Mercurial > repos > lecorguille > xcms_retcor
changeset 5:d0efb2c07577 draft
planemo upload
| author | lecorguille |
|---|---|
| date | Mon, 22 Feb 2016 17:05:29 -0500 |
| parents | dc31e4459a11 |
| children | fcd93f47dcbf |
| files | Makefile README.rst abims_xcms_retcor.xml planemo.sh test-data/log.txt |
| diffstat | 5 files changed, 69 insertions(+), 52 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Mon Feb 22 17:05:29 2016 -0500 @@ -0,0 +1,23 @@ +# USAGE: make [install|clean] + +# -------- VARIABLE -------- + +OBJ=xcms_retcor.tgz +DEP=abims_xcms_retcor.xml tool_dependencies.xml repository_dependencies.xml static test-data + + +# ------------------------ + +all: $(OBJ) + +$(OBJ): $(DEP) + tar --exclude=".svn" -zchf $@ $^ + +# ------------------------ + +install: $(OBJ) + mv *.tgz ~ + +clean: + rm *.tgz +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Feb 22 17:05:29 2016 -0500 @@ -0,0 +1,21 @@ + +Changelog/News +-------------- + +**Version 2.0.5 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- BUGFIX: some pdf remained empty even when the process succeed + +- UPDATE: refactoring of internal management of inputs/outputs + +- UPDATE: refactoring to feed the new report tool + + +**Version 2.0.2 - 02/06/2015** + +- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. + +- IMPROVEMENT: parameter labels have changed to facilitate their reading. +
--- a/abims_xcms_retcor.xml Tue Jan 19 16:35:24 2016 -0500 +++ b/abims_xcms_retcor.xml Mon Feb 22 17:05:29 2016 -0500 @@ -291,6 +291,30 @@ .. image:: xcms_retcor.png + +--------------------------------------------------- + +Changelog/News +-------------- + +**Version 2.0.5 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- BUGFIX: some pdf remained empty even when the process succeed + +- UPDATE: refactoring of internal management of inputs/outputs + +- UPDATE: refactoring to feed the new report tool + + +**Version 2.0.2 - 02/06/2015** + +- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. + +- IMPROVEMENT: parameter labels have changed to facilitate their reading. + + ]]></help> <citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo.sh Mon Feb 22 17:05:29 2016 -0500 @@ -0,0 +1,1 @@ +planemo shed_init -f --name=xcms_retcor --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - Correct retention time from different samples" --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\nRetention Time Correction using retcor function from xcms R package\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics"
--- a/test-data/log.txt Tue Jan 19 16:35:24 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ - PACKAGE INFO -parallel 3.1.2 -BiocGenerics 0.14.0 -Biobase 2.28.0 -Rcpp 0.12.0 -mzR 2.2.2 -xcms 1.44.0 -snow 0.3.13 -batch 1.1.4 - - - ARGUMENTS INFO -image test-data/xset.group.RData -xfunction retcor -xsetRdataOutput test-data/xset.group.retcor.RData -ticspdf xset.group.retcor.TICs_corrected.pdf -bicspdf xset.group.retcor.BPCs_corrected.pdf -rplotspdf xset.group.retcor.Rplots.pdf -method obiwarp -profStep 1 -zipfile test-data/sacuri.zip - - - INFILE PROCESSING INFO - - - ARGUMENTS PROCESSING INFO - - - MAIN PROCESSING INFO -center sample: HU_neg_060 -Processing: HU_neg_028 HU_neg_051 HU_neg_017 HU_neg_034 Blanc09 Blanc06 Blanc12 Blanc04 -null device - 1 - - - XSET OBJECT INFO -An "xcmsSet" object with 9 samples - -Time range: 0.7-1139.9 seconds (0-19 minutes) -Mass range: 50.0019-999.9863 m/z -Peaks: 135846 (about 15094 per sample) -Peak Groups: 0 -Sample classes: bio, blank - -Profile settings: method = bin - step = 0.01 - -Memory usage: 13.8 MB - - - DONE