Question: R tool in galaxy
0
gravatar for chaimae0azouggarh
19 months ago by
chaimae0azouggarh10 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

galaxy tools R • 583 views
ADD COMMENTlink modified 19 months ago by Martin Čech ♦♦ 4.2k • written 19 months ago by chaimae0azouggarh10

So far it looks good. Can you tell me what is the error or what means, it does not work?

ADD REPLYlink written 19 months ago by Bjoern Gruening4.8k

When i restart galaxy, my tool doesn't appear in the tool list at left

ADD REPLYlink written 19 months ago by chaimae0azouggarh10

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.

ADD REPLYlink written 19 months ago by Bjoern Gruening4.8k

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 :(

ADD REPLYlink written 19 months ago by chaimae0azouggarh10
2
gravatar for Martin Čech
19 months ago by
Martin Čech ♦♦ 4.2k
United States
Martin Čech ♦♦ 4.2k wrote:

do not add it to the tool_conf.xml.sample but to the tool_conf.xml

ADD COMMENTlink written 19 months ago by Martin Čech ♦♦ 4.2k

I tried but still it doesn't work

ADD REPLYlink written 19 months ago by chaimae0azouggarh10
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