Mercurial > repos > lecorguille > xcms_fillpeaks
changeset 22:a6938c381d4e draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
| author | lecorguille |
|---|---|
| date | Fri, 10 Feb 2017 11:03:13 -0500 |
| parents | 99094333f540 |
| children | 7e289788d37d |
| files | README.rst abims_xcms_fillPeaks.xml macros.xml |
| diffstat | 3 files changed, 11 insertions(+), 15 deletions(-) [+] |
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--- a/README.rst Thu Feb 09 04:51:18 2017 -0500 +++ b/README.rst Fri Feb 10 11:03:13 2017 -0500 @@ -2,12 +2,10 @@ Changelog/News -------------- -**Version 2.1.1 - 07/02/2017** +**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) -**Version 2.1.0 - 03/02/2017** - - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data **Version 2.0.8 - 22/12/2016**
--- a/abims_xcms_fillPeaks.xml Thu Feb 09 04:51:18 2017 -0500 +++ b/abims_xcms_fillPeaks.xml Fri Feb 10 11:03:13 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.1"> +<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> @@ -12,9 +12,9 @@ <command><![CDATA[ @COMMAND_XCMS_SCRIPT@ xfunction fillPeaks - image $image + image '$image' - xsetRdataOutput $xsetRData + xsetRdataOutput '$xsetRData' method $method @@ -272,12 +272,10 @@ Changelog/News -------------- -**Version 2.1.1 - 07/02/2017** +**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) -**Version 2.1.0 - 03/02/2017** - - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data **Version 2.0.8 - 22/12/2016**
--- a/macros.xml Thu Feb 09 04:51:18 2017 -0500 +++ b/macros.xml Fri Feb 10 11:03:13 2017 -0500 @@ -25,8 +25,8 @@ <token name="@COMMAND_LOG_EXIT@"> ; return=\$?; - mv log.txt $log; - cat $log; + mv log.txt '$log'; + cat '$log'; sh -c "exit \$return" </token> @@ -35,12 +35,12 @@ <token name="@COMMAND_FILE_LOAD@"> #if $file_load_conditional.file_load_select == "yes": #if $file_load_conditional.inputs.input == "zip_file": - zipfile $file_load_conditional.inputs.zip_file + zipfile '$file_load_conditional.inputs.zip_file' #else #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] ) #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] ) - singlefile_galaxyPath $singlefile_galaxyPath singlefile_sampleName $singlefile_sampleName + singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' #end if #end if </token> @@ -72,8 +72,8 @@ <token name="@COMMAND_PEAKLIST@"> #if $peaklist.peaklistBool - variableMetadataOutput $variableMetadata - dataMatrixOutput $dataMatrix + variableMetadataOutput '$variableMetadata' + dataMatrixOutput '$dataMatrix' convertRTMinute $peaklist.convertRTMinute numDigitsMZ $peaklist.numDigitsMZ numDigitsRT $peaklist.numDigitsRT