Mercurial > repos > siwaa > carboseq_s
changeset 9:2af4b1e46d90 draft
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/0376c8590ba7b401f91db9be50a49e03cf5044fb/toos/CarboSeqSimulator commit 0376c8590ba7b401f91db9be50a49e03cf5044fb-dirty"
| author | siwaa |
|---|---|
| date | Tue, 17 Sep 2024 10:41:39 +0000 |
| parents | 5fdc9d0c223b |
| children | 20886bc40659 |
| files | carboseqSimulator.xml carboseqUnsplit.R carboseqUnsplit.xml |
| diffstat | 3 files changed, 14 insertions(+), 28 deletions(-) [+] |
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--- a/carboseqSimulator.xml Fri Aug 30 13:29:48 2024 +0000 +++ b/carboseqSimulator.xml Tue Sep 17 10:41:39 2024 +0000 @@ -1,7 +1,7 @@ -<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.14"> +<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.15"> <description>To run the CarboSeq simulator</description> <requirements> - <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwaa</container> + <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container> </requirements> <command detect_errors="exit_code"><![CDATA[ (env | grep DOCKER_IMAGE) && @@ -32,7 +32,7 @@ <param name="semantifier" value="modeltoolbox_sem_local" /> <output name="output" ftype="rdata" > <assert_contents> - <has_size value="38654" negate="false" /> + <has_size value="1202" negate="false" /> <has_size value="0" negate="true" /> </assert_contents> </output> @@ -42,7 +42,7 @@ <param name="semantifier" value="modeltoolbox_sem_remote" /> <output name="output" ftype="rdata" > <assert_contents> - <has_size value="38654" negate="false" /> + <has_size value="1202" negate="false" /> <has_size value="0" negate="true" /> </assert_contents> </output>
--- a/carboseqUnsplit.R Fri Aug 30 13:29:48 2024 +0000 +++ b/carboseqUnsplit.R Tue Sep 17 10:41:39 2024 +0000 @@ -1,23 +1,13 @@ - -resU <- data.frame() +library(data.table) +library(dplyr) -listFiles <- list.files('./inputs') - -# restoring the order first - -orderVec <- c() +resU <- data.table(); -for (i in list.files('./inputs')) { - load(file.path('.', 'inputs',i)) - orderVec <- c(orderVec, res$ID[1]); - rm(res) - } +listFiles <- commandArgs(trailingOnly = TRUE) -listFilesReOrder <- listFiles[order(orderVec)] - -for (i in listFilesReOrder) { - load(file.path('.', 'inputs',i)) - resU<- rbind(resU, res); +for (i in listFiles) { + load(i) + resU<- dplyr::bind_rows(resU, res); rm(res) }
--- a/carboseqUnsplit.xml Fri Aug 30 13:29:48 2024 +0000 +++ b/carboseqUnsplit.xml Tue Sep 17 10:41:39 2024 +0000 @@ -1,14 +1,10 @@ -<tool id="CarboSeqUnsplit" name="CarboSeqUnsplit" version="1.0.3"> +<tool id="CarboSeqUnsplit" name="CarboSeqUnsplit" version="1.0.4"> <description>To unsplit CarboSeq results</description> <requirements> - <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwa</container> + <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/record-projet-carboseq/carboseq_r_4_siwaa</container> </requirements> <command detect_errors="exit_code"><![CDATA[ - mkdir inputs && - #for $input in $inputList - cp $input inputs && - #end for - Rscript $__tool_directory__/carboseqUnsplit.R && + Rscript $__tool_directory__/carboseqUnsplit.R #for $input in $inputList# $input #end for# && cp csopraRes.Rdata $output ]]> </command>