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changeset 27:30410a052ab3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
author lecorguille
date Tue, 24 Oct 2017 11:47:49 -0400
parents dcca50c5e1cb
children 13885e67b123
files README.rst abims_xcms_retcor.xml lib.r macros.xml test-data/ko15-BPC_corrected_mqc.out test-data/ko15-TIC_corrected_mqc.out test-data/ko16-BPC_corrected_mqc.out test-data/ko16-TIC_corrected_mqc.out test-data/wt15-BPC_corrected_mqc.out test-data/wt15-TIC_corrected_mqc.out test-data/wt16-BPC_corrected_mqc.out test-data/wt16-TIC_corrected_mqc.out xcms.r
diffstat 13 files changed, 10495 insertions(+), 106 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Mon Apr 03 07:52:52 2017 -0400
+++ b/README.rst	Tue Oct 24 11:47:49 2017 -0400
@@ -2,6 +2,10 @@
 Changelog/News
 --------------
 
+**Version 2.2.0 - 19/10/2017**
+
+- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC.
+
 **Version 2.1.0 - 03/02/2017**
 
 - IMPROVEMENT: xcms.retcor can deal with merged individual data
--- a/abims_xcms_retcor.xml	Mon Apr 03 07:52:52 2017 -0400
+++ b/abims_xcms_retcor.xml	Tue Oct 24 11:47:49 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.1.0">
+<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.2.0">
 
     <description>Retention Time Correction using retcor function from xcms R package </description>
 
@@ -15,9 +15,6 @@
         xfunction retcor
 
         xsetRdataOutput '$xsetRData'
-        ticspdf '$ticsCorPdf'
-        bicspdf '$bpcsCorPdf'
-        rplotspdf '$rplotsPdf'
 
         method $methods.method
         #if $methods.method == "obiwarp":
@@ -83,19 +80,32 @@
         </conditional>
 
         <expand macro="input_file_load"/>
+        <expand macro="input_tic_bpc_pdf"/>
 
     </inputs>
 
     <outputs>
         <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" />
-        <data name="rplotsPdf" format="pdf"  label="${image.name[:-6]}.retcor.Rplots.pdf">
+        <data name="rplotsPdf" format="pdf"  from_work_dir="Rplots.pdf" label="${image.name[:-6]}.retcor.Rplots.pdf">
             <filter>(methods['method'] == 'peakgroups')</filter>
-            <filter>(options['option'] == 'show')</filter>
-            <filter>(family == 'symmetric')</filter>
-            <filter>(plottype != 'none')</filter>
+            <filter>(methods['options']['option'] == 'show')</filter>
+            <filter>(methods['options']['family'] == 'symmetric')</filter>
+            <filter>(methods['options']['plottype'] != 'none')</filter>
+        </data>
+        <data name="ticsCorPdf" format="pdf" from_work_dir="TICs.pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf">
+            <filter>tic_bpc_pdf</filter>
         </data>
-        <data name="ticsCorPdf"   format="pdf"  label="${image.name[:-6]}.retcor.TICs_corrected.pdf" />
-        <data name="bpcsCorPdf"   format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" />
+        <data name="bpcsCorPdf" format="pdf" from_work_dir="BPCs.pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf">
+            <filter>tic_bpc_pdf</filter>
+        </data>
+        <collection name="ticsCorrectedTabCollection" type="list" label="TIC corrected tabular">
+            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
+           <discover_datasets pattern="(?P&lt;designation&gt;.+)-TIC_corrected_mqc\.out" ext="tabular" visible="true" />
+        </collection>
+        <collection name="bpcsCorrectedTabCollection" type="list" label="BPC corrected tabular">
+            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
+           <discover_datasets pattern="(?P&lt;designation&gt;.+)-BPC_corrected_mqc\.out" ext="tabular" visible="true" />
+        </collection>
         <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
     </outputs>
 
@@ -125,47 +135,15 @@
         </test>-->
         <test>
             <param name="image" value="faahKO.xset.group.RData"/>
-            <param name="methods|method" value="peakgroups"/>
-            <param name="methods|smooth" value="loess"/>
-            <param name="methods|extra" value="1"/>
-            <param name="methods|missing" value="1"/>
-            <param name="methods|options|option" value="show"/>
-            <param name="methods|options|span" value="0.2"/>
-            <param name="methods|options|family" value="gaussian"/>
-            <param name="methods|options|plottype" value="deviation"/>
+            <expand macro="test_retcor_param"/>
             <expand macro="test_file_load_zip"/>
-            <output name="log">
-                <assert_contents>
-                    <has_text text="object with 4 samples" />
-                    <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
-                    <has_text text="Mass range: 200.1-600 m/z" />
-                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
-                    <has_text text="Peak Groups: 0" />
-                    <has_text text="Sample classes: KO, WT" />
-                </assert_contents>
-            </output>
+            <expand macro="test_retcor_output" raworcorrected="_corrected" />
         </test>
         <test>
             <param name="image" value="faahKO-single-class.xset.group.RData"/>
-            <param name="methods|method" value="peakgroups"/>
-            <param name="methods|smooth" value="loess"/>
-            <param name="methods|extra" value="1"/>
-            <param name="methods|missing" value="1"/>
-            <param name="methods|options|option" value="show"/>
-            <param name="methods|options|span" value="0.2"/>
-            <param name="methods|options|family" value="gaussian"/>
-            <param name="methods|options|plottype" value="deviation"/>
-            <expand macro="test_file_load_single"/>
-            <output name="log">
-                <assert_contents>
-                    <has_text text="object with 4 samples" />
-                    <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
-                    <has_text text="Mass range: 200.1-600 m/z" />
-                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
-                    <has_text text="Peak Groups: 0" />
-                    <has_text text="Sample classes: KO, WT" />
-                </assert_contents>
-            </output>
+            <expand macro="test_retcor_param" />
+	    <expand macro="test_file_load_single"/>
+            <expand macro="test_retcor_output" raworcorrected="_corrected" />
         </test>
     </tests>
 
@@ -177,7 +155,6 @@
 Xcms.retcor
 ===========
 
------------
 Description
 -----------
 
@@ -196,18 +173,17 @@
 
 
 
------------------
 Workflow position
 -----------------
 
 
 **Upstream tools**
 
-========================= ================= ======= ==========
-Name                      output file       format  parameter
-========================= ================= ======= ==========
-xcms.group                xset.group.RData  RData   RData file
-========================= ================= ======= ==========
++------------------------+------------------+--------------------+------------+
+| Name                   | output file      | format             | parameter  |
++========================+==================+====================+============+
+| xcms.group             | xset.group.RData | RData              | RData file |
++------------------------+------------------+--------------------+------------+
 
 
 **Downstream tools**
@@ -218,14 +194,13 @@
 |xcms.group                 | xset.retcor.RData| RData  |
 +---------------------------+------------------+--------+
 
-The output file **xset.retcor.RData** is an RData file. You can continue your analysis using it in **xcms.group** tool as an next step.
-
-
 **General schema of the metabolomic workflow**
 
 .. image:: xcms_retcor_workflow.png
 
 
+---------------------------------------------------
+
 -----------
 Input files
 -----------
@@ -260,24 +235,11 @@
 Output files
 ------------
 
-xset.group.retcor.TICs_corrected.pdf
-
-    | "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step.
-
-xset.group.retcor.BPCs_corrected.pdf
-
-    | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step
-
 xset.group.retcor.RData: rdata.xcms.retcor format
 
     | Rdata file that will be necessary in the **xcms.group** step of the workflow.
 
-
-------
-
-.. class:: infomark
-
-The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool.
+@HELP_BCP_TIC@
 
 
 ---------------------------------------------------
@@ -294,24 +256,14 @@
 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
+    | **Method**: peakgroups
+    | **smooth**: loess
+    | **extra**: 1
+    | **missing**: 5
+    | **Advanced options**: show
+    | **span**: 0.4
+    | **family**: gaussian
+    | **plottype**: deviation
 
 
 ---------------------------------------------------
@@ -319,6 +271,10 @@
 Changelog/News
 --------------
 
+**Version 2.2.0 - 19/10/2017**
+
+- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC.
+
 **Version 2.1.0 - 03/02/2017**
 
 - IMPROVEMENT: xcms.retcor can deal with merged individual data
--- a/lib.r	Mon Apr 03 07:52:52 2017 -0400
+++ b/lib.r	Tue Oct 24 11:47:49 2017 -0400
@@ -51,6 +51,42 @@
     write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
 }
 
+#@author G. Le Corguille
+exportTicBpcTabular <- function(dataset, filenameBase, ticORbpc, rt='raw') {
+
+        rawORcorrected = ''
+        title = ''
+        if (rt=='corrected') {
+            rawORcorrected = '_corrected'
+            title = ' corrected by retcor'
+        }
+
+        if (ticORbpc == "TIC") {
+            section_name = paste0('TIC',rawORcorrected)
+            title = paste0('Total Ion Current (TIC) chromatogram',title)
+            description = 'Sum of intensity (Y) of all ions detected at each retention time(X)'
+        } else if (ticORbpc == "BPC") {
+            section_name = paste0('BPC',rawORcorrected)
+            title = paste0('Base Peak Chromatogram (BPC)',title)
+            description = 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
+        }
+
+        filename=paste0(basename(file_path_sans_ext(filenameBase)),"-",ticORbpc,rawORcorrected,"_mqc.out")
+
+        # Headers for MultiQC
+        cat("# file_format: 'tsv'\n", sep="", file = filename)
+        cat("# section_name: '",section_name,"'\n", sep="", file = filename, append = T)
+        cat("# title: '",title,"'\n", sep="", file = filename, append = T)
+        cat("# description: '",description,"'\n", sep="", file = filename, append = T)
+        cat("# plot_type: 'linegraph'\n", sep="", file = filename, append = T)
+        cat("# pconfig:\n", sep="", file = filename, append = T)
+        cat("#     id: '",ticORbpc,rawORcorrected,"_lineplot'\n", sep="", file = filename, append = T)
+        cat("#     ylab: 'Base Peak Intensity'\n", sep="", file = filename, append = T)
+        cat("#     xlab: 'Retention Time'\n", sep="", file = filename, append = T)
+        cat("Intensity\tRT\n", file = filename, append = T)
+        write.table(dataset, filename ,row.names = F, col.names = F, sep = "\t", append = T, quote = F)
+}
+
 #@author Y. Guitton
 getBPC <- function(file,rtcor=NULL, ...) {
     object <- xcmsRaw(file)
@@ -94,6 +130,9 @@
             rtcor <- NULL
 
         TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
+
+        exportTicBpcTabular(TIC[[j]], files[j], "BPC", rt=rt)
+
         # TIC[[j]][,1]<-rtcor
     }
 
@@ -221,6 +260,8 @@
             rtcor <- xcmsSet@rt$corrected[[i]] else
         rtcor <- NULL
         TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
+
+        exportTicBpcTabular(TIC[[i]], files[i], "TIC", rt=rt)
     }
 
     pdf(pdfname,w=16,h=10)
@@ -476,7 +517,7 @@
 
 
 # This function get the raw file path from the arguments
-getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {    
+getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {
     if (!is.null(listArguments[["zipfile"]]))           zipfile = listArguments[["zipfile"]]
     if (!is.null(listArguments[["zipfilePositive"]]))   zipfile = listArguments[["zipfilePositive"]]
     if (!is.null(listArguments[["zipfileNegative"]]))   zipfile = listArguments[["zipfileNegative"]]
--- a/macros.xml	Mon Apr 03 07:52:52 2017 -0400
+++ b/macros.xml	Tue Oct 24 11:47:49 2017 -0400
@@ -12,6 +12,7 @@
             <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
         </requirements>
     </xml>
+
     <xml name="stdio">
         <stdio>
             <exit_code range="1" level="fatal" />
@@ -116,14 +117,55 @@
         </data>
     </xml>
 
+    <xml name="input_tic_bpc_pdf">
+        <param name="tic_bpc_pdf" type="boolean" checked="False" label="Do you want TIC and BCP in PDF Format" help="Whatever, you will be able to use MultiQC tools on the tabular files" />
+    </xml>
+
+    <xml name="test_retcor_param">
+        <param name="methods|method" value="peakgroups"/>
+        <param name="methods|smooth" value="loess"/>
+        <param name="methods|extra" value="1"/>
+        <param name="methods|missing" value="1"/>
+        <param name="methods|options|option" value="show"/>
+        <param name="methods|options|span" value="0.2"/>
+        <param name="methods|options|family" value="gaussian"/>
+        <param name="methods|options|plottype" value="deviation"/>
+    </xml>
+
+    <xml name="test_retcor_output" token_raworcorrected="">
+        <output name="log">
+            <assert_contents>
+                <has_text text="object with 4 samples" />
+                <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
+                <has_text text="Mass range: 200.1-600 m/z" />
+                <has_text text="Peaks: 9251 (about 2313 per sample)" />
+                <has_text text="Peak Groups: 0" />
+                <has_text text="Sample classes: KO, WT" />
+            </assert_contents>
+        </output>
+        <output_collection name="ticsCorrectedTabCollection" type="list">
+            <element name="ko15" value="ko15-TIC@RAWORCORRECTED@_mqc.out" />
+            <element name="ko16" value="ko16-TIC@RAWORCORRECTED@_mqc.out" />
+            <element name="wt15" value="wt15-TIC@RAWORCORRECTED@_mqc.out" />
+            <element name="wt16" value="wt16-TIC@RAWORCORRECTED@_mqc.out" />
+        </output_collection>
+        <output_collection name="bpcsCorrectedTabCollection" type="list">
+            <element name="ko15" value="ko15-BPC@RAWORCORRECTED@_mqc.out" />
+            <element name="ko16" value="ko16-BPC@RAWORCORRECTED@_mqc.out" />
+            <element name="wt15" value="wt15-BPC@RAWORCORRECTED@_mqc.out" />
+            <element name="wt16" value="wt16-BPC@RAWORCORRECTED@_mqc.out" />
+        </output_collection>
+    </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
 
 .. 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 - UPMC/CNRS - Station Biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
 
  | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
 
@@ -131,6 +173,57 @@
 
     </token>
 
+    <token name="@HELP_BCP_TIC@">
+
+BPCs and TICs: tabular
+
+    | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs
+    | Import BPC and TIC from xcmsSet and retcor [at once] within MultiQC_ (in or outside Galaxy) to display and navigate in the graphs.
+    | - In MultiQC: as tool, use the Custom Content
+
+.. _MultiQC: http://multiqc.info/
+
+BPCs and TICs: pdf [if using zip]
+
+    | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs in pdf format.
+
+    </token>
+
+    <token name="@HELP_GET_PEAK_LIST@">
+
+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_GET_PEAK_LIST_OUTPUTS@">
+
+xset.variableMetadata.tsv : tabular format [If Get a Peak List == Yes]
+
+    | Table containing information about ions - Can be used in **Normalisation/Generic_filter** and **Statitics** tools.
+
+xset.dataMatrix.tsv : tabular format
+
+    | Table containing ions' intensities - Can be used **Normalisation/Generic_filter** and **Statitics** tools.
+
+    </token>
 
     <xml name="citation">
         <citations>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ko15-BPC_corrected_mqc.out	Tue Oct 24 11:47:49 2017 -0400
@@ -0,0 +1,1288 @@
+# file_format: 'tsv'
+# section_name: 'BPC_corrected'
+# title: 'Base Peak Chromatogram (BPC) corrected by retcor'
+# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
+# plot_type: 'linegraph'
+# pconfig:
+#     id: 'BPC_corrected_lineplot'
+#     ylab: 'Base Peak Intensity'
+#     xlab: 'Retention Time'
+Intensity	RT
+2502.98928676082	43888
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ko15-TIC_corrected_mqc.out	Tue Oct 24 11:47:49 2017 -0400
@@ -0,0 +1,1288 @@
+# file_format: 'tsv'
+# section_name: 'TIC_corrected'
+# title: 'Total Ion Current (TIC) chromatogram corrected by retcor'
+# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)'
+# plot_type: 'linegraph'
+# pconfig:
+#     id: 'TIC_corrected_lineplot'
+#     ylab: 'Base Peak Intensity'
+#     xlab: 'Retention Time'
+Intensity	RT
+2502.98928676082	621512
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ko16-BPC_corrected_mqc.out	Tue Oct 24 11:47:49 2017 -0400
@@ -0,0 +1,1288 @@
+# file_format: 'tsv'
+# section_name: 'BPC_corrected'
+# title: 'Base Peak Chromatogram (BPC) corrected by retcor'
+# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
+# plot_type: 'linegraph'
+# pconfig:
+#     id: 'BPC_corrected_lineplot'
+#     ylab: 'Base Peak Intensity'
+#     xlab: 'Retention Time'
+Intensity	RT
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ko16-TIC_corrected_mqc.out	Tue Oct 24 11:47:49 2017 -0400
@@ -0,0 +1,1288 @@
+# file_format: 'tsv'
+# section_name: 'TIC_corrected'
+# title: 'Total Ion Current (TIC) chromatogram corrected by retcor'
+# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)'
+# plot_type: 'linegraph'
+# pconfig:
+#     id: 'TIC_corrected_lineplot'
+#     ylab: 'Base Peak Intensity'
+#     xlab: 'Retention Time'
+Intensity	RT
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wt15-BPC_corrected_mqc.out	Tue Oct 24 11:47:49 2017 -0400
@@ -0,0 +1,1288 @@
+# file_format: 'tsv'
+# section_name: 'BPC_corrected'
+# title: 'Base Peak Chromatogram (BPC) corrected by retcor'
+# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
+# plot_type: 'linegraph'
+# pconfig:
+#     id: 'BPC_corrected_lineplot'
+#     ylab: 'Base Peak Intensity'
+#     xlab: 'Retention Time'
+Intensity	RT
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wt15-TIC_corrected_mqc.out	Tue Oct 24 11:47:49 2017 -0400
@@ -0,0 +1,1288 @@
+# file_format: 'tsv'
+# section_name: 'TIC_corrected'
+# title: 'Total Ion Current (TIC) chromatogram corrected by retcor'
+# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)'
+# plot_type: 'linegraph'
+# pconfig:
+#     id: 'TIC_corrected_lineplot'
+#     ylab: 'Base Peak Intensity'
+#     xlab: 'Retention Time'
+Intensity	RT
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wt16-BPC_corrected_mqc.out	Tue Oct 24 11:47:49 2017 -0400
@@ -0,0 +1,1288 @@
+# file_format: 'tsv'
+# section_name: 'BPC_corrected'
+# title: 'Base Peak Chromatogram (BPC) corrected by retcor'
+# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
+# plot_type: 'linegraph'
+# pconfig:
+#     id: 'BPC_corrected_lineplot'
+#     ylab: 'Base Peak Intensity'
+#     xlab: 'Retention Time'
+Intensity	RT
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wt16-TIC_corrected_mqc.out	Tue Oct 24 11:47:49 2017 -0400
@@ -0,0 +1,1288 @@
+# file_format: 'tsv'
+# section_name: 'TIC_corrected'
+# title: 'Total Ion Current (TIC) chromatogram corrected by retcor'
+# description: 'Sum of intensity (Y) of all ions detected at each retention time(X)'
+# plot_type: 'linegraph'
+# pconfig:
+#     id: 'TIC_corrected_lineplot'
+#     ylab: 'Base Peak Intensity'
+#     xlab: 'Retention Time'
+Intensity	RT
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--- a/xcms.r	Mon Apr 03 07:52:52 2017 -0400
+++ b/xcms.r	Tue Oct 24 11:47:49 2017 -0400
@@ -13,7 +13,7 @@
 # ----- PACKAGE -----
 cat("\tPACKAGE INFO\n")
 #pkgs=c("xcms","batch")
-pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
+pkgs=c("tools","parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
 for(pkg in pkgs) {
     suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
     cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
@@ -65,10 +65,6 @@
 }
 
 #saving the specific parameters
-rplotspdf = "Rplots.pdf"
-if (!is.null(listArguments[["rplotspdf"]])){
-    rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
-}
 sampleMetadataOutput = "sampleMetadata.tsv"
 if (!is.null(listArguments[["sampleMetadataOutput"]])){
     sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
@@ -94,11 +90,6 @@
     intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL
 }
 
-if (thefunction %in% c("xcmsSet","retcor")) {
-    ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
-    bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
-}
-
 
 if (thefunction %in% c("xcmsSet","retcor","fillPeaks"))  {
     if (!exists("singlefile")) singlefile=NULL
@@ -147,7 +138,7 @@
 
 #change the default display settings
 #dev.new(file="Rplots.pdf", width=16, height=12)
-pdf(file=rplotspdf, width=16, height=12)
+pdf(file="Rplots.pdf", width=16, height=12)
 if (thefunction == "group") {
     par(mfrow=c(2,2))
 }
@@ -197,12 +188,12 @@
 if (thefunction == "xcmsSet") {
     cat("\t\tGET TIC GRAPH\n")
     sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
-    getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
-    getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
+    getTICs(xcmsSet=xset, rt="raw")
+    getBPCs(xcmsSet=xset, rt="raw")
 } else if (thefunction == "retcor") {
     cat("\t\tGET TIC GRAPH\n")
-    getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
-    getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
+    getTICs(xcmsSet=xset, rt="corrected")
+    getBPCs(xcmsSet=xset, rt="corrected")
 }
 
 if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) {