PMCC-BioinformaticsCore / janis-core

Core python modules for Janis Pipeline workflow assistant
GNU General Public License v3.0
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Failed translation of Galaxy tool with output collections containing data with same name #118

Open ddeepwell opened 8 months ago

ddeepwell commented 8 months ago

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?