Question: Error unavailable variable in Galaxy
0
sharma.ram.h • 0 wrote:
I have very simple Galaxy wrapper for simple R function. The following mergefun.xml file.
<tool id="mergefun" name="mergefun" version="1.0.0">
<description>merge two datasets </description>
<command><![CDATA[
Rscript ~/Documents/galaxy_development/galaxy/tools/mergefun/mergefun.R --input1 $input1 --input2 $input2 --output $output
]]></command>
<inputs>
<param name="input1" type="data"
label="encoded data" help="encoded must be a rda file"
/>
<param name="input2" type="data"
label="encoded data" help=" must be rda file"
/>
</inputs>
<outputs>
<data format="tabular" name = "output" label="output" />
</outputs>
<help>
merge two datasets
</help>
</tool>
Here is simple R script with the function.
mergefun <- function(input1, input2){
in1 <- input1
in2 <- input2
output <- merge(in1, in2)
return(output)
}
output <- mergefun(input1=input1, input2=input2)
write.csv(output, file="merged_data.csv")
When I run I am getting the following error.
An error occurred with this dataset:
Error in mergefun(input1 = input1, input2 = input2) :
object 'input1' not found
Execution halted
It may be simple error as I am new to galaxy. Help appreciated.
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modified 16 months ago
by
Hotz, Hans-Rudolf • 1.8k
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written
16 months ago by
sharma.ram.h • 0
