multiple Rdata output

1

Hi,

I’m developping my own tool in a local Galaxy and I would like to dynamically output multiple Rdata… It works very well with my table in tsv files with the following lines :

<collection name="table_result" type="list" label="result_tables">
     <discover_datasets pattern="__designation_and_ext__" directory="tsv" format="tsv" />
</collection>

I use nearly the same lines for output Rdata :

<collection name="rdata_result" type="list" label="rdata_results">
      <discover_datasets pattern="__designation_and_ext__" directory="rdata" format="rdata"/>
</collection>

But I obtain the following error :
Error in gzfile(file, "wb") : cannot open the connection Calls: save -> save.default -> <Anonymous> -> gzfile In addition: Warning message: In gzfile(file, "wb") : cannot open compressed file './rdata/f4fresult_for_run1_class.Rdata', probable reason 'No such file or directory' Execution halted

So first thing : is it possible to make something like this with as result two collection, one with tables in tsv format and one collection with Rdata ?
Second thing : if yes, how can I do it ?

Thanks a lot !

Julien

2

My bad… I foget to create the directory to save my Rdata files…

So don’t forget : dir.create("my_directory") before runing your save !! Finally it looks like this :

dir.create("rdata",showWarnings=FALSE)
save(pa,file=paste0(args$out_dir, "/rdata/f4fresult_for_",names(final_pa)[o],"_class.Rdata"))
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