If I donwload the file it displays no problem.. I checked the whitelist config file and the tool that produced it is listed there. FastQC works fine.
qname_input_sorted.bamand the subsequent tools will require that as input. However, it seems galaxy will not accept this format for upload(?) - i.e. i don't know how to write a test that has this param:
<param name="mapping_output" value="mapped_reads.bam" ftype="qname_input_sorted.bam"/>- the error message I get is: `An invalid option was selected for file_type qname_input_sorted please verify'
qname_input_sorted.bamis for aligners that were run in galaxy and that output the reads in the order that they were read in. This isn't the official "SO:queryname", but
qname_sorted.bamis compatible with
qname_input_sorted.bam, so there will be no additional conversion