# HG changeset patch # User lecorguille # Date 1460126020 14400 # Node ID 1ea35f88f3c42932a88e6e581fbf4b70832b388a # Parent dc6b3773f8de6c35ef5ba7c5f45273d7b6b8ee28 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 diff -r dc6b3773f8de -r 1ea35f88f3c4 README.rst --- a/README.rst Fri Apr 08 06:18:24 2016 -0400 +++ b/README.rst Fri Apr 08 10:33:40 2016 -0400 @@ -16,5 +16,8 @@ ----------- Planemo test using conda: failed + Planemo test using source env.sh: passed +Planemo shed_test : passed + diff -r dc6b3773f8de -r 1ea35f88f3c4 planemo_test.sh --- a/planemo_test.sh Fri Apr 08 06:18:24 2016 -0400 +++ b/planemo_test.sh Fri Apr 08 10:33:40 2016 -0400 @@ -10,4 +10,12 @@ planemo test --install_galaxy #All 1 test(s) executed passed. -#abims_xcms_summary[0]: passed \ No newline at end of file +#abims_xcms_summary[0]: passed + + +planemo shed_test --install_galaxy --galaxy_branch "dev" + +#All 2 test(s) executed passed. +#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.0.8[0]: passed +#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.0.8[1]: passed + diff -r dc6b3773f8de -r 1ea35f88f3c4 test-data/summary.html --- a/test-data/summary.html Fri Apr 08 06:18:24 2016 -0400 +++ b/test-data/summary.html Fri Apr 08 10:33:40 2016 -0400 @@ -4,23 +4,26 @@ [W4M] XCMS analysis summary -

_ XCMS analysis summary using Workflow4Metabolomics _

Samples used:

- +

sample	filename
HU_neg_051	sacuri//bio2/HU_neg_051.mzXML
HU_neg_060	sacuri//bio2/HU_neg_060.mzXML
HU_neg_017	sacuri//bio/HU_neg_017.mzXML
HU_neg_028	sacuri//bio/HU_neg_028.mzXML
Blanc04	sacuri//blank/Blanc04.mzXML
Blanc06	sacuri//blank/Blanc06.mzXML
HU_neg_051	sacuri//bio2/HU_neg_051.mzXML
HU_neg_060	sacuri//bio2/HU_neg_060.mzXML
HU_neg_017	sacuri//bio/HU_neg_017.mzXML
HU_neg_028	sacuri//bio/HU_neg_028.mzXML
Blanc04	sacuri//blank/Blanc04.mzXML
Blanc06	sacuri//blank/Blanc06.mzXML

+ +

Function launched:

- - +

timestamp (ymd-h:m:s)	function	argument	value

+ @@ -35,8 +38,10 @@

timestamp^***	function	argument	value
151221-16:20:54	xcmsSet	nSlaves	1
		method	matchedFilter
		151221-16:37:20	fillPeaks	method	chrom

Information about the xcmsSet object:

+
^***timestamp format: yymmdd-hh:mm:ss
+
+Informations about the xcmsSet object:
+ An "xcmsSet" object with 6 samples
 
 Time range: 16.3-1138.9 seconds (0.3-19 minutes)
@@ -49,9 +54,9 @@
                   step = 0.01
 
 Memory usage: 0.421 MB
-
+

Citations:

To cite the XCMS package in publications use:
- Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)
- Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813

___ XCMS analysis summary using Workflow4Metabolomics ___

___ XCMS analysis summary using Workflow4Metabolomics ___

Samples used:

Function launched:

Information about the xcmsSet object:

Informations about the xcmsSet object:

Citations:

_ XCMS analysis summary using Workflow4Metabolomics _

_ XCMS analysis summary using Workflow4Metabolomics _