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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
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## Application
Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_alpha_diversity.py (version : 3.1)
Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_alpha_diversity.py --varExp EnvType --rdata res/14-phylo_import.Rdata --alpha-measures Observed Chao1 Shannon --alpha-out res/16-phylo_alpha_div.tsv --html res/16-phylo_alpha_div.html --log-file res/16-phylo_alpha_div.log

########################################################################################################
# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)"
[1] "Rmarkdown version:  1.10"
[1] "Phyloseq version:  1.19.1")
Command:
	Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_alpha_diversity.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/16-phylo_alpha_div.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', measures='Observed,Chao1,Shannon', varExp='EnvType',fileAlpha='/home/maria/workspace/git/FROGS/FROGS_master/test/res/16-phylo_alpha_div.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620149.26_24026_rmarkdown.stderr

Execution:
	start: 08 Feb 2019 11:02:32
	end:   08 Feb 2019 11:02:57

## Application
Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_alpha_diversity.py (version : 3.1)
Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_alpha_diversity.py --varExp EnvType --rdata res/14-phylo_import.Rdata --alpha-measures Observed Chao1 Shannon --alpha-out res/16-phylo_alpha_div.tsv --html res/16-phylo_alpha_div.html --log-file res/16-phylo_alpha_div.log

########################################################################################################
# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)"
[1] "Rmarkdown version:  1.10"
[1] "Phyloseq version:  1.19.1")
Command:
	Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_alpha_diversity.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/16-phylo_alpha_div.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', measures='Observed,Chao1,Shannon', varExp='EnvType',fileAlpha='/home/maria/workspace/git/FROGS/FROGS_master/test/res/16-phylo_alpha_div.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623031.57_25477_rmarkdown.stderr

Execution:
	start: 08 Feb 2019 11:50:35
	end:   08 Feb 2019 11:50:58