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+galaxy3 |
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2 (this tool) |
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 |
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 |
attributes: name |
sam_to_bam_in1.sam name |
Test-2 |
input: sam_to_bam_in1.sam 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 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 |
input: test.cram addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.cram test.fa name |
Test-5 |
input: 1_sort.bam |
attributes: name |
1_sort.bam name |
Test-6 |
input: 1_sort.bam mode|output_options|output_format|oformat: input |
attributes: name |
1_sort.bam name |
Test-7 |
input: 1_sort_read_names.bam |
attributes: name |
1_sort_read_names.bam name |
Test-8 |
input: 1_sort_read_names.bam mode|output_options|output_format|oformat: input |
attributes: name |
1_sort_read_names.bam name |
Test-9 |
input: 1_sort_read_names.bam |
attributes: name |
1_sort_read_names.bam name |
Test-10 |
input: 1_sort_read_names.bam mode|output_options|output_format|oformat: input |
attributes: name |
1_sort_read_names.bam name |
Test-11 |
input: bam_to_sam_in1.bam mode|output_options|output_format|oformat: sam mode|output_options|output_format|with_header: True |
attributes: name |
bam_to_sam_in1.bam name |
Test-12 |
input: bam_to_sam_in1.bam mode|output_options|output_format|oformat: sam mode|outtype: header |
attributes: name |
bam_to_sam_in1.bam name |
Test-13 |
input: bam_to_sam_in1.bam mode|output_options|output_format|oformat: sam mode|output_options|output_format|with_header: False |
attributes: name |
bam_to_sam_in1.bam name |
Test-14 |
input: test.bam mode|output_options|reads_report_type: count mode|outtype: all_reads |
attributes: name |
test.bam name |
Test-15 |
mode|filter_config|cond_region|select_region: no input: test.sam mode|outtype: selected_reads mode|output_options|output_format|oformat: cram addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.sam test.fa name |
Test-16 |
mode|filter_config|cond_region|select_region: no input: test.bam mode|outtype: selected_reads mode|output_options|output_format|oformat: cram addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.bam test.fa name |
Test-17 |
mode|filter_config|cond_region|select_region: no input: test2.cram mode|outtype: selected_reads mode|output_options|output_format|oformat: bam addref_cond|addref_select: cached addref_cond|ref: equCab2chrM |
attributes: name |
test2.cram name |
Test-18 |
mode|filter_config|cond_region|regions: CHROMOSOME_I mode|filter_config|cond_region|select_region: text input: test.bam mode|outtype: selected_reads mode|output_options|output_format|oformat: cram addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.bam test.fa name |
Test-19 |
mode|filter_config|cond_region|regions: CHROMOSOME_I mode|filter_config|cond_region|select_region: text input: test.cram mode|outtype: selected_reads mode|output_options|output_format|oformat: bam addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.cram test.fa name |
Test-20 |
mode|filter_config|cond_region|bedfile: test.bed mode|filter_config|cond_region|select_region: bed input: test.cram mode|outtype: selected_reads mode|output_options|output_format|oformat: bam addref_cond|addref_select: history addref_cond|ref: test.fa |
attributes: name |
test.cram test.bed test.fa name |
Test-21 |
input: test.sam mode|subsample_config|subsampling_mode|select_subsample: target mode|subsample_config|subsampling_mode|target: 2 mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
attributes: name |
test.sam name |
Test-22 |
input: test.sam mode|subsample_config|subsampling_mode|select_subsample: target mode|subsample_config|subsampling_mode|target: 20 mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
attributes: name |
test.sam name |
Test-23 |
input: no_reads.sam mode|subsample_config|subsampling_mode|select_subsample: target mode|subsample_config|subsampling_mode|target: 20 mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
attributes: name |
no_reads.sam name |
Test-24 |
input: no_reads.bam mode|subsample_config|subsampling_mode|select_subsample: target mode|subsample_config|subsampling_mode|target: 20 mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
attributes: name |
no_reads.bam name |
Test-25 |
mode|subsample_config|subsampling_mode|target: 2 mode|subsample_config|subsampling_mode|seed: 7 mode|subsample_config|subsampling_mode|select_subsample: target input: test.sam mode|outtype: selected_reads mode|output_options|output_format|oformat: input |
attributes: name |
test.sam name |
Test-26 |
mode|subsample_config|subsampling_mode|target: 2 mode|subsample_config|subsampling_mode|seed: 7 mode|subsample_config|subsampling_mode|select_subsample: target input: test.bam mode|outtype: selected_reads mode|output_options|output_format|oformat: input |
attributes: name |
test.bam name |
Test-27 |
mode|subsample_config|subsampling_mode|target: 20 mode|subsample_config|subsampling_mode|seed: 7 mode|subsample_config|subsampling_mode|select_subsample: target input: test.bam mode|outtype: selected_reads mode|output_options|output_format|oformat: input |
attributes: name |
test.bam name |
Test-28 |
mode|subsample_config|subsampling_mode|seed: 7 mode|subsample_config|subsampling_mode|select_subsample: fraction input: test.bam mode|outtype: selected_reads mode|output_options|output_format|oformat: input mode|subsample_config|subsampling_mode|factor: 5 |
attributes: name |
test.bam name |
Test-29 |
input: test.bam mode|subsample_config|subsampling_mode|seed: 7 mode|subsample_config|subsampling_mode|select_subsample: fraction mode|outtype: selected_reads mode|output_options|reads_report_type: dropped mode|output_options|output_format|oformat: input mode|subsample_config|subsampling_mode|factor: 1.25 |
attributes: name |
test.bam name |