| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13 |
| toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2 |
| 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 |
name: value |
sam_to_bam_in1.sam value |
| Test-2 |
input: sam_to_bam_in1.sam addref_cond|ref: equCab2chrM addref_cond|addref_select: cached |
name: value |
sam_to_bam_in1.sam value |
| Test-3 |
input: sam_to_bam_noheader_in2.sam addref_cond|ref: chr_m.fasta addref_cond|addref_select: history |
name: value |
sam_to_bam_noheader_in2.sam chr_m.fasta value |
| Test-4 |
input: test.cram addref_cond|ref: test.fa addref_cond|addref_select: history |
name: value |
test.cram test.fa value |
| Test-5 |
input: 1_sort.bam |
name: value |
1_sort.bam value |
| Test-6 |
input: 1_sort.bam mode|output_options|output_format|oformat: input |
name: value |
1_sort.bam value |
| Test-7 |
input: 1_sort_read_names.bam |
name: value |
1_sort_read_names.bam value |
| Test-8 |
input: 1_sort_read_names.bam mode|output_options|output_format|oformat: input |
name: value |
1_sort_read_names.bam value |
| Test-9 |
input: 1_sort_read_names.bam |
name: value |
1_sort_read_names.bam value |
| Test-10 |
input: 1_sort_read_names.bam mode|output_options|output_format|oformat: input |
name: value |
1_sort_read_names.bam value |
| Test-11 |
input: bam_to_sam_in1.bam mode|output_options|output_format|with_header: True mode|output_options|output_format|oformat: sam |
name: value |
bam_to_sam_in1.bam value |
| Test-12 |
input: bam_to_sam_in1.bam mode|output_options|output_format|oformat: sam mode|outtype: header |
name: value |
bam_to_sam_in1.bam value |
| Test-13 |
input: bam_to_sam_in1.bam mode|output_options|output_format|with_header: False mode|output_options|output_format|oformat: sam |
name: value |
bam_to_sam_in1.bam value |
| Test-14 |
input: test.bam mode|output_options|reads_report_type: count mode|outtype: all_reads |
name: value |
test.bam value |
| Test-15 |
input: test.sam mode|filter_config|cond_region|select_region: no mode|output_options|output_format|oformat: cram mode|outtype: selected_reads addref_cond|ref: test.fa addref_cond|addref_select: history |
name: value |
test.sam test.fa value |
| Test-16 |
input: test.bam mode|filter_config|cond_region|select_region: no mode|output_options|output_format|oformat: cram mode|outtype: selected_reads addref_cond|ref: test.fa addref_cond|addref_select: history |
name: value |
test.bam test.fa value |
| Test-17 |
input: test2.cram mode|filter_config|cond_region|select_region: no mode|output_options|output_format|oformat: bam mode|outtype: selected_reads addref_cond|ref: equCab2chrM addref_cond|addref_select: cached |
name: value |
test2.cram value |
| Test-18 |
input: test.bam mode|filter_config|cond_region|regions: CHROMOSOME_I mode|filter_config|cond_region|select_region: text mode|output_options|output_format|oformat: cram mode|outtype: selected_reads addref_cond|ref: test.fa addref_cond|addref_select: history |
name: value |
test.bam test.fa value |
| Test-19 |
input: test.cram mode|filter_config|cond_region|regions: CHROMOSOME_I mode|filter_config|cond_region|select_region: text mode|output_options|output_format|oformat: bam mode|outtype: selected_reads addref_cond|ref: test.fa addref_cond|addref_select: history |
name: value |
test.cram test.fa value |
| Test-20 |
input: test.cram mode|filter_config|cond_region|bedfile: test.bed mode|filter_config|cond_region|select_region: bed mode|output_options|output_format|oformat: bam mode|outtype: selected_reads addref_cond|ref: test.fa addref_cond|addref_select: history |
name: value |
test.cram test.bed test.fa value |
| Test-21 |
input: test.sam mode|subsample_config|subsampling_mode|target: 2 mode|subsample_config|subsampling_mode|select_subsample: target mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
name: value |
test.sam value |
| Test-22 |
input: test.sam mode|subsample_config|subsampling_mode|target: 20 mode|subsample_config|subsampling_mode|select_subsample: target mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
name: value |
test.sam value |
| Test-23 |
input: no_reads.sam mode|subsample_config|subsampling_mode|target: 20 mode|subsample_config|subsampling_mode|select_subsample: target mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
name: value |
no_reads.sam value |
| Test-24 |
input: no_reads.bam mode|subsample_config|subsampling_mode|target: 20 mode|subsample_config|subsampling_mode|select_subsample: target mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
name: value |
no_reads.bam value |
| Test-25 |
input: test.sam mode|subsample_config|subsampling_mode|target: 2 mode|subsample_config|subsampling_mode|seed: 7 mode|subsample_config|subsampling_mode|select_subsample: target mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
name: value |
test.sam value |
| Test-26 |
input: test.bam mode|subsample_config|subsampling_mode|target: 2 mode|subsample_config|subsampling_mode|seed: 7 mode|subsample_config|subsampling_mode|select_subsample: target mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
name: value |
test.bam value |
| Test-27 |
input: test.bam mode|subsample_config|subsampling_mode|target: 20 mode|subsample_config|subsampling_mode|seed: 7 mode|subsample_config|subsampling_mode|select_subsample: target mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
name: value |
test.bam value |
| Test-28 |
input: test.bam mode|subsample_config|subsampling_mode|factor: 5 mode|subsample_config|subsampling_mode|seed: 7 mode|subsample_config|subsampling_mode|select_subsample: fraction mode|output_options|output_format|oformat: input mode|outtype: selected_reads |
name: value |
test.bam value |
| Test-29 |
input: test.bam mode|subsample_config|subsampling_mode|factor: 1.25 mode|subsample_config|subsampling_mode|seed: 7 mode|subsample_config|subsampling_mode|select_subsample: fraction mode|output_options|output_format|oformat: input mode|output_options|reads_report_type: dropped mode|outtype: selected_reads |
name: value |
test.bam value |