Miscellaneous |
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 |