I'm trying to incorporate a pipeline tool into our instance of Galaxy. My tool xml uses the <repeat> tag to allow an end-user to enter a number of different fasta/fastq files with information about each of those files so that RSEM can be run on all of the files one at a time with minimal end-user input. My repeat name is Files.

To do this, I need the tool xml to loop over each file and its input parameters to put together a string of input to a perl wrapper (file is in same directory as the xml). I tried using 'enumerate' to do this within the <command> tag with perl as the interpreter, but I'm noticing some some strange behavior with ordering of statements in the tag.

Here's what I have for the tool xml's command tag (aforementioned perl wrapper is run-rsem-1.2.3.pl).

#for $i, $s in enumerate( $Files )

#if $s.input.fastqmatepair.matepair=="single" #/opt/galaxy/galaxy-dist-dev/tools/ngs_rna/run-rsem-1.2.3.pl

--seed-length $s.seedlength --forward-prob $s.fprob -p $s.cpus --single_fastq $s.input.fastqmatepair.singlefastq /opt/galaxy/references/rhesus/rheMac2_ensembl_1.64/RSEM_rheMac2_ensembl_1.64

#if $s.need_bam.yes_bamfile=="yes":

--output-genome-bam

--bamfile $s.bam_res

#end if

#if $s.dostats.stat==1:

--fragment-length-mean $s.dostats.fraglenmean

--fragment-length-sd $s.dostats.fraglensd

#end if

#if $s.dorspd.rspd==1:

--estimate-rspd

--num-rspd-bins $s.dorspd.rspd_num

#end if

#end for

</command>

I must be missing something above because it does not call run-rsem-1.2.3 for each loop iteration. Do I need a break or pause or something within the tag to make this enumerate loop work correctly?

FWIW, to debug I added a print statement between the last '#end if' and the '#end for' above:

'print "loop iteration $i.\n";'

and this correctly resulted in a number of separate calls to run-rsem-1.2.3, but the literal statement "print loop iteration #.\n" was also added as an argument to the perl wrapper that caused it to quit early because too many input arguments were received.