Repository revision
8:bf328cec6a42

Repository 'samtools_view'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/samtools_view

Samtools view tool metadata
Miscellaneous
- reformat, filter, or subsample SAM, BAM or CRAM
samtools_view
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
1.9+galaxy2
samtools 2>&1 | grep Version
True
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