Repository revision
10:3a0efe14891f

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

Samtools stats tool metadata
Miscellaneous
generate statistics for BAM dataset
samtools_stats
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4
2.0.4
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_stats/samtools_stats/2.0.5
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4 (this tool)
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.3
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy1
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0
samtools_stats
Requirements (dependencies defined in the <requirements> tag set)
name version type
samtools 1.13 package
Functional tests
name inputs outputs required files
Test-1 input: 1_map_cigar.sam
addref_cond|ref: test.fa
addref_cond|addref_select: history
name: value
1_map_cigar.sam
test.fa
value
Test-2 input: 2_equal_cigar_full_seq.sam
addref_cond|ref: test.fa
addref_cond|addref_select: history
name: value
2_equal_cigar_full_seq.sam
test.fa
value
Test-3 input: 5_insert_cigar.sam
insert_size: 0
addref_cond|ref: test.fa
addref_cond|addref_select: history
name: value
5_insert_cigar.sam
test.fa
value
Test-4 input: 11_target.sam
addref_cond|addref_select: no
cond_region|targetregions: 11.stats.targets
cond_region|select_region: tab
name: value
11_target.sam
11.stats.targets
value
Test-5 input: 11_target.bam
addref_cond|addref_select: no
cond_region|regions_repeat_0|region: ref1:10-24
cond_region|regions_repeat_1|region: ref1:30-46
cond_region|regions_repeat_2|region: ref1:39-56
cond_region|select_region: text
name: value
11_target.bam
value
Test-6 input: 11_target.sam
addref_cond|addref_select: no
cond_region|targetregions: 11.stats.targets
cond_region|select_region: tab
cov_threshold: 4
name: value
11_target.sam
11.stats.targets
value
Test-7 input: 11_target.bam
addref_cond|addref_select: no
cond_region|regions_repeat_0|region: ref1:10-24
cond_region|regions_repeat_1|region: ref1:30-46
cond_region|regions_repeat_2|region: ref1:39-56
cond_region|select_region: text
cov_threshold: 4
name: value
11_target.bam
value
Test-8 input: 12_overlaps.bam
addref_cond|addref_select: no
cond_region|targetregions: 12_3reads.bed
cond_region|select_region: tab
name: value
12_overlaps.bam
12_3reads.bed
value
Test-9 input: 12_overlaps.bam
addref_cond|addref_select: no
cond_region|targetregions: 12_3reads.bed
cond_region|select_region: tab
remove_overlaps: True
name: value
12_overlaps.bam
12_3reads.bed
value
Test-10 input: 12_overlaps.bam
addref_cond|addref_select: no
cond_region|targetregions: 12_2reads.bed
cond_region|select_region: tab
name: value
12_overlaps.bam
12_2reads.bed
value
Test-11 input: 12_overlaps.bam
addref_cond|addref_select: no
cond_region|targetregions: 12_2reads.bed
cond_region|select_region: tab
remove_overlaps: True
name: value
12_overlaps.bam
12_2reads.bed
value
Test-12 input: samtools_stats_input.bam
addref_cond|ref: samtools_stats_ref.fa
addref_cond|addref_select: history
name: value
samtools_stats_input.bam
samtools_stats_ref.fa
value
Test-13 input: samtools_stats_input.bam
split_output_cond|generate_tables: ['SN', 'MPC', 'GCC']
split_output_cond|split_output_selector: yes
addref_cond|ref: samtools_stats_ref.fa
addref_cond|addref_select: history
samtools_stats_input.bam
samtools_stats_ref.fa