matrix with p rows (ppm) and n columns (samples) containing the aligned intensities\r\n+ |\r\n \r\n graphOut.pdf\r\n-\t| pdf output\r\n-\t| Graphical chart of raw and aligned data: whole spectral width, "zoomed" zones depending on the exclusion zones, spectral zone between 2.8 and 2.4ppm corresponding to the citric acid\r\n+ | pdf output\r\n+ | Graphical chart of raw and aligned data: whole spectral width, "zoomed" zones depending on the exclusion zones, spectral zone between 2.8 and 2.4ppm corresponding to the citric acid\r\n \r\n \r\n ---------------------------------------------------\r\n' |
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| diff -r 908e1345d7ca -r f3ec6799c435 nmr_alignement/test-data/MTBLS1.zip |
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| Binary file nmr_alignement/test-data/MTBLS1.zip has changed |
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| diff -r 908e1345d7ca -r f3ec6799c435 nmr_alignement/test-data/MTBLS1_alignedSpectra.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_alignement/test-data/MTBLS1_alignedSpectra.tabular Wed Apr 12 04:32:23 2017 -0400 |
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|
| b |
| diff -r 908e1345d7ca -r f3ec6799c435 nmr_alignement/test-data/MTBLS1_bucketedData.tabular --- a/nmr_alignement/test-data/MTBLS1_bucketedData.tabular Fri Mar 31 09:56:39 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r 908e1345d7ca -r f3ec6799c435 nmr_alignement/test-data/MTBLS1_sampleMetadata.tabular --- a/nmr_alignement/test-data/MTBLS1_sampleMetadata.tabular Fri Mar 31 09:56:39 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ -Sample SampleOrder -ADG10003u_007 1 -ADG10003u_008 2 -ADG10003u_009 3 -ADG10003u_010 4 -ADG10003u_015 5 -ADG10003u_016 6 -ADG10003u_017 7 -ADG10003u_021 8 -ADG10003u_022 9 -ADG10003u_023 10 -ADG10003u_051 11 -ADG10003u_052 12 -ADG10003u_053 13 -ADG10003u_066 14 -ADG10003u_067 15 -ADG10003u_071 16 -ADG10003u_072 17 -ADG10003u_073 18 -ADG10003u_087 19 -ADG10003u_088 20 -ADG10003u_089 21 -ADG10003u_097 22 -ADG10003u_098 23 |
| b |
| diff -r 908e1345d7ca -r f3ec6799c435 nmr_alignement/test-data/MTBLS1_variableMetadata.tabular --- a/nmr_alignement/test-data/MTBLS1_variableMetadata.tabular Fri Mar 31 09:56:39 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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