I'm attempting to translate the Galaxy Tool Trimmomatic, but the translation fails because of a duplicate values error on the output collections. Here is the final error message:
Exception: There are 2 duplicate values in trimmomatic's outputs: out_forward1, out_reverse1
The relevant tool output definition (shown below) shows that the duplicate values seem to come from data within separate collections.
<collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
<filter>readtype['single_or_paired'] == "collection"</filter>
<data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
<data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
</collection>
<collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
<filter>readtype['single_or_paired'] == "collection"</filter>
<data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
<data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
</collection>
Is there an issue with the parsing of a Galaxy tool of this form?
I'm attempting to translate the Galaxy Tool Trimmomatic, but the translation fails because of a duplicate values error on the output collections. Here is the final error message:
Exception: There are 2 duplicate values in trimmomatic's outputs: out_forward1, out_reverse1
The relevant tool output definition (shown below) shows that the duplicate values seem to come from data within separate collections.
Is there an issue with the parsing of a Galaxy tool of this form?