| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy1 (this tool) |
| 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 | 1.9 | package |
| gnuplot | 5.2.3 | package |
| perl | 5.26 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: 1_map_cigar.sam addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
1_map_cigar.sam test.fa name |
| Test-2 |
input: 2_equal_cigar_full_seq.sam addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
2_equal_cigar_full_seq.sam test.fa name |
| Test-3 |
input: 5_insert_cigar.sam addref_cond|addref_select: history insert_size: 0 addref_cond|ref: test.fa |
attributes: name |
5_insert_cigar.sam test.fa name |
| Test-4 |
cond_region|targetregions: 11.stats.targets input: 11_target.sam addref_cond|addref_select: no cond_region|select_region: tab |
attributes: name |
11_target.sam 11.stats.targets name |
| Test-5 |
cond_region|regions_repeat_2|region: ref1:39-56 cond_region|regions_repeat_1|region: ref1:30-46 cond_region|regions_repeat_0|region: ref1:10-24 cond_region|select_region: text input: 11_target.bam addref_cond|addref_select: no |
attributes: name |
11_target.bam name |
| Test-6 |
cond_region|targetregions: 11.stats.targets input: 11_target.sam cond_region|select_region: tab addref_cond|addref_select: no cov_threshold: 4 |
attributes: name |
11_target.sam 11.stats.targets name |
| Test-7 |
cond_region|regions_repeat_2|region: ref1:39-56 cov_threshold: 4 cond_region|regions_repeat_1|region: ref1:30-46 cond_region|regions_repeat_0|region: ref1:10-24 input: 11_target.bam cond_region|select_region: text addref_cond|addref_select: no |
attributes: name |
11_target.bam name |
| Test-8 |
cond_region|targetregions: 12_3reads.bed input: 12_overlaps.bam addref_cond|addref_select: no cond_region|select_region: tab |
attributes: name |
12_overlaps.bam 12_3reads.bed name |
| Test-9 |
cond_region|targetregions: 12_3reads.bed input: 12_overlaps.bam remove_overlaps: True addref_cond|addref_select: no cond_region|select_region: tab |
attributes: name |
12_overlaps.bam 12_3reads.bed name |
| Test-10 |
cond_region|targetregions: 12_2reads.bed input: 12_overlaps.bam addref_cond|addref_select: no cond_region|select_region: tab |
attributes: name |
12_overlaps.bam 12_2reads.bed name |
| Test-11 |
cond_region|targetregions: 12_2reads.bed input: 12_overlaps.bam remove_overlaps: True addref_cond|addref_select: no cond_region|select_region: tab |
attributes: name |
12_overlaps.bam 12_2reads.bed name |
| Test-12 |
input: samtools_stats_input.bam addref_cond|ref: samtools_stats_ref.fa cond_plot|select_plot: yes addref_cond|addref_select: history |
attributes: name |
samtools_stats_input.bam samtools_stats_ref.fa name |
| Test-13 |
split_output_cond|split_output_selector: yes input: samtools_stats_input.bam addref_cond|ref: samtools_stats_ref.fa addref_cond|addref_select: history split_output_cond|generate_tables: ['SN', 'MPC', 'GCC'] |
samtools_stats_input.bam samtools_stats_ref.fa |