Mercurial > repos > lecorguille > xcms_fillpeaks

changeset 34:d8bac1291473 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:40:32 -0400
parents ea611367e1da
children e67cbb96d9e9
files abims_xcms_fillPeaks.xml lib.r macros.xml macros_xcms.xml repository_dependencies.xml static/images/xcms_fillpeaks_workflow.png xcms_fillpeaks.r
diffstat 7 files changed, 357 insertions(+), 236 deletions(-) [+]
line wrap: on
line diff
--- a/abims_xcms_fillPeaks.xml	Thu Mar 08 05:55:04 2018 -0500
+++ b/abims_xcms_fillPeaks.xml	Tue Apr 03 11:40:32 2018 -0400
@@ -4,13 +4,14 @@
 
     <macros>
         <import>macros.xml</import>
+        <import>macros_xcms.xml</import>
     </macros>
 
     <expand macro="requirements"/>
     <expand macro="stdio"/>
 
     <command><![CDATA[
-        @COMMAND_XCMS_SCRIPT@/xcms_fillpeaks.r
+        @COMMAND_RSCRIPT@/xcms_fillpeaks.r
 
         image '$image'
 
@@ -49,7 +50,7 @@
 
     <tests>
         <!--<test>
-            <param name="image" value="xset.group.retcor.group.RData"/>
+            <param name="image" value="xset.group.retcor.group.RData" ftype="rdata"/>
             <param name="method" value="chrom"/>
             <param name="zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
             <assert_stdout>
@@ -63,7 +64,7 @@
         </test>-->
         <!-- Issue with fillpeaks because it seems that there are too many NA
         <test>
-            <param name="image" value="faahKO.xset.group.retcor.group.RData"/>
+            <param name="image" value="faahKO.xset.group.retcor.group.RData" ftype="rdata"/>
             <param name="method" value="chrom"/>
             <conditional name="peaklist">
                 <param name="peaklistBool" value="true" />
@@ -84,7 +85,7 @@
             <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
         </test>
         <test>
-            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData"/>
+            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData" ftype="rdata"/>
             <param name="method" value="chrom"/>
             <conditional name="peaklist">
                 <param name="peaklistBool" value="true" />
@@ -105,7 +106,7 @@
             <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
         </test>-->
         <test>
-            <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData"/>
+            <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/>
             <conditional name="peaklist">
                 <param name="peaklistBool" value="true" />
                 <param name="convertRTMinute" value="false" />
@@ -163,33 +164,20 @@
 
 **Downstream tools**
 
-+---------------------------+------------------+-----------------------+
-| Name                      | Output file      | Format                |
-+===========================+==================+=======================+
-|CAMERA.annotate            | xset.retcor.RData| rdata.xcms.fillpeaks  |
-+---------------------------+------------------+-----------------------+
-|xcms.summary               | xset.retcor.RData| rdata.xcms.fillpeaks  |
-+---------------------------+------------------+-----------------------+
-
-The output file **xset.fillpeaks** is a RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool as a following step of your workflow.
+=========================== ================== =======================
+Name                        Output file        Format
+=========================== ================== =======================
+CAMERA.annotate             xset.retcor.RData  rdata.xcms.fillpeaks
+--------------------------- ------------------ -----------------------
+xcms.summary                xset.retcor.RData  rdata.xcms.fillpeaks
+=========================== ================== =======================
 
 
 **General schema of the metabolomic workflow**
 
 .. image:: xcms_fillpeaks_workflow.png
 
-
-
------------
-Input files
------------
-
-+---------------------------+-----------------------+
-| Parameter : num + label   |   Format              |
-+===========================+=======================+
-| 1 : RData file            |   rdata.xcms.group    |
-+---------------------------+-----------------------+
-
+---------------------------------------------------
 
 ----------
 Parameters
@@ -211,43 +199,7 @@
 
     | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.
 
-xset.variableMetadata.tsv : tabular format
-
-    | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
-
-xset.dataMatrix.tsv : tabular format
-
-    | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
-
-------
-
-.. class:: infomark
-
-The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool.
-
-
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
------------
-
-    | RData file -> **xset.retcor.RData**
-
-Parameters
-----------
-
-    | method -> **chrom**
-    | Get a Peak List -> **false**
-
-
-Output files
-------------
-
-    | **xset.fillPeaks.RData: RData file**
+@HELP_PEAKLIST_OUTPUT@
 
 
 ---------------------------------------------------
--- a/lib.r	Thu Mar 08 05:55:04 2018 -0500
+++ b/lib.r	Tue Apr 03 11:40:32 2018 -0400
@@ -28,6 +28,58 @@
 }
 
 #@author G. Le Corguille
+# This function merge several xdata into one.
+mergeXData <- function(args) {
+    for(image in args$images) {
+        load(image)
+        # Handle infiles
+        if (!exists("singlefile")) singlefile <- NULL
+        if (!exists("zipfile")) zipfile <- NULL
+        rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
+        zipfile <- rawFilePath$zipfile
+        singlefile <- rawFilePath$singlefile
+        retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+        if (exists("raw_data")) xdata <- raw_data
+        if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
+        cat(sampleNamesList$sampleNamesOrigin,"\n")
+        if (!exists("xdata_merged")) {
+            xdata_merged <- xdata
+            singlefile_merged <- singlefile
+            md5sumList_merged <- md5sumList
+            sampleNamesList_merged <- sampleNamesList
+        } else {
+            if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
+            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
+            else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
+            singlefile_merged <- c(singlefile_merged,singlefile)
+            md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
+            sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
+            sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
+        }
+    }
+    rm(image)
+    xdata <- xdata_merged; rm(xdata_merged)
+    singlefile <- singlefile_merged; rm(singlefile_merged)
+    md5sumList <- md5sumList_merged; rm(md5sumList_merged)
+    sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
+
+    if (!is.null(args$sampleMetadata)) {
+        cat("\tXSET PHENODATA SETTING...\n")
+        sampleMetadataFile <- args$sampleMetadata
+        sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
+        xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
+
+        if (any(is.na(pData(xdata)$sample_group))) {
+            sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
+            error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
+            print(error_message)
+            stop(error_message)
+        }
+    }
+    return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList))
+}
+
+#@author G. Le Corguille
 # This function convert if it is required the Retention Time in minutes
 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
     if (convertRTMinute){
@@ -79,9 +131,11 @@
 
     # Color by group
     group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
-    names(group_colors) <- unique(xdata$sample_group)
-    plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
-    legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
+    if (length(group_colors) > 1) {
+        names(group_colors) <- unique(xdata$sample_group)
+        plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
+        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
+    }
 
     # Color by sample
     plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
@@ -109,6 +163,19 @@
 }
 
 #@author G. Le Corguille
+# It allow different of field separators
+getDataFrameFromFile <- function(filename, header=T) {
+    myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
+    if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
+    if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
+    if (ncol(myDataFrame) < 2) {
+        error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
+        print(error_message)
+        stop(error_message)
+    }
+    return(myDataFrame)
+}
+
 getPlotChromatogram <- function(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
 
     chrom <- chromatogram(xdata, aggregationFun = aggregationFun)
@@ -127,9 +194,11 @@
 
     # Color by group
     group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
-    names(group_colors) <- unique(xdata$sample_group)
-    plot(chrom, col = group_colors[chrom$sample_group], main=main)
-    legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
+    if (length(group_colors) > 1) {
+        names(group_colors) <- unique(xdata$sample_group)
+        plot(chrom, col = group_colors[chrom$sample_group], main=main)
+        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
+    }
 
     # Color by sample
     plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
@@ -345,10 +414,7 @@
             singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
         }
     }
-    for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
-        args[[argument]] <- NULL
-    }
-    return(list(zipfile=zipfile, singlefile=singlefile, args=args))
+    return(list(zipfile=zipfile, singlefile=singlefile))
 }
 
 
@@ -559,3 +625,9 @@
 c.XCMSnExp <- function(...) {
     .concatenate_XCMSnExp(...)
 }
+
+#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
+# https://github.com/sneumann/xcms/issues/247
+c.MSnbase <- function(...) {
+    .concatenate_OnDiskMSnExp(...)
+}
--- a/macros.xml	Thu Mar 08 05:55:04 2018 -0500
+++ b/macros.xml	Tue Apr 03 11:40:32 2018 -0400
@@ -1,22 +1,13 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@WRAPPER_VERSION@">3.0.0</token>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement>
-            <requirement type="package" version="1.1_4">r-batch</requirement>
-            <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
-            <requirement type="package" version="6.0">unzip</requirement>
-            <yield />
-        </requirements>
-    </xml>
     <xml name="stdio">
         <stdio>
             <exit_code range="1" level="fatal" />
         </stdio>
     </xml>
 
-    <token name="@COMMAND_XCMS_SCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
+    <!-- COMMAND -->
+    <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
 
     <token name="@COMMAND_LOG_EXIT@">
         ;
@@ -25,6 +16,7 @@
         sh -c "exit \$return"
     </token>
 
+    <!-- INPUT_VALIDATORS -->
     <xml name="input_validator_range_integer">
         <validator type="regex" message="The format is 'min,max'" >[0-9]+ *, *[0-9]+</validator>
     </xml>
@@ -37,155 +29,24 @@
         <validator type="regex" message="The format is '1,2,4,6'" >[0-9, ]+</validator>
     </xml>
 
+
     <token name="@INPUT_IMAGE_LABEL@">RData file</token>
     <token name="@INPUT_IMAGE_HELP@">It contain a xcms3::XCMSnExp object (named xdata)</token>
 
-    <!-- zipfile load for planemo test -->
 
-    <token name="@COMMAND_FILE_LOAD@">
-        #if $file_load_section.file_load_conditional.file_load_select == "yes":
-            #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
-                #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
-                #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
-
-                singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
-            #else
-                zipfile '$file_load_section.file_load_conditional.input'
-            #end if
-        #end if
-    </token>
-
-    <xml name="input_file_load">
-        <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
-            <conditional name="file_load_conditional">
-                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
-                    <option value="no" >no need</option>
-                    <option value="yes" >yes</option>
-                </param>
-                <when value="no">
-                </when>
-                <when value="yes">
-                    <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
-                </when>
-            </conditional>
-        </section>
-    </xml>
-
-    <xml name="test_file_load_zip">
-        <section name="file_load_section">
-            <conditional name="file_load_conditional">
-                <param name="file_load_select" value="yes" />
-                <param name="input" value="faahKO_reduce.zip" ftype="zip" />
-            </conditional>
-        </section>
-    </xml>
-
-    <xml name="test_file_load_zip_sacuri">
-        <section name="file_load_section">
-            <conditional name="file_load_conditional">
-                <param name="file_load_select" value="yes" />
-                <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
-            </conditional>
-        </section>
-    </xml>
-
-    <xml name="test_file_load_single">
-        <section name="file_load_section">
-            <conditional name="file_load_conditional">
-                <param name="file_load_select" value="yes" />
-                <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
-            </conditional>
-        </section>
-    </xml>
-
-    <token name="@COMMAND_PEAKLIST@">
-        #if $peaklist.peaklistBool
-            convertRTMinute $peaklist.convertRTMinute
-            numDigitsMZ $peaklist.numDigitsMZ
-            numDigitsRT $peaklist.numDigitsRT
-            intval $peaklist.intval
-        #end if
-    </token>
-
-    <xml name="input_peaklist">
-        <conditional name="peaklist">
-            <param name="peaklistBool" type="boolean" label="Get a Peak List" />
-            <when value="true">
-              <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
-              <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
-              <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
-              <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
-                  <option value="into" selected="true">into</option>
-                  <option value="maxo">maxo</option>
-                  <option value="intb">intb</option>
-              </param>
-            </when>
-            <when value="false" />
-        </conditional>
-    </xml>
-
-    <xml name="output_peaklist"  token_function="">
-        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" >
-            <filter>(peaklist['peaklistBool'])</filter>
-        </data>
-        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" >
-            <filter>(peaklist['peaklistBool'])</filter>
-        </data>
-    </xml>
-
-    <token name="@HELP_AUTHORS@">
-.. class:: infomark
-
-**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
+    <!-- MISC -->
+    <token name="@HELP_AUTHORS_WRAPPERS@">
 
 .. class:: infomark
 
-**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
+**Galaxy integration** ABiMS TEAM - SU/CNRS - Station biologique de Roscoff and Yann Guitton - LABERCA
+Part of Workflow4Metabolomics.org [W4M]
 
  | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
 
----------------------------------------------------
-
-    </token>
-
-    <token name="@HELP_XCMS_MANUAL@">
-
-For details and explanations for all the parameters and the workflow of xcms_ package, see its manual_ and this example_
-
-.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
-.. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
-.. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
-
     </token>
 
-    <token name="@HELP_PEAKLIST@">
-
-Get a Peak List
----------------
-
-If 'true', the module generates two additional files corresponding to the peak list:
-- the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
-- the data matrix (corresponding to related intensities)
-
-**decimal places for [mass or retention time] values in identifiers**
-
-    | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
-    | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
-    | Theses parameters do not affect decimal places in columns other than the identifier one.
-
-**Reported intensity values**
-
-    | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
-    | - into: integrated area of original (raw) peak
-    | - maxo: maximum intensity of original (raw) peak
-    | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
-
-    </token>
-
-    <xml name="citation">
-        <citations>
-            <citation type="doi">10.1021/ac051437y</citation>
+    <xml name="citation_w4m">
             <citation type="doi">10.1093/bioinformatics/btu813</citation>
-        </citations>
     </xml>
 </macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_xcms.xml	Tue Apr 03 11:40:32 2018 -0400
@@ -0,0 +1,242 @@
+<?xml version="1.0"?>
+<macros>
+
+    <token name="@WRAPPER_VERSION@">3.0.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement>
+            <requirement type="package" version="1.1_4">r-batch</requirement>
+            <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
+            <requirement type="package" version="6.0">unzip</requirement>
+            <yield />
+        </requirements>
+    </xml>
+
+    <!-- FILE_LOAD for planemo test -->
+    <token name="@COMMAND_FILE_LOAD@">
+        #if $file_load_section.file_load_conditional.file_load_select == "yes":
+            #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
+                #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
+                #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
+
+                singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
+            #else
+                zipfile '$file_load_section.file_load_conditional.input'
+            #end if
+        #end if
+    </token>
+
+    <xml name="input_file_load">
+        <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
+                    <option value="no" >no need</option>
+                    <option value="yes" >yes</option>
+                </param>
+                <when value="no">
+                </when>
+                <when value="yes">
+                    <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
+                </when>
+            </conditional>
+        </section>
+    </xml>
+
+    <xml name="test_file_load_zip">
+        <section name="file_load_section">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <param name="input" value="faahKO_reduce.zip" ftype="zip" />
+            </conditional>
+        </section>
+    </xml>
+
+    <xml name="test_file_load_zip_sacuri">
+        <section name="file_load_section">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
+            </conditional>
+        </section>
+    </xml>
+
+    <xml name="test_file_load_single">
+        <section name="file_load_section">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
+            </conditional>
+        </section>
+    </xml>
+
+    <xml name="test_file_load_single_ko15">
+        <section name="file_load_section">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <param name="input" value="ko15.CDF" ftype="netcdf" />
+            </conditional>
+        </section>
+    </xml>
+
+    <!-- PEAKLIST -->
+    <token name="@COMMAND_PEAKLIST@">
+        #if $peaklist.peaklistBool
+            convertRTMinute $peaklist.convertRTMinute
+            numDigitsMZ $peaklist.numDigitsMZ
+            numDigitsRT $peaklist.numDigitsRT
+            intval $peaklist.intval
+        #end if
+    </token>
+
+    <xml name="input_peaklist">
+        <conditional name="peaklist">
+            <param name="peaklistBool" type="boolean" label="Get a Peak List" />
+            <when value="true">
+              <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
+              <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
+              <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
+              <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
+                  <option value="into" selected="true">into</option>
+                  <option value="maxo">maxo</option>
+                  <option value="intb">intb</option>
+              </param>
+            </when>
+            <when value="false" />
+        </conditional>
+    </xml>
+
+    <xml name="output_peaklist"  token_function="">
+        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" >
+            <filter>(peaklist['peaklistBool'])</filter>
+        </data>
+        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" >
+            <filter>(peaklist['peaklistBool'])</filter>
+        </data>
+    </xml>
+
+    <token name="@HELP_PEAKLIST@">
+
+Get a Peak List
+---------------
+
+If 'true', the module generates two additional files corresponding to the peak list:
+- the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
+- the data matrix (corresponding to related intensities)
+
+**decimal places for [mass or retention time] values in identifiers**
+
+    | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
+    | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
+    | Theses parameters do not affect decimal places in columns other than the identifier one.
+
+**Reported intensity values**
+
+    | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
+    | - into: integrated area of original (raw) peak
+    | - maxo: maximum intensity of original (raw) peak
+    | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
+
+    </token>
+
+    <token name="@HELP_PEAKLIST_OUTPUT@">
+xset.variableMetadata.tsv : tabular format
+
+    | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
+
+xset.dataMatrix.tsv : tabular format
+
+    | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
+    </token>
+
+    <!-- CENTWAVE -->
+    <token name="@COMMAND_CENTWAVE@">
+            ppm $methods.ppm
+            peakwidth "c($methods.peakwidth)"
+
+            ## Advanced
+            snthresh $methods.CentWaveAdv.snthresh
+            prefilter "c($methods.CentWaveAdv.prefilter)"
+            mzCenterFun $methods.CentWaveAdv.mzCenterFun
+            integrate $methods.CentWaveAdv.integrate
+            mzdiff $methods.CentWaveAdv.mzdiff
+            fitgauss $methods.CentWaveAdv.fitgauss
+            noise $methods.CentWaveAdv.noise
+            verboseColumns $methods.CentWaveAdv.verboseColumns
+    </token>
+
+    <xml name="input_centwave">
+        <param argument="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." />
+        <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space.">
+            <expand macro="input_validator_range_float"/>
+        </param>
+    </xml>
+
+    <xml name="input_centwaveAdv">
+        <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" />
+        <param argument="prefilter" type="text" value="3,100" label="Prefilter step for for the first analysis step (ROI detection)" help="Separate by coma k, I. Mass traces are only retained if they contain at least ‘k‘ peaks with intensity ‘>= I‘.">
+            <expand macro="input_validator_range_integer"/>
+        </param>
+        <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" >
+            <option value="wMean">intensity weighted mean of the peak's m/z values</option>
+            <option value="mean">mean of the peak's m/z values</option>
+            <option value="apex">use the m/z value at the peak apex</option>
+            <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
+            <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>
+        </param>
+        <param argument="integrate" type="select" label="Integration method" >
+            <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option>
+            <option value="2">peak limits based on real data (more accurate but prone to noise)</option>
+        </param>
+        <param argument="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="can be negative to allow overlap" />
+        <param argument="fitgauss" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="fitgauss" help="whether or not a Gaussian should be fitted to each peak" />
+        <param argument="noise" type="integer" value="0" label="Noise filter" help="allowing to set a minimum intensity required for centroids to be considered in the first analysis step (centroids with intensity lower than ‘noise’ are omitted from ROI detection)." />
+        <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" />
+    </xml>
+
+    <token name="@COMMAND_CENTWAVEADVROI@">
+            #if $sectionROI.roiList:
+                roiList '$sectionROI.roiList'
+                firstBaselineCheck $sectionROI.firstBaselineCheck
+                #if $sectionROI.roiScales != "":
+                    roiScales "c($sectionROI.roiScales)"
+                #end if
+            #end if
+    </token>
+
+    <xml name="input_centwaveAdvROI" token_optional="true">
+        <param argument="roiList" type="data" format="tabular" optional="@OPTIONAL@" label="List of regions-of-interest (ROI) representing detected mass traces" help="If ROIs are submitted the first analysis step is omitted and chromatographic peak detection is performed on the submitted ROIs. Each ROI is expected to have the following elements specified: ‘scmin’ (start scan index), ‘scmax’ (end scan index), ‘mzmin’ (minimum m/z), ‘mzmax’ (maximum m/z), ‘length’ (number of scans), ‘intensity’ (summed intensity)." />
+        <param argument="firstBaselineCheck" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Is continuous data within regions of interest is checked to be above the first baseline." />
+        <param argument="roiScales" type="text" value="" optional="true" label="Numeric vector defining the scale for each region of interest in ‘roiList’" help="Length equal to ‘roiList’ - Should be used for the centWave-wavelets (format 0.9,1,0.2)">
+            <expand macro="input_validator_range_float"/>
+        </param>
+    </xml>
+
+    <!-- MISC -->
+    <token name="@HELP_AUTHORS@">
+.. class:: infomark
+
+**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
+
+@HELP_AUTHORS_WRAPPERS@
+
+---------------------------------------------------
+
+    </token>
+
+    <token name="@HELP_XCMS_MANUAL@">
+
+For details and explanations for all the parameters and the workflow of xcms_ package, see its manual_ and this example_
+
+.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
+.. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
+.. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
+
+    </token>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1021/ac051437y</citation>
+            <expand macro="citation_w4m"/>
+        </citations>
+    </xml>
+</macros>
--- a/repository_dependencies.xml	Thu Mar 08 05:55:04 2018 -0500
+++ b/repository_dependencies.xml	Tue Apr 03 11:40:32 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories>
     <repository changeset_revision="91815b6d07fe" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-	<repository changeset_revision="bff835d58914" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+	<repository changeset_revision="8ce71291b600" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
Binary file static/images/xcms_fillpeaks_workflow.png has changed
--- a/xcms_fillpeaks.r	Thu Mar 08 05:55:04 2018 -0500
+++ b/xcms_fillpeaks.r	Tue Apr 03 11:40:32 2018 -0400
@@ -31,18 +31,10 @@
 #saving the specific parameters
 method <- "FillChromPeaks"
 
-if (!is.null(args$convertRTMinute)){
-    convertRTMinute <- args$convertRTMinute; args$convertRTMinute <- NULL
-}
-if (!is.null(args$numDigitsMZ)){
-    numDigitsMZ <- args$numDigitsMZ; args$numDigitsMZ <- NULL
-}
-if (!is.null(args$numDigitsRT)){
-    numDigitsRT <- args$numDigitsRT; args$numDigitsRT <- NULL
-}
-if (!is.null(args$intval)){
-    intval <- args$intval; args$intval <- NULL
-}
+if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
+if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
+if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
+if (!is.null(args$intval)) intval <- args$intval
 
 cat("\n\n")
 
@@ -51,7 +43,7 @@
 cat("\tINFILE PROCESSING INFO\n")
 
 #image is an .RData file necessary to use xset variable given by previous tools
-load(args$image); args$image=NULL
+load(args$image)
 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
 
 #Verification of a group step before doing the fillpeaks job.
@@ -63,7 +55,6 @@
 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
 zipfile <- rawFilePath$zipfile
 singlefile <- rawFilePath$singlefile
-args <- rawFilePath$args
 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
 
 # Check some character issues
@@ -82,6 +73,9 @@
 cat("\t\tCOMPUTE\n")
 
 cat("\t\t\tFilling missing peaks using default settings\n")
+# clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
+args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
+
 fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
 print(fillChromPeaksParam)
 xdata <- fillChromPeaks(xdata, param=fillChromPeaksParam)