# 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 @@
+
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+ r-snow
+ bioconductor-xcms
+ r-batch
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+ bioconductor-xcms
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+ LANG=C Rscript $__tool_directory__/xcms.r
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+ ;
+ return=\$?;
+ mv log.txt $log;
+ cat $log;
+ sh -c "exit \$return"
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+
+
+ #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 ] )
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+ singlefile_galaxyPath $singlefile_galaxyPath singlefile_sampleName $singlefile_sampleName
+ #end if
+ #end if
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+ #if $peaklist.peaklistBool
+ variableMetadataOutput $variableMetadata
+ dataMatrixOutput $dataMatrix
+ convertRTMinute $peaklist.convertRTMinute
+ numDigitsMZ $peaklist.numDigitsMZ
+ numDigitsRT $peaklist.numDigitsRT
+ intval $peaklist.intval
+ #end if
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+ (peaklist['peaklistBool'])
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+ (peaklist['peaklistBool'])
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+.. 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
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diff -r 000000000000 -r 9063eaae5112 test-data/ko16-xset.RData
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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
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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
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+ Merge xcms.xcmsSet xset in one to be used by group
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+ macros.xml
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