Mercurial > repos > lecorguille > xcms_fillpeaks
diff abims_xcms_fillPeaks.xml @ 11:de0d85537ee3 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author | lecorguille |
---|---|
date | Fri, 07 Apr 2017 07:37:05 -0400 |
parents | ee29f0a6e361 |
children | dcb9041cb9ea |
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--- a/abims_xcms_fillPeaks.xml Tue Feb 07 04:05:02 2017 -0500 +++ b/abims_xcms_fillPeaks.xml Fri Apr 07 07:37:05 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.8"> +<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.0"> <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description> @@ -12,22 +12,15 @@ <command><![CDATA[ @COMMAND_XCMS_SCRIPT@ xfunction fillPeaks - image $image + image '$image' - xsetRdataOutput $xsetRData + xsetRdataOutput '$xsetRData' method $method - #if $peaklist.peaklistBool - variableMetadataOutput $variableMetadata - dataMatrixOutput $dataMatrix - convertRTMinute $peaklist.convertRTMinute - numDigitsMZ $peaklist.numDigitsMZ - numDigitsRT $peaklist.numDigitsRT - intval $peaklist.intval - #end if + @COMMAND_PEAKLIST@ - @COMMAND_ZIPFILE_LOAD@ + @COMMAND_FILE_LOAD@ @COMMAND_LOG_EXIT@ @@ -39,32 +32,16 @@ <option value="chrom" selected="true">chrom</option> <option value="MSW" >MSW</option> </param> - <conditional name="peaklist"> - <param name="peaklistBool" type="boolean" label="Get a Peak List" /> - <when value="true"> - <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> - <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> - <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> - <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> - <option value="into" selected="true">into</option> - <option value="maxo">maxo</option> - <option value="intb">intb</option> - </param> - </when> - <when value="false" /> - </conditional> - <expand macro="zipfile_load"/> + + <expand macro="input_peaklist"/> + + <expand macro="input_file_load"/> </inputs> <outputs> <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${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> + <expand macro="output_peaklist" function="fillpeaks" /> <data name="log" format="txt" label="xset.log.txt" hidden="true" /> </outputs> @@ -93,8 +70,30 @@ <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" /> + <expand macro="test_file_load_zip"/> + <output name="log"> + <assert_contents> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" /> + <has_text text="Mass range: 200.1-600 m/z" /> + <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> + <test> + <param name="image" value="faahKO-single.xset.merged.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> + <expand macro="test_file_load_single"/> <output name="log"> <assert_contents> <has_text text="object with 4 samples" /> @@ -269,6 +268,12 @@ Changelog/News -------------- +**Version 2.1.0 - 07/02/2017** + +- IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom) + +- IMPROVEMENT: xcms.fillpeaks can deal with merged individual data + **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 @@ -281,7 +286,6 @@ - TEST: refactoring to pass planemo test using conda dependencies - **Version 2.0.5 - 10/02/2016** - BUGFIX: better management of errors. Datasets remained green although the process failed