| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.7.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.4.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.3.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/0.11.5 |
| medaka_consensus |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| medaka | 1.7.2 | package |
| Additional information about this tool |
## initialize
ln -s '${bam}' alignment.bam &&
ln -s '${bam.metadata.bam_index}' alignment.bam.bai &&
## Possibly new options bam_chunk and bam_workers. Should we be setting these?
## run
medaka consensus
## optional
--debug ## increase log level
--threads \${GALAXY_SLOTS:-4}
--batch_size $batch_size
#if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed'
--regions
#if $regions_cond.regions_sel == 'custom'
'$regions_cond.custom'
#else if $regions_cond.regions_sel == 'bed'
'$regions_cond.bed'
#end if
#end if
--chunk_len $chunk_len
--chunk_ovlp $chunk_ovlp
--model $model
$check_output
$save_features
#if $RG
--RG '$RG'
#end if
#if $tag_name
--tag_name '$tag_name'
#end if
#if str($tag_value):
--tag_value $tag_value
#end if
$tag_keep_missing
## required
alignment.bam ## bam
'$out_result' ## output
2>&1 | tee '$out_log'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
bam: alignment.bam |
name: value |
alignment.bam value |
| Test-2 |
bam: alignment.bam model: r941_min_fast_g303 batch_size: 99 chunk_len: 9999 chunk_ovlp: 999 check_output: True save_features: True tag_keep_missing: True out: ['result', 'log'] |
name: value name: value |
alignment.bam value |