xcms_fillpeaks: abims_xcms_fillPeaks.xml comparison

comparison 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

comparison

equal deleted inserted replaced

-:cce30b3398e0
+:ee29f0a6e361
-<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>
 </macros>
 <expand macro="requirements"/>
 <expand macro="stdio"/>
 <command><![CDATA[
 @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 $peaklist.intval
+#end if
 @COMMAND_ZIPFILE_LOAD@
 @COMMAND_LOG_EXIT@
 ]]></command>
 <inputs>
-<param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" />
+<param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />
 <param name="method" type="select" label="Filling method" help="[method] See the help section below">
 <option value="chrom" selected="true">chrom</option>
 <option value="MSW" >MSW</option>
 </param>
+<conditional name="peaklist">
+<param name="peaklistBool" type="boolean" label="Get a Peak List" />
+<when value="true">
+<param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
+<param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
+<param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
+<param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
+<option value="into" selected="true">into</option>
+<option value="maxo">maxo</option>
+<option value="intb">intb</option>
+</param>
+</when>
+<when value="false" />
+</conditional>
 <expand macro="zipfile_load"/>
 </inputs>
 <outputs>
 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${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"/>
 <param name="method" value="chrom"/>
 <param name="zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
 </output>
 </test>-->
 <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">
 <assert_contents>
 <has_text text="object with 4 samples" />
 <has_text text="Peaks: 32720 (about 8180 per sample)" />
 <has_text text="Peak Groups: 8157" />
 <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@
 ==============
 Xcms.fillPeaks
 ==============
 -----------
 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.
 According to the type of raw-data there are 2
 **Downstream tools**
 +---------------------------+------------------+-----------------------+
 | 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**
 .. image:: xcms_fillpeaks_workflow.png
 **MSW**
 | "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
-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.
 ---------------------------------------------------
 ---------------
 Working example
 ---------------
 Parameters
 ----------
 | method -> **chrom**
+| Get a Peak List -> **false**
 Output files
 ------------
 | **xset.fillPeaks.RData: RData file**
 ---------------------------------------------------
 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
 **Version 2.0.6 - 04/04/2016**

Mercurial > repos > lecorguille > xcms_fillpeaks

comparison abims_xcms_fillPeaks.xml @ 9:ee29f0a6e361 draft