# HG changeset patch # User lecorguille # Date 1460110704 14400 # Node ID dc6b3773f8de6c35ef5ba7c5f45273d7b6b8ee28 # Parent 78fb71c535d0f6c90d85fd861b5965faf0375420 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c diff -r 78fb71c535d0 -r dc6b3773f8de README.rst --- a/README.rst Tue Mar 22 17:00:35 2016 -0400 +++ b/README.rst Fri Apr 08 06:18:24 2016 -0400 @@ -2,7 +2,19 @@ Changelog/News -------------- +**Version 1.0.1 - 04/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + + **Version 1.0.0 - 10/02/2016** - NEW: Create a summary of XCMS analysis + +Test Status +----------- + +Planemo test using conda: failed +Planemo test using source env.sh: passed + diff -r 78fb71c535d0 -r dc6b3773f8de abims_xcms_summary.xml --- a/abims_xcms_summary.xml Tue Mar 22 17:00:35 2016 -0400 +++ b/abims_xcms_summary.xml Fri Apr 08 06:18:24 2016 -0400 @@ -1,20 +1,21 @@ - + Create a summary of XCMS analysis - + + + macros.xml + + R - Rscript - xcms - camera + bioconductor-camera + r-batch - - - + - - + @@ -34,20 +35,14 @@ - - + + - - 10.1093/bioinformatics/btu813 - + diff -r 78fb71c535d0 -r dc6b3773f8de macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Apr 08 06:18:24 2016 -0400 @@ -0,0 +1,51 @@ + + + + + R + r-snow + bioconductor-xcms + r-batch + + + + + + + + + + LANG=C Rscript $__tool_directory__/xcms.r + + + + ; + return=\$?; + mv log.txt $log; + cat $log; + sh -c "exit \$return" + + + +.. 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 78fb71c535d0 -r dc6b3773f8de planemo.sh --- a/planemo.sh Tue Mar 22 17:00:35 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -planemo shed_init -f --name=xcms_summary --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - HTML Summary for XCMS analysis" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nThis tool create a HTML summary of XCMS analysis" --category="Metabolomics" diff -r 78fb71c535d0 -r dc6b3773f8de planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_test.sh Fri Apr 08 06:18:24 2016 -0400 @@ -0,0 +1,13 @@ +planemo conda_init +planemo conda_install . +#Linking packages ... +#Error: ERROR: placeholder '/root/miniconda3/envs/_build_placehold_placehold_placehold_placehold_placehold_p' too short in: ncurses-5.9-4 + + + +source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh +source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-camera/1.22.0/lecorguille/package_bioconductor_camera_1_22_0/22cec61d66c2/env.sh +planemo test --install_galaxy + +#All 1 test(s) executed passed. +#abims_xcms_summary[0]: passed \ No newline at end of file diff -r 78fb71c535d0 -r dc6b3773f8de test-data/summary.html --- a/test-data/summary.html Tue Mar 22 17:00:35 2016 -0400 +++ b/test-data/summary.html Fri Apr 08 06:18:24 2016 -0400 @@ -4,26 +4,23 @@ [W4M] XCMS analysis summary -

___ XCMS analysis summary using Workflow4Metabolomics ___

-
+

___ XCMS analysis summary using Workflow4Metabolomics ___

Samples used:

-
+
- +
samplefilename
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***functionargumentvalue
+ @@ -38,10 +35,8 @@
timestamp
(ymd-h:m:s)
functionargumentvalue
151221-16:20:54xcmsSet nSlaves1
methodmatchedFilter
151221-16:37:20fillPeaks methodchrom
-
***timestamp format: yymmdd-hh:mm:ss -
-

Informations about the xcmsSet object:

-
+

Information about the xcmsSet object:

+
 An "xcmsSet" object with 6 samples
 
 Time range: 16.3-1138.9 seconds (0.3-19 minutes)
@@ -54,9 +49,9 @@
                   step = 0.01
 
 Memory usage: 0.421 MB
-
+

Citations:

-
+ diff -r 78fb71c535d0 -r dc6b3773f8de tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 22 17:00:35 2016 -0400 +++ b/tool_dependencies.xml Fri Apr 08 06:18:24 2016 -0400 @@ -3,7 +3,7 @@ - + diff -r 78fb71c535d0 -r dc6b3773f8de xcms_summary.r --- a/xcms_summary.r Tue Mar 22 17:00:35 2016 -0400 +++ b/xcms_summary.r Fri Apr 08 06:18:24 2016 -0400 @@ -1,5 +1,5 @@ -#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file -# version="0.1.0" +#!/usr/bin/env Rscript +# version="1.0.0" #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM