Question: R tool in galaxy
0
chaimae0azouggarh • 10 wrote:
Hey so i just started using galaxy and i really need your help so i have a simple script in R
library(xlsx)
test<-read.xlsx("Data.xls", sheetIndex=1,colIndex=(c(4:5)),header=TRUE)
attach(datafile)
stem(pC50)
stem(A)
plot(A,pC50)
cor(A,pC50)
cov(A,pC50)
model = lm(pC50 ~ A)
summary(model)
abline(model)
I want to create a galaxy tool with this script so i know i have to create a xml file like this
<tool id="PLS_1" name="PLS">
<command interpreter="Rscript">
PLS.R $value $output
</command>
<inputs>
<param type="tabular" name="value" label="data"/>
</inputs>
<outputs>
<data format="tabular" type="data" name="output" />
</outputs>
</tool>
And i added the xml file in the tool_conf.xml.sample
<section name="R_tools" id="PLS_1">
<tool file="R_tools/PLS.xml" /></section>
But it doesn't work so if you could help me lease i will be so grateful
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modified 2.5 years ago
by
Martin Čech ♦♦ 4.9k
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written
2.5 years ago by
chaimae0azouggarh • 10
So far it looks good. Can you tell me what is the error or what means, it does not work?
When i restart galaxy, my tool doesn't appear in the tool list at left
Can you send me your original tool.xml file? Also try to add your tool into the tool_conf.xml file not the sample file.
The xml file i posted is my original tool.xml. And i tried to add it in the tool_config.xml file but still it doesn't work :(