| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9 (this tool) |
| samtools_view |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| samtools | 1.9 | package |
| gawk | not provided | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: sam_to_bam_in1.sam outtype: bam addref_cond|addref_select: history addref_cond|ref: chr_m.fasta |
attributes: name |
sam_to_bam_in1.sam chr_m.fasta name |
| Test-2 |
input: sam_to_bam_in1.sam outtype: bam addref_cond|addref_select: cached addref_cond|ref: equCab2chrM |
attributes: name |
sam_to_bam_in1.sam name |
| Test-3 |
input: sam_to_bam_noheader_in2.sam outtype: bam addref_cond|addref_select: history addref_cond|ref: chr_m.fasta |
attributes: name |
sam_to_bam_noheader_in2.sam chr_m.fasta name |
| Test-4 |
outtype: cram cond_filter|select_filter: yes input: test.bam cond_filter|cond_region|select_region: no addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.bam test.fa name |
| Test-5 |
input: test.bam outtype: count |
attributes: name |
test.bam name |
| Test-6 |
outtype: cram cond_filter|select_filter: yes input: test.sam cond_filter|cond_region|select_region: no addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.sam test.fa name |
| Test-7 |
cond_filter|cond_region|regions: CHROMOSOME_I outtype: cram cond_filter|select_filter: yes input: test.bam cond_filter|cond_region|select_region: text addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.bam test.fa name |
| Test-8 |
input: bam_to_sam_in1.bam outtype: sam adv_output|header: -h |
attributes: name |
bam_to_sam_in1.bam name |
| Test-9 |
input: bam_to_sam_in1.bam outtype: sam adv_output|header: -H |
attributes: name |
bam_to_sam_in1.bam name |
| Test-10 |
input: bam_to_sam_in1.bam outtype: sam adv_output|header: |
attributes: name |
bam_to_sam_in1.bam name |
| Test-11 |
input: test.cram outtype: bam addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.cram test.fa name |
| Test-12 |
input: test.cram outtype: bam addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.cram test.fa name |
| Test-13 |
input: test.cram outtype: bam addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.cram test.fa name |
| Test-14 |
input: test2.cram outtype: bam cond_filter|cond_region|select_region: no addref_cond|addref_select: cached addref_cond|ref: equCab2chrM |
attributes: name |
test2.cram name |
| Test-15 |
cond_subsample|select_subsample: target outtype: sam cond_subsample|target: 2 input: test.sam |
attributes: name |
test.sam name |
| Test-16 |
input: test.sam outtype: sam cond_subsample|seed: 7 cond_subsample|target: 2 cond_subsample|select_subsample: target |
attributes: name |
test.sam name |
| Test-17 |
input: test.bam outtype: bam cond_subsample|seed: 7 cond_subsample|target: 2 cond_subsample|select_subsample: target |
attributes: name |
test.bam name |
| Test-18 |
input: test.bam cond_subsample|fraction: .2 cond_subsample|seed: 7 outtype: bam cond_subsample|select_subsample: fraction |
attributes: name |
test.bam name |