Hi,
Is there a way to pipe in the same xml wrapper two scripts in different languages, the output of the first script becoming the input of the second ? I know that the spirit of galaxy would be to make a workflow, but the intermediate output in the present case is not interesting at all and may confuse the user.
I am testing something like : <command interpreter="python">plotter.py $input $minsize $maxsize $factor $output</command> <command interpreter="bash">r_wrapper.sh $Rplotter</command> <inputs> <param name="input" type="data" format="tabular" label="Compute Plot table from this bowtie standard output"/> <param name="minsize" type="integer" size="3" value="20" label="Min size of small RNA to plot" help="'20' = 20 nucleotides"/> <param name="maxsize" type="integer" size="3" value="22" label="Max size of small RNA to plot" help="'22' = 22 nucleotides"/> <param name="factor" type="float" size="6" value="1.00" label="Normalization factort" help="leave at 1.00 for no normalization"/> <param name="title" type="text" size="15" value="Main Title" label="Main Titles"/> <param name="xlabel" type="text" size="15" value="Coordinates (nt)" label="x axis label"/> <param name="ylabel" type="text" size="15" value="Normalized number of reads" label="y axis label"/> <param name="yrange" type="integer" size="6" value="400" label="y axis range"/>
</inputs> <configfiles> <configfile name="Rplotter"> ## Setup R error handling to go to stderr options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) tab = read.delim("${output}", header=TRUE) ## Open output PDF file pdf( "${outputFinal}" )
#determining y and x axis ranges MAXcoord = max(tab[,1]) + 100 MINcoord = min(tab[,1]) MMAX = ${yrange} plot(tab[,1], tab[,2], type="h", xaxt="n", xlim=c(MINcoord , MAXcoord), ylim=c(-MMAX , MMAX), frame.plot=FALSE, lwd=2, las=2, xlab= "${xlabel}", ylab="${ylabel}", main = "${title}") lines(tab[,1], tab[,3], type="h", lwd=2) axis(1)
## Close the PDF file devname = dev.off() </configfile> </configfiles>
<outputs> <data name="output" format="tabular" label= "Data Frame"/> <data name="outputFinal" format="pdf" label= "PDF plot"/> </outputs>
but the second script output is empty. I suspect that the second script is launched when the output of the first script is not available yet.
Thanks for the help
Chris