Empty table output

Question: Empty table output

2.7 years ago by

hortowe • 10 wrote:

Hi all,

I'm attempting to run an Rscript that outputs a few tables, but can't get that to work. I then created a super simple test script that just prints a table, but the output is empty. When I go to the tool on the galaxy interface, I run it and everything works fine, but when I click on the output in my history, it says it is empty. One potential issue is that the path to the output file is a directory outside of the galaxy install...not sure if there is a specific place within galaxy that I should point to.

Script:

foo <- matrix(seq(1:100), nrow=10, ncol=10)

out.file <- "/path/to/output/test.txt"

write.table(foo, sep="\t", file=out.file, row.names=F)

xml:

<tool id="test" name="Testing" version="0.1">

<description>Print a table.</description>

<command>R --vanilla --file=/path/to/galaxy/tools/my_tools/test.R --args $out </command>

<inputs> </inputs>

<outputs>

<data name="out" format="tabular" label="Test output"/>

</outputs>

</tool>

Here is what I see on my galaxy interface:

galaxy • 681 views

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modified 2.7 years ago by Hotz, Hans-Rudolf • 1.8k • written 2.7 years ago by hortowe • 10

2.7 years ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k wrote:

looks like you are mixing up two things..... what do you want to achieve? Do you want the output as a Galaxy history item or do you want to store the data outside of the Galaxy tree?

Normally, you want the data as a Galaxy history item (and I assume this is what you want, since you 'complain' about the empty output). Hence, you have to read the arguments (i.e "$out") in your R script.

Your example R script will then look like:

foo <- matrix(seq(1:100), nrow=10, ncol=10)

out.file <- commandArgs(trailingOnly = TRUE)

write.table(foo, sep="\t", file=out.file, row.names=F)

Be careful, this works only as long as you have just one argument. If you have more than one argument 'commandArgs' will give you a character vector of those arguments (see also '?commandArgs')

Hope this helps, Hans-Rudolf

ADD COMMENT • link written 2.7 years ago by Hotz, Hans-Rudolf • 1.8k

Hanz,

That worked like a charm, thank you! I am looking to have more than one argument eventually, but I believe I saw a few questions and maybe a wiki entry about it that I will check out. Thanks again.

ADD REPLY • link written 2.7 years ago by hortowe • 10

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