# HG changeset patch # User lecorguille # Date 1486553238 18000 # Node ID 9063eaae51129a86805d6fdd64de985315c80f45 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty diff -r 000000000000 -r 9063eaae5112 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Feb 08 06:27:18 2017 -0500 @@ -0,0 +1,132 @@ + + + + + r-snow + bioconductor-xcms + r-batch + + + + + bioconductor-xcms + + + + + + + + + + LANG=C Rscript $__tool_directory__/xcms.r + + + + ; + return=\$?; + mv log.txt $log; + cat $log; + sh -c "exit \$return" + + + + + + #if $file_load_conditional.file_load_select == "yes": + #if $file_load_conditional.inputs.input == "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 + #end if + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #if $peaklist.peaklistBool + variableMetadataOutput $variableMetadata + dataMatrixOutput $dataMatrix + convertRTMinute $peaklist.convertRTMinute + numDigitsMZ $peaklist.numDigitsMZ + numDigitsRT $peaklist.numDigitsRT + intval $peaklist.intval + #end if + + + + + + + + + + + + + + + + + + + + + + (peaklist['peaklistBool']) + + + (peaklist['peaklistBool']) + + + + +.. class:: infomark + +**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu + +.. class:: infomark + +**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + +--------------------------------------------------- + + + + + + + 10.1021/ac051437y + 10.1093/bioinformatics/btu813 + + + diff -r 000000000000 -r 9063eaae5112 test-data/MM14-xset.RData Binary file test-data/MM14-xset.RData has changed diff -r 000000000000 -r 9063eaae5112 test-data/MM8-xset.RData Binary file test-data/MM8-xset.RData has changed diff -r 000000000000 -r 9063eaae5112 test-data/ko15-xset.RData Binary file test-data/ko15-xset.RData has changed diff -r 000000000000 -r 9063eaae5112 test-data/ko16-xset.RData Binary file test-data/ko16-xset.RData has changed diff -r 000000000000 -r 9063eaae5112 test-data/sampleMetadata.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tab Wed Feb 08 06:27:18 2017 -0500 @@ -0,0 +1,6 @@ +wt16 WT +ko16 KO +wt15 WT +ko15 KO +ko10 KO +foobar01 FOOBAR diff -r 000000000000 -r 9063eaae5112 test-data/wt15-xset.RData Binary file test-data/wt15-xset.RData has changed diff -r 000000000000 -r 9063eaae5112 test-data/wt16-xset.RData Binary file test-data/wt16-xset.RData has changed diff -r 000000000000 -r 9063eaae5112 xcms_merge.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_merge.xml Wed Feb 08 06:27:18 2017 -0500 @@ -0,0 +1,224 @@ + + Merge xcms.xcmsSet xset in one to be used by group + + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +