Mercurial > repos > lecorguille > xcms_fillpeaks
diff abims_xcms_fillPeaks.xml @ 9:ee29f0a6e361 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
| author | lecorguille |
|---|---|
| date | Mon, 30 Jan 2017 08:53:48 -0500 |
| parents | cce30b3398e0 |
| children | de0d85537ee3 |
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--- a/abims_xcms_fillPeaks.xml Wed Jul 06 17:43:29 2016 -0400 +++ b/abims_xcms_fillPeaks.xml Mon Jan 30 08:53:48 2017 -0500 @@ -1,6 +1,6 @@ -<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.7"> +<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.8"> - <description>Integrate the signal in the region of that peak group not represented and create a new peak</description> + <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description> <macros> <import>macros.xml</import> @@ -10,36 +10,64 @@ <expand macro="stdio"/> <command><![CDATA[ - @COMMAND_XCMS_SCRIPT@ - xfunction fillPeaks - image $image + @COMMAND_XCMS_SCRIPT@ + xfunction fillPeaks + image $image xsetRdataOutput $xsetRData method $method + #if $peaklist.peaklistBool + variableMetadataOutput $variableMetadata + dataMatrixOutput $dataMatrix + convertRTMinute $peaklist.convertRTMinute + numDigitsMZ $peaklist.numDigitsMZ + numDigitsRT $peaklist.numDigitsRT + intval $peaklist.intval + #end if + @COMMAND_ZIPFILE_LOAD@ - @COMMAND_LOG_EXIT@ - + @COMMAND_LOG_EXIT@ + ]]></command> <inputs> - <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" /> + <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" /> <param name="method" type="select" label="Filling method" help="[method] See the help section below"> <option value="chrom" selected="true">chrom</option> <option value="MSW" >MSW</option> </param> - + <conditional name="peaklist"> + <param name="peaklistBool" type="boolean" label="Get a Peak List" /> + <when value="true"> + <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> + <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> + <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> + <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> + <option value="into" selected="true">into</option> + <option value="maxo">maxo</option> + <option value="intb">intb</option> + </param> + </when> + <when value="false" /> + </conditional> <expand macro="zipfile_load"/> </inputs> <outputs> <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> + <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv"> + <filter>(peaklist['peaklistBool'])</filter> + </data> + <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" > + <filter>(peaklist['peaklistBool'])</filter> + </data> <data name="log" format="txt" label="xset.log.txt" hidden="true" /> </outputs> - + <tests> <!--<test> <param name="image" value="xset.group.retcor.group.RData"/> @@ -59,6 +87,12 @@ <test> <param name="image" value="faahKO.xset.group.retcor.group.RData"/> <param name="method" value="chrom"/> + <conditional name="peaklist"> + <param name="convertRTMinute" value="false" /> + <param name="peaklistBool" value="true" /> + <param name="numDigitsMZ" value="4" /> + <param name="numDigitsRT" value="1" /> + </conditional> <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> <output name="log"> @@ -71,11 +105,13 @@ <has_text text="Sample classes: KO, WT" /> </assert_contents> </output> + <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" /> + <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" /> </test> </tests> <help><![CDATA[ - + @HELP_AUTHORS@ ============== @@ -86,6 +122,7 @@ Description ----------- +**Integrate areas of missing peaks** For each sample, identify peak groups where that sample is not represented. For each of those peak groups, integrate the signal in the region of that peak group and create a new peak. @@ -117,12 +154,12 @@ +---------------------------+------------------+-----------------------+ | Name | Output file | Format | +===========================+==================+=======================+ -|xcms.diffreport | xset.retcor.RData| rdata.xcms.fillpeaks | +|CAMERA.annotate | xset.retcor.RData| rdata.xcms.fillpeaks | +---------------------------+------------------+-----------------------+ -|xcms.annotateDiffreport | xset.retcor.RData| rdata.xcms.fillpeaks | +|xcms.summary | xset.retcor.RData| rdata.xcms.fillpeaks | +---------------------------+------------------+-----------------------+ -The output file **xset.fillpeaks** is an RData file. You can continue your analysis using it in **xcms.diffreport** or **xcms.annotateDiffreport** tool as an next step of the workflow. +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. **General schema of the metabolomic workflow** @@ -159,21 +196,50 @@ | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra. + +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’) + ------------ Output files ------------ xset.fillPeaks.RData : rdata.xcms.fillpeaks format - | Rdata file that will be used in the **xcms.diffreport** or **xcms.annotateDiffreport** step of the workflow. - + | 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 +.. class:: infomark -The output file is an group.RData file. You can continue your analysis using it in **xcms.diffreport** or **xcms.annotateDiffreport** tool. +The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool. - + --------------------------------------------------- --------------- @@ -189,7 +255,8 @@ ---------- | method -> **chrom** - + | Get a Peak List -> **false** + Output files ------------ @@ -202,6 +269,10 @@ Changelog/News -------------- +**Version 2.0.8 - 22/12/2016** + +- IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate + **Version 2.0.7 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0