| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.4.4+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.3.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.1+galaxy0 |
| medaka_variant_pipeline |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| medaka | 1.4.4 | package |
| Additional information about this tool |
## initialize
#if $reference_source.reference_source_selector == 'history':
#if $reference_source.ref_file.ext.endswith(".gz")
gunzip -c '$reference_source.ref_file' > reference.fa &&
#else
ln -f -s '$reference_source.ref_file' reference.fa &&
#end if
#else:
ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
#end if
## link doesn't work
cp '${i}' alignment.bam &&
cp '${i.metadata.bam_index}' alignment.bam.bai &&
## run
medaka_variant
## optional
#if $r:
-r '$r'
#end if
-o results
-s $s
-m $m
-t \${GALAXY_SLOTS:-4}
-p
-b $b
-N $N
-P $P
$U
$S
## required
-i alignment.bam
-f reference.fa
2>&1 | tee '$out_log'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
i: medaka_test.bam reference_source|ref_file: ref_fasta reference_source|reference_source_selector: cached out: ['round_0_hap_mixed_probs_hdf', 'round_0_hap_mixed_unphased_vcf', 'log'] |
name: value name: value name: value |
medaka_test.bam value |