Mercurial > repos > ethevenot > transformation
changeset 3:cc0e9eff0de2 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 60ebb3e8919c09c18f89a5362750ae45ca84d0c2
| author | ethevenot |
|---|---|
| date | Wed, 28 Feb 2018 09:15:47 -0500 |
| parents | 0ccfc3e15710 |
| children | |
| files | build.xml runit/output/information.txt runit/transformation_runtests.R transformation_config.xml transformation_wrapper.R |
| diffstat | 4 files changed, 40 insertions(+), 5 deletions(-) [+] |
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--- a/build.xml Tue Jun 06 11:55:21 2017 -0400 +++ b/build.xml Wed Feb 28 09:15:47 2018 -0500 @@ -36,7 +36,7 @@ <arg value="--conda_prefix"/> <arg value="${conda.dir}"/> <arg value="--galaxy_branch"/> - <arg value="release_16.01"/> + <arg value="release_17.05"/> <arg value="--conda_dependency_resolution"/> <arg value="${tool.xml}"/> </exec>
--- a/runit/output/information.txt Tue Jun 06 11:55:21 2017 -0400 +++ b/runit/output/information.txt Wed Feb 28 09:15:47 2018 -0500 @@ -1,5 +1,5 @@ -Start of the 'Transformation' module: Thu 04 Aug 2016 08:58:11 PM +Start of the 'Transformation' module: Thu 03 Aug 2017 16:41:30 Missing values in the 'dataMatrix': 4 (4%) @@ -7,4 +7,24 @@ 'Square root' transformation -End of the 'Transformation' Galaxy module call: Thu 04 Aug 2016 08:58:11 PM +End of the 'Transformation' Galaxy module call: Thu 03 Aug 2017 16:41:30 + + + +============================================================================ +Additional information about the call: + +1) Parameters: + value +dataMatrix_in "runit/input/dataMatrix.tsv" +dataMatrix_out "runit/output/dataMatrix.tsv" +information "runit/output/information.txt" +method "sqrt" + +2) Session Info: +R version 3.4.1 (2017-06-30) +Main packages: +batch 1.1.4 +Other loaded packages: +compiler 3.4.1 +============================================================================
--- a/transformation_config.xml Tue Jun 06 11:55:21 2017 -0400 +++ b/transformation_config.xml Wed Feb 28 09:15:47 2018 -0500 @@ -2,7 +2,7 @@ <description>Transforms the dataMatrix intensity values</description> <requirements> - <requirement type="package">r-batch</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> <stdio> @@ -78,7 +78,6 @@ | .. image:: transformation_workflowPositionImage.png -:width: 600
--- a/transformation_wrapper.R Tue Jun 06 11:55:21 2017 -0400 +++ b/transformation_wrapper.R Wed Feb 28 09:15:47 2018 -0500 @@ -2,6 +2,22 @@ library(batch) ## parseCommandArgs +# Constants +argv <- commandArgs(trailingOnly = FALSE) +script.path <- sub("--file=","",argv[grep("--file=",argv)]) +prog.name <- basename(script.path) + +# Print help +if (length(grep('-h', argv)) >0) { + cat("Usage:", prog.name, + "dataMatrix_in myDataMatrixInput.tsv", + "method log2|log10|sqrt", + "dataMatrix_out myDataMatrixOutput.tsv", + "information information.txt", + "\n") + quit(status = 0) +} + source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE) base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))