| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mitobim/mitobim/1.9.1 (this tool) |
| mitobim |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| mitobim | 1.9.1 | package |
| Additional information about this tool |
export LC_ALL=C &&
cp '$readpool' readpool.fastq &&
cp '$reference' reference.$reference.ext &&
MITObim.pl
#if str($start) != ""
--start $start
#end if
#if str($end) != ""
--end $end
#end if
--sample '$sample'
--ref '$ref'
--readpool readpool.fastq
#if $reference.ext == "fasta"
--quick
#else
--maf
#end if
reference.$reference.ext
--kbait $kbait
--platform $platform
$denovo
$pair
$split
$trimreads
$trimoverhang
#if str($mismatch) != ""
--mismatch $mismatch
#end if
#if str($min_cov) != ""
--min_cov $min_cov
#end if
#if str($min_len) != ""
--min_len $min_len
#end if
## does not work with 3rd test --redirect_tmp \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
--NFS_warn_only | tee log.txt &&
if grep -q "^Final assembly result will be written to file:" log.txt; then
cp \$(grep "^Final assembly result will be written to file:" log.txt | cut -d":" -f 2) '$assembly';
else
exit 1;
fi
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reference: initial-mapping-testpool-to-Salpinus-mt_out.maf ref: Salpinus_mt_genome readpool: Tthymallus-150bp-300sd50-interleaved.fastq sample: testpool start: 1 end: 10 |
name: value |
initial-mapping-testpool-to-Salpinus-mt_out.maf Tthymallus-150bp-300sd50-interleaved.fastq value |
| Test-2 |
reference: Salpinus-mt-genome-NC_000861.fasta ref: Salpinus_mt_genome readpool: Tthymallus-150bp-300sd50-interleaved.fastq sample: testpool start: 1 end: 30 |
name: value |
Salpinus-mt-genome-NC_000861.fasta Tthymallus-150bp-300sd50-interleaved.fastq value |
| Test-3 |
reference: Tthymallus-COI-partial-HQ961018.fasta ref: Tthymallus-COI readpool: Tthymallus-150bp-300sd50-interleaved.fastq sample: testpool end: 50 pair: True |
name: value |
Tthymallus-COI-partial-HQ961018.fasta Tthymallus-150bp-300sd50-interleaved.fastq value |