# HG changeset patch
# User lecorguille
# Date 1492681292 14400
# Node ID 47f9b1fd5ce63cfa25bfd8b74303a2c5bffcea9f
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
diff -r 000000000000 -r 47f9b1fd5ce6 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Apr 20 05:41:32 2017 -0400
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+ r-snow
+ bioconductor-xcms
+ r-batch
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+ bioconductor-xcms
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+ LANG=C Rscript $__tool_directory__/xcms.r
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+
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+ ;
+ return=\$?;
+ mv log.txt '$log';
+ cat '$log';
+ sh -c "exit \$return"
+
+
+
+
+
+ #if $file_load_section.file_load_conditional.file_load_select == "yes":
+ #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
+ #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
+ #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
+
+ singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
+ #else
+ zipfile '$file_load_section.file_load_conditional.input'
+ #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 47f9b1fd5ce6 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Thu Apr 20 05:41:32 2017 -0400
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diff -r 000000000000 -r 47f9b1fd5ce6 static/images/xcms_merge_workflow.png
Binary file static/images/xcms_merge_workflow.png has changed
diff -r 000000000000 -r 47f9b1fd5ce6 test-data/MM14-xset.RData
Binary file test-data/MM14-xset.RData has changed
diff -r 000000000000 -r 47f9b1fd5ce6 test-data/MM8-xset.RData
Binary file test-data/MM8-xset.RData has changed
diff -r 000000000000 -r 47f9b1fd5ce6 test-data/ko15-xset.RData
Binary file test-data/ko15-xset.RData has changed
diff -r 000000000000 -r 47f9b1fd5ce6 test-data/ko16-xset.RData
Binary file test-data/ko16-xset.RData has changed
diff -r 000000000000 -r 47f9b1fd5ce6 test-data/sampleMetadata.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleMetadata.tab Thu Apr 20 05:41:32 2017 -0400
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+wt16 WT
+ko16 KO
+wt15 WT
+ko15 KO
+ko10 KO
+foobar01 FOOBAR
diff -r 000000000000 -r 47f9b1fd5ce6 test-data/wt15-xset.RData
Binary file test-data/wt15-xset.RData has changed
diff -r 000000000000 -r 47f9b1fd5ce6 test-data/wt16-xset.RData
Binary file test-data/wt16-xset.RData has changed
diff -r 000000000000 -r 47f9b1fd5ce6 xcms_merge.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_merge.xml Thu Apr 20 05:41:32 2017 -0400
@@ -0,0 +1,225 @@
+
+ Merge xcms.xcmsSet xset in one to be used by group
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+ macros.xml
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