| 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+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13 (this tool) |
| 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 |
| 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 | 1.13 | package |
| gawk | not provided | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: in_test_1.sam |
name: value |
in_test_1.sam value |
| Test-2 |
input: in_test_1.sam addref_cond|ref: equCab2chrM addref_cond|addref_select: cached |
name: value |
in_test_1.sam value |
| Test-3 |
input: in_test_3.sam addref_cond|ref: chr_m.fasta addref_cond|addref_select: history |
name: value |
in_test_3.sam chr_m.fasta value |
| Test-4 |
input: in_test_4.cram addref_cond|ref: test.fa addref_cond|addref_select: history |
name: value |
in_test_4.cram test.fa value |
| Test-5 |
input: in_test_5.bam |
name: value |
in_test_5.bam value |
| Test-6 |
input: in_test_5.bam mode|output_options|output_format|oformat: input |
name: value |
in_test_5.bam value |
| Test-7 |
input: in_test_7.bam |
name: value |
in_test_7.bam value |
| Test-8 |
input: in_test_7.bam mode|output_options|output_format|oformat: input |
name: value |
in_test_7.bam value |
| Test-9 |
input: in_test_7.bam |
name: value |
in_test_7.bam value |
| Test-10 |
input: in_test_7.bam mode|output_options|output_format|oformat: input |
name: value |
in_test_7.bam value |
| Test-11 |
input: in_test_11.bam mode|output_options|output_format|with_header: True mode|output_options|output_format|oformat: sam |
name: value |
in_test_11.bam value |
| Test-12 |
input: in_test_11.bam mode|output_options|output_format|oformat: sam mode|outtype: header |
name: value |
in_test_11.bam value |
| Test-13 |
input: in_test_11.bam mode|output_options|output_format|with_header: False mode|output_options|output_format|oformat: sam |
name: value |
in_test_11.bam value |
| Test-14 |
input: in_test_14.bam mode|output_options|reads_report_type: count mode|outtype: all_reads |
name: value |
in_test_14.bam value |
| Test-15 |
input: in_test_15.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 |
in_test_15.sam test.fa value |
| Test-16 |
input: in_test_14.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 |
in_test_14.bam test.fa value |
| Test-17 |
input: in_test_17.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 |
in_test_17.cram value |
| Test-18 |
input: in_test_14.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 |
in_test_14.bam test.fa value |
| Test-19 |
input: test_15.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_15.cram test.fa value |
| Test-20 |
input: test_15.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_15.cram test.bed test.fa value |
| Test-21 |
input: in_test_15.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 |
in_test_15.sam value |
| Test-22 |
input: in_test_15.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 |
in_test_15.sam value |
| Test-23 |
input: in_test_23.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 |
in_test_23.sam value |
| Test-24 |
input: in_test_24.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 |
in_test_24.bam value |
| Test-25 |
input: in_test_15.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 |
in_test_15.sam value |
| Test-26 |
input: in_test_14.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 |
in_test_14.bam value |
| Test-27 |
input: in_test_14.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 |
in_test_14.bam value |
| Test-28 |
input: in_test_14.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 |
in_test_14.bam value |
| Test-29 |
input: in_test_14.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 |
in_test_14.bam value |
| Test-30 |
input: in_test_30.bam mode|filter_config|tag: XS:-18 mode|output_options|output_format|oformat: bam mode|outtype: selected_reads |
name: value |
in_test_30.bam value |
| Test-31 |
input: in_test_30.bam mode|filter_config|qname_file: readnames.txt mode|output_options|output_format|oformat: bam mode|outtype: selected_reads |
name: value |
in_test_30.bam readnames.txt value |