Repository revision
4:06dc50b7b711

Repository 'samtools_calmd'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd

CalMD tool metadata
Miscellaneous
CalMD
recalculate MD/NM tags
samtools_calmd
toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2
2.0.2
samtools 2>&1 | grep Version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.3
toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2 (this tool)
toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.1
toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0
samtools_calmd
Requirements (dependencies defined in the <requirements> tag set)
name version type
samtools 1.9 package
Functional tests
name inputs outputs required files
Test-1 reference_source|reference_source_selector: history
input_bam: phiX.bam
reference_source|ref_fasta: phiX.fasta
baq_settings|use_baq:
option_set|option_sets: default
attributes: name
phiX.bam
phiX.fasta
name
Test-2 baq_settings|use_baq: -r
option_set|option_sets: advanced
reference_source|reference_source_selector: history
reference_source|ref_fasta: phiX.fasta
baq_settings|extended_baq: True
option_set|adjust_mq: 50
input_bam: phiX.bam
option_set|change_identical: True
attributes: name
phiX.bam
phiX.fasta
name