| Next changeset 1:da716e2937f2 (2016-02-22) |
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Commit message:
planemo upload |
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added:
Makefile abims_xcms_retcor.xml planemo.sh repository_dependencies.xml static/images/xcms_retcor.png static/images/xcms_retcor_workflow.png 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 tool_dependencies.xml |
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| diff -r 000000000000 -r 19c1d2598eb5 Makefile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Fri Aug 07 10:57:36 2015 -0400 |
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| @@ -0,0 +1,23 @@ +# USAGE: make [install|clean] + +# -------- VARIABLE -------- + +OBJ=xcms_retcor.tgz +DEP=abims_xcms_retcor.xml tool_dependencies.xml repository_dependencies.xml static test-data + + +# ------------------------ + +all: $(OBJ) + +$(OBJ): $(DEP) + tar --exclude=".svn" -zchf $@ $^ + +# ------------------------ + +install: $(OBJ) + mv *.tgz ~ + +clean: + rm *.tgz + |
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| diff -r 000000000000 -r 19c1d2598eb5 abims_xcms_retcor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_retcor.xml Fri Aug 07 10:57:36 2015 -0400 |
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| b'@@ -0,0 +1,276 @@\n+<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.2">\n+\n+ <description>Retention Time Correction using retcor function from xcms R package </description>\n+\n+ <requirements>\n+ <requirement type="package" version="3.1.2">R</requirement>\n+ <requirement type="binary">Rscript</requirement>\n+ <requirement type="package" version="1.44.0">xcms</requirement>\n+ <requirement type="package" version="2.1">xcms_w4m_script</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <exit_code range="1:" level="fatal" />\n+ </stdio>\n+\n+ <command>\n+ xcms.r \n+ image $image xfunction retcor method $methods.method\n+ #if $methods.method == "obiwarp":\n+ profStep $methods.profStep\n+ #else\n+ smooth $methods.smooth\n+ extra $methods.extra\n+ missing $methods.missing\n+ #if $methods.options.option == "show":\n+ span $methods.options.span\n+ family $methods.options.family\n+ plottype $methods.options.plottype\n+ #end if\n+ #end if\n+ && ( mv retcor.RData $xsetRData;\n+ mv TICs_corrected.pdf $ticsCorPdf ;\n+ mv BPCs_corrected.pdf $bpcsCorPdf ;\n+ mv Rplots.pdf $rplotsPdf 2> /dev/null);\n+ cat xset.log; \n+ \n+ </command>\n+\n+ <inputs>\n+ <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.)" />\n+ <conditional name="methods">\n+ <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >\n+ <option value="obiwarp" >obiwarp</option>\n+ <option value="peakgroups" selected="peakgroups">peakgroups</option>\n+ </param>\n+ <when value="obiwarp">\n+ <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" />\n+ </when> \n+ <when value="peakgroups"> \n+ <param name="smooth" type="select" label="Smooth method" help="[smooth] either \'loess\xe2\x80\x99 for non-linear alignment or \xe2\x80\x98linear\xe2\x80\x99 for linear alignment" >\n+ <option value="loess">loess</option>\n+ <option value="linear">linear</option>\n+ </param>\n+ <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />\n+ <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" />\n+ <conditional name="options">\n+ <param name="option" type="select" label="Advanced options">\n+ <option value="show">show</option>\n+ <option value="hide" selected="true">hide</option>\n+ </param>\n+ <when value="show">\n+ <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>\n+ \n+ <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">\n+ <option value="gaussian" selected="true">gaussian</option>\n+ <option value="symmetric">symmetric</option>\n+ </param>\n+\n+ <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'..b'== ==========\n+\n+\n+**Downstream tools**\n+\n++---------------------------+------------------+--------+\n+| Name | Output file | Format |\n++===========================+==================+========+\n+|xcms.group | xset.retcor.RData| RData |\n++---------------------------+------------------+--------+\n+\n+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.\n+\n+\n+**General schema of the metabolomic workflow**\n+\n+.. image:: xcms_retcor_workflow.png\n+\n+\n+-----------\n+Input files\n+-----------\n+\n++---------------------------+----------------------+\n+| Parameter : num + label | Format |\n++===========================+======================+\n+| 1 : RData file | rdata.xcms.group |\n++---------------------------+----------------------+\n+\n+\n+----------\n+Parameters\n+----------\n+\n+Method\n+------\n+\n+**peakgroups**\n+\n+ | 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.)\n+ | 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.\n+ | However, it is possible to enable outlier detection and removal by setting the **family** argument to **symmetric**.\n+\n+**obiwarp**\n+\n+ | 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.\n+ | 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.**\n+\n+\n+------------\n+Output files\n+------------\n+\n+xset.group.retcor.TICs_corrected.pdf\n+\n+ | "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step.\n+\n+xset.group.retcor.BPCs_corrected.pdf\n+\n+ | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step\n+\n+xset.group.retcor.RData: rdata.xcms.retcor format\n+\n+ | Rdata file that will be necessary in the **xcms.group** step of the workflow.\n+ \n+ \n+------\n+\n+.. class:: infomark \n+\n+The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool.\n+\n+ \n+---------------------------------------------------\n+\n+---------------\n+Working example\n+---------------\n+\n+Input files\n+-----------\n+\n+ | RData file -> **xset.group.RData**\n+\n+Parameters\n+----------\n+\n+ | Method: -> **peakgroups**\n+ | smooth: -> **loess**\n+ | extra: -> **1**\n+ | missing -> **1**\n+ | Advanced options: -> **show**\n+ | span -> **0.2**\n+ | family -> **gaussian**\n+ | plottype -> **deviation**\n+ \n+\n+Output files\n+------------\n+\n+ | **1) xset.group.retcor.RData: RData file**\n+\n+ | **2) Example of an xset.group.retcor.TICs_corrected pdf file**\n+\n+.. image:: xcms_retcor.png\n+\n+ </help>\n+\n+ <citations>\n+ <citation type="doi">10.1021/ac051437y</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+ </citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r 19c1d2598eb5 planemo.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo.sh Fri Aug 07 10:57:36 2015 -0400 |
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| @@ -0,0 +1,1 @@ +planemo shed_init -f --name=xcms_retcor --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - Correct retention time from different samples" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nRetention Time Correction using retcor function from xcms R package\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics" |
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| diff -r 000000000000 -r 19c1d2598eb5 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Aug 07 10:57:36 2015 -0400 |
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| @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="12afb0ecb55f" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d64562a4ebb3" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r 19c1d2598eb5 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Aug 07 10:57:36 2015 -0400 |
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| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.1.2"> + <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="xcms" version="1.44.0"> + <repository changeset_revision="a1c3fc774157" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="xcms_w4m_script" version="2.1"> + <repository changeset_revision="c94c8ef520c8" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
