Mercurial > repos > lecorguille > xcms_xcmsset
changeset 25:dc4d3e2b9968 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312
| author | lecorguille |
|---|---|
| date | Thu, 02 Mar 2017 08:20:04 -0500 |
| parents | d8915395681f |
| children | 626d3db664ef |
| files | abims_xcms_xcmsSet.xml xcms.r |
| diffstat | 2 files changed, 17 insertions(+), 16 deletions(-) [+] |
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--- a/abims_xcms_xcmsSet.xml Wed Mar 01 16:56:01 2017 -0500 +++ b/abims_xcms_xcmsSet.xml Thu Mar 02 08:20:04 2017 -0500 @@ -163,17 +163,18 @@ </inputs> <outputs> - <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" /> - <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" /> - <data name="ticsRawPdf" format="pdf" label="xset.TICs_raw.pdf" /> - <data name="bpcsRawPdf" format="pdf" label="xset.BPCs_raw.pdf" /> - <data name="log" format="txt" label="xset.log.txt" /> + <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" /> + <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv"> + <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> + </data> + <data name="ticsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" /> + <data name="bpcsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" /> + <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" /> </outputs> <tests> <!--<test> - <param name="inputs|input" value="zip_file" /> - <param name="inputs|zip_file" value="sacuri_dir_root.zip" ftype="zip" /> + <param name="input" value="sacuri_dir_root.zip" ftype="zip" /> <param name="methods|method" value="matchedFilter" /> <param name="methods|step" value="0.01" /> <param name="methods|fwhm" value="4" /> @@ -193,8 +194,7 @@ </output> </test> <test> - <param name="inputs|input" value="zip_file" /> - <param name="inputs|zip_file" value="sacuri_current_root.zip" ftype="zip" /> + <param name="input" value="sacuri_current_root.zip" ftype="zip" /> <param name="methods|method" value="centWave" /> <param name="methods|ppm" value="25" /> <param name="methods|peakwidth" value="20,50" /> @@ -227,8 +227,7 @@ </test> <!-- Passed but disable to save time for Travis" --> <!--<test> - <param name="inputs|input" value="single_file" /> - <param name="inputs|single_file" value="ko15.CDF" ftype="netcdf" /> + <param name="input" value="ko15.CDF" ftype="netcdf" /> <param name="methods|method" value="centWave" /> <param name="methods|ppm" value="25" /> <param name="methods|peakwidth" value="20,50" /> @@ -244,8 +243,7 @@ </output> </test> <test> - <param name="inputs|input" value="single_file" /> - <param name="inputs|single_file" value="ko16.CDF" ftype="netcdf" /> + <param name="input" value="ko16.CDF" ftype="netcdf" /> <param name="methods|method" value="centWave" /> <param name="methods|ppm" value="25" /> <param name="methods|peakwidth" value="20,50" /> @@ -261,8 +259,7 @@ </output> </test> <test> - <param name="inputs|input" value="single_file" /> - <param name="inputs|single_file" value="wt15.CDF" ftype="netcdf" /> + <param name="input" value="wt15.CDF" ftype="netcdf" /> <param name="methods|method" value="centWave" /> <param name="methods|ppm" value="25" /> <param name="methods|peakwidth" value="20,50" />
--- a/xcms.r Wed Mar 01 16:56:01 2017 -0500 +++ b/xcms.r Thu Mar 02 08:20:04 2017 -0500 @@ -161,6 +161,11 @@ cat("\t\tCOMPUTE\n") xset = do.call(thefunction, listArguments) +# check if there are no peaks +if (nrow(peaks(xset)) == 0) { + stop("No peaks were detected. You should review your settings") +} + cat("\n\n") @@ -170,7 +175,6 @@ #transform the files absolute pathways into relative pathways xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths) - print(zipfile) if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) { #Modify the samples names (erase the path)