Mercurial > repos > lecorguille > xcms_report
changeset 10:753cde95b6a8 draft
Uploaded
| author | lecorguille |
|---|---|
| date | Tue, 19 Jan 2016 10:02:28 -0500 |
| parents | 17d585d877ee |
| children | 467dc9b12da5 |
| files | abims_xcms_report.xml abims_xcms_retcor.xml repository_dependencies.xml static/images/xcms_retcor.png static/images/xcms_retcor_workflow.png test-data/fillpeaks.RData test-data/log.txt test-data/report.html test-data/sacuri.zip test-data/xset.group.RData test-data/xset.group.retcor.BPCs_corrected.pdf test-data/xset.group.retcor.RData test-data/xset.group.retcor.Rplots.pdf test-data/xset.group.retcor.TICs_corrected.pdf |
| diffstat | 14 files changed, 144 insertions(+), 355 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_report.xml Tue Jan 19 10:02:28 2016 -0500 @@ -0,0 +1,69 @@ +<tool id="abims_xcms_report" name="xcms.report" version="0.1.0"> + + <description>Create a report of XCMS analysis</description> + + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + <requirement type="binary">Rscript</requirement> + <requirement type="package" version="1.44.0">xcms</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command interpreter="Rscript"><![CDATA[ + xcms_report.r + + image $image + htmlOutput $htmlOutput + user_email $__user_email__ + + ]]></command> + + <inputs> + + <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" /> + + </inputs> + + <outputs> + <data name="htmlOutput" format="html" label="xcms report html" /> + </outputs> + + <tests> + <test> + <param name="image" value="fillpeaks.RData" /> + <output name="htmlOutput" file="report.html" /> + </test> + </tests> + + <help><![CDATA[ + +.. class:: infomark + +**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff part of Workflow4Metabolomics.org [W4M] + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + +--------------------------------------------------- + +============ +Xcms.report +============ + +----------- +Description +----------- + +This tool provide a HTML report which summarizes your analysis using the [W4M] XCMS and CAMERA tools + + + ]]></help> + + + <citations> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + +</tool>
--- a/abims_xcms_retcor.xml Fri Jan 15 05:06:08 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,301 +0,0 @@ -<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.4"> - - <description>Retention Time Correction using retcor function from xcms R package </description> - - <requirements> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="binary">Rscript</requirement> - <requirement type="package" version="1.44.0">xcms</requirement> - <requirement type="package" version="2.1">xcms_w4m_script</requirement> - </requirements> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - - <command><![CDATA[ - xcms.r - image $image - xfunction retcor - - xsetRdataOutput $xsetRData - ticspdf $ticsCorPdf - bicspdf $bpcsCorPdf - rplotspdf $rplotsPdf - - method $methods.method - #if $methods.method == "obiwarp": - profStep $methods.profStep - #else - smooth $methods.smooth - extra $methods.extra - missing $methods.missing - #if $methods.options.option == "show": - span $methods.options.span - family $methods.options.family - plottype $methods.options.plottype - #end if - #end if - #if $zip_file: - zipfile $zip_file - #end if - ; - return=\$?; - mv log.txt $log; - cat $log; - sh -c "exit \$return" - - ]]></command> - - <inputs> - <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> - <conditional name="methods"> - <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" > - <option value="obiwarp" >obiwarp</option> - <option value="peakgroups" selected="peakgroups">peakgroups</option> - </param> - <when value="obiwarp"> - <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" /> - </when> - <when value="peakgroups"> - <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" > - <option value="loess">loess</option> - <option value="linear">linear</option> - </param> - <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" /> - <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" /> - <conditional name="options"> - <param name="option" type="select" label="Advanced options"> - <option value="show">show</option> - <option value="hide" selected="true">hide</option> - </param> - <when value="show"> - <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/> - - <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> - <option value="gaussian" selected="true">gaussian</option> - <option value="symmetric">symmetric</option> - </param> - - <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> - <option value="none" selected="true">none</option> - <option value="deviation">deviation</option> - <option value="mdevden">mdevden</option> - </param> - </when> - <when value="hide"> - </when> - </conditional> - </when> - </conditional> - <!-- To pass planemo test --> - <param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" /> - </inputs> - - <outputs> - <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" /> - <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf"> - <filter>(methods['method'] == 'peakgroups')</filter> - <filter>(options['option'] == 'show')</filter> - <filter>(family == 'symmetric')</filter> - <filter>(plottype != 'none')</filter> - </data> - <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" /> - <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" /> - <data name="log" format="txt" label="xset.log.txt" hidden="true" /> - </outputs> - - <tests> - <test> - <param name="image" value="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"/> - <param name="zip_file" value="sacuri.zip"/> - <!--<output name="xsetRData" file="xset.group.retcor.RData" />--> - <!--<output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />--> - <!--<output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />--> - <!--<output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" />--> - <output name="log"> - <assert_contents> - <has_text text="object with 9 samples" /> - <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" /> - <has_text text="Mass range: 50.0019-999.9863 m/z" /> - <has_text text="Peaks: 135846 (about 15094 per sample)" /> - <has_text text="Peak Groups: 0" /> - <has_text text="Sample classes: bio, blank" /> - </assert_contents> - </output> - </test> - </tests> - - <help><![CDATA[ - - -.. 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@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M] - - | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. - - - ---------------------------------------------------- - -=========== -Xcms.retcor -=========== - ------------ -Description ------------ - -After matching peaks into groups, xcms can use those groups to identify and correct -correlated drifts in retention time from run to run. The aligned peaks can then be -used for a second pass of peak grouping which will be more accurate than the first. -The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful -for identifying retention time drifts. Some groups may be missing peaks from a large -fraction of samples and thus provide an incomplete picture of the drift at that time point. -Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping. - -.. class:: warningmark - -**After an retcor step, it is mandatory to do a group step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is -discarded)** - - - ------------------ -Workflow position ------------------ - - -**Upstream tools** - -========================= ================= ======= ========== -Name output file format parameter -========================= ================= ======= ========== -xcms.group xset.group.RData RData RData file -========================= ================= ======= ========== - - -**Downstream tools** - -+---------------------------+------------------+--------+ -| Name | Output file | Format | -+===========================+==================+========+ -|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 ------------ - -+---------------------------+----------------------+ -| Parameter : num + label | Format | -+===========================+======================+ -| 1 : RData file | rdata.xcms.group | -+---------------------------+----------------------+ - - ----------- -Parameters ----------- - -Method ------- - -**peakgroups** - - | xcms ignores those groups by only considering well-behaved peak groups which are missing at most one sample and have at most one extra peak. (Those values can be changed with the **missing** and **extra** arguments.) - | For each of those well-behaved groups, the algorithm calculates a median retention time and, for every sample, a deviation from that median. Within a sample, the observed deviation generally changes over time in a nonlinear fashion. Those changes are approximated using a local polynomial regression technique implemented in the **loess** function. By default, the curve fitting is done using least-squares on all data points. - | However, it is possible to enable outlier detection and removal by setting the **family** argument to **symmetric**. - -**obiwarp** - - | Calculate retention time deviations for each sample using the obiwarp code at "http://obi-warp.sourceforge.net/". This function is able to align multiple samples by a center-star strategy. Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. OBI-Warp harnesses the non-linear, comprehensive alignment power of DTW and builds on the discrete, non-bijective output of DTW to give natural interpolants that can be used across multiple datasets. - | For the original publication see :**Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpo-lated Warping John T. Prince and, Edward M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152.** - - ------------- -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. - - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files ------------ - - | RData file -> **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 - - ]]></help> - - <citations> - <citation type="doi">10.1021/ac051437y</citation> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> - -</tool>
--- a/repository_dependencies.xml Fri Jan 15 05:06:08 2016 -0500 +++ b/repository_dependencies.xml Tue Jan 19 10:02:28 2016 -0500 @@ -1,5 +1,4 @@ <?xml version="1.0"?> <repositories> - <repository changeset_revision="9ed593071db2" 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="bff835d58914" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- a/test-data/log.txt Fri Jan 15 05:06:08 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ - 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.html Tue Jan 19 10:02:28 2016 -0500 @@ -0,0 +1,74 @@ +<!DOCTYPE html> +<HTML lang='en'> +<HEAD> +<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' /> +<title>[W4M] XCMS analysis report</title> +<style> +table { min-width: 500px; border:1px solid #D6B161; border-collapse:collapse;} +th { background: #898989; text-align:left;} +tr { border: 1px solid #000000 } +h2 { color: #FFA212; } +ul li { margin-bottom:10px; } +</style> +</HEAD> +<BODY> +<h1>___ XCMS analysis report using Workflow4Metabolomics ___</h1> +<h2>Samples used:</h2> +<table +<tr><th>sample</th><th>filename</th></tr> +<tr><td> HU_neg_051 </td><td> sacuri//bio2/HU_neg_051.mzXML </td></tr><tr><td> HU_neg_060 </td><td> sacuri//bio2/HU_neg_060.mzXML </td></tr><tr><td> HU_neg_017 </td><td> sacuri//bio/HU_neg_017.mzXML </td></tr><tr><td> HU_neg_028 </td><td> sacuri//bio/HU_neg_028.mzXML </td></tr><tr><td> Blanc04 </td><td> sacuri//blank/Blanc04.mzXML </td></tr><tr><td> Blanc06 </td><td> sacuri//blank/Blanc06.mzXML </td></tr> +</table> +<h2>Function launched:</h2> +<table> +<tr><th>timestamp<br />(ymd-h:m:s)</th><th>function</th><th>argument</th><th>value</th></tr> +<tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td> +<td>nSlaves</td><td>1</td></tr> +<tr><td>method</td><td>matchedFilter</td></tr> +<tr><td>step</td><td>0.01</td></tr> +<tr><td>fwhm</td><td>30</td></tr> +<tr><td rowspan='5'>151221-16:37:00</td><td rowspan='5'>group</td> +<td>method</td><td>density</td></tr> +<tr><td>sleep</td><td>0.001</td></tr> +<tr><td>minfrac</td><td>0.5</td></tr> +<tr><td>bw</td><td>30</td></tr> +<tr><td>mzwid</td><td>0.25</td></tr> +<tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td> +<td>method</td><td>chrom</td></tr> +</table> +<h2>Information about the xcmsSet object:</h2> +<pre> +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 +</pre> +<h2>Citations:</h2> +<ul> +<li>To cite the <b>XCMS</b> package in publications use: +<ul> +<li>Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)</li> +<li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li> +<li>H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)</li> +</ul> +</li> +<li>To cite the <b>CAMERA</b> package in publications use: +<ul> +<li>Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)</li> +</ul> +</li> +<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use: +<ul> +<li>Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813</li> +</ul> +</li> +</ul> +</BODY> +</HTML>