Mark this script as executable
Sample paired Illumina HiSeq 2000 reads from SRR639755

$ wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/SRR639755/SRR639755_1.fastq.gz
$ wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/SRR639755/SRR639755_2.fastq.gz
$ ~/picobio/blooming_reads/interlace_fastq.py SRR639755_1.fastq.gz SRR639755_2.fastq.gz | gzip > SRR639755_12.fastq.gz
Interlacing SRR639755_1.fastq.gz and SRR639755_2.fastq.gz
Decompressing SRR639755_1.fastq.gz
Decompressing SRR639755_2.fastq.gz
Interlacing paired FASTQ files to stdout...
Interlacing paired FASTQ files done.

That gives us an interlaced FASTQ file with /1 and /2 naming. Select mitochondria reads:

$ mirabait -f fastq -t fastq NC_010642.fasta SRR639755_12.fastq.gz SRR639755_12_mito
...

The FASTQ file is still sorted, but now a mix of pairs and orphans which some tools hate:

$ ~/pico_galaxy/tools/fastq_paired_unpaired/fastq_paired_unpaired.py sanger SRR639755_12_mito.fastq SRR639755_mito_pairs.fastq SRR639755_mito_orphans.fastq
1965 reads (965 forward, 1000 reverse), 1064 in pairs, 901 as singles
Commented out tests for mira4_de_novo.xml
Simple test for mira4_de_novo.xml (failing)

$ ./run_functional_tests.sh -id mira_4_0_de_novo
...
======================================================================
ERROR: MIRA v4.0 de novo assember ( mira_4_0_de_novo ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
  File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 216, in test_tool
    self.do_it( td, shed_tool_id=shed_tool_id )
  File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 25, in do_it
    data_list = self.__run_tool( testdef )
  File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 106, in __run_tool
    page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs)
  File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 172, in __expand_grouping
    expanded_inputs.update( self.__expand_grouping( { new_prefix : r_value }, declared_inputs, prefix=new_prefix ) )
  File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 159, in __expand_grouping
    if declared_inputs[ value.test_param.name ] == case.value:
KeyError: 'type'
...