Question: Use paired collection on wrapper
0
benoit.valot • 0 wrote:
Hi,
I'm try to write a wrapper for a tool that performed subsampling of fastq file. The script is also able to handle paired-end files. My problem is to run on paired collection.
See the input parameter
<conditional name="fastq" >
<param name="choice" type="select" label="Type of reads to subsampling" help="" >
<option value="choice1" selected="true">Single</option>
<option value="choice2">Paired (separated)</option>
<option value="choice3">Paired</option>
</param>
<when value="choice1">
<param name="single" type="data" format="fastq,fastq.gz"
label="Single read file" help="Fastq(gz) format" />
</when>
<when value="choice2">
<param name="forward" type="data" format="fastq,fastq.gz"
label="Forward read file" help="Fastq(gz) format" />
<param name="reverse" type="data" format="fastq,fastq.gz"
label="Reverse read file" help="Fastq(gz) format" />
</when>
<when value="choice3">
<param name="pairedfile" type="data_collection" format="fastq,fastq.gz"
label="Paired of read files" help="Fastq(gz) format"
collection_type="paired" />
</when>
</conditional>
And the command line:
#if $fastq.choice == "choice3"
#if $fastq.pairedfile
-r '${fastq.pairedfile.forward}'
-l '${fastq.pairedfile.reverse}'
#end if
#end if
When I run the wrapper, I got the following message:
Error executing tool: Paired instance must define 'forward' and 'reverse' datasets .
I have look at other tools like bwa-mem that use also paired collection, but don't see where is the problem in my code.
Thanks in advance
Benoit