Mercurial > repos > pieterlukasse > prims_metabolomics
changeset 2:627ddbd15823
using tool_dependencies file
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 24 Oct 2014 16:44:03 +0200 |
| parents | 071a185c2ced |
| children | f8e804258dda |
| files | metams_lcms_annotate.xml repository_dependencies.xml static/images/test/out2/fig_box/001.png static/images/test/out2/fig_box/002.png static/images/test/out2/fig_box/003.png static/images/test/out2/fig_box/004.png static/images/test/out2/fig_box/005.png static/images/test/out2/fig_box/006.png static/images/test/out2/fig_box/007.png static/images/test/out2/fig_box/008.png static/images/test/out2/fig_box/009.png static/images/test/out2/fig_box/010.png static/images/test/outplot1.png static/images/test/outplot2.png static/images/test/outplot3.png static/images/test/outplot4.png tool_dependencies.xml xcms_differential_analysis.r |
| diffstat | 18 files changed, 21 insertions(+), 6 deletions(-) [+] |
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--- a/metams_lcms_annotate.xml Fri Oct 24 12:52:56 2014 +0200 +++ b/metams_lcms_annotate.xml Fri Oct 24 16:44:03 2014 +0200 @@ -1,10 +1,9 @@ <tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate" version="0.0.1"> <description> Runs metaMS process for LC/MS feature grouping and annotation</description> <requirements> - <!-- <requirement type="set_environment">XTANDEM_12_10_01_PATH</requirement>--> <requirement type="package" version="3.1.1">R_bioc_metams</requirement> </requirements> - <command interpreter="/home/lukas007/R/R-3.1.1/bin/Rscript"> + <command interpreter="Rscript"> metaMS_cmd_interface.r $constructed_db $data_files
--- a/repository_dependencies.xml Fri Oct 24 12:52:56 2014 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Required metaMS dependencies."> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="prims_metabolomics_dependencies" owner="pieterlukasse" changeset_revision="62b3f4d6e015" /> -</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Oct 24 16:44:03 2014 +0200 @@ -0,0 +1,17 @@ +<?xml version="1.0"?> +<tool_dependency> +<!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help + --> + <package name="R_bioc_metams" version="3.1.1"> + <repository changeset_revision="71356c62e5cd" name="prims_metabolomics_dependencies" owner=pieterlukasse prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <readme> + This dependency: + Ensures R 3.1.1 is installed. + Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed. + R is a free software environment for statistical computing and graphics. + </readme> + </package> + + +</tool_dependency> \ No newline at end of file
--- a/xcms_differential_analysis.r Fri Oct 24 12:52:56 2014 +0200 +++ b/xcms_differential_analysis.r Fri Oct 24 16:44:03 2014 +0200 @@ -30,6 +30,7 @@ tryCatch( { + library(metaMS) library(xcms) #library("R2HTML") @@ -47,6 +48,8 @@ # report dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE) # setwd(file.path(args.htmlReportFile.files_path)) + file.rename("fig_eic", paste(args.htmlReportFile.files_path, "/fig_eic")) + cat("<html><body><h1>Differential analysis report</h1>", file= args.htmlReportFile) #HTML(reporttab[1:args.topcount,], file= args.htmlReportFile)