blob: 9f11cc63ddc312e520b35467f7d0b98362da4711 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
|
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
doc: "samtools view to convert sam format to bam format"
requirements:
DockerRequirement:
dockerPull: quay.io/biocontainers/samtools:1.9--h8571acd_11
baseCommand: [samtools, view]
inputs:
threads:
type: int
label: "Number of additional threads to use"
default: 4
inputBinding:
prefix: -@
output_bam:
type: boolean
label: "output BAM"
default: true
inputBinding:
prefix: -b
output_filename:
type: string
label: "output file name"
default: "aln.bam"
inputBinding:
prefix: -o
input_file:
type: File
label: "input file"
inputBinding:
position: 1
include_header:
type: boolean
label: "include the header in the output"
default: false
inputBinding:
prefix: -h
ignore_previous_version:
type: boolean
label: "ignored for compatibility with previous samtools versions"
default: false
inputBinding:
prefix: -S
filter_alignments:
type: string?
label: "Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0]."
inputBinding:
prefix: -F
skip_alignments:
type: int?
label: "Skip alignments with MAPQ smaller than INT [0]."
inputBinding:
prefix: -q
outputs:
bam:
type: File
outputBinding:
glob: "$(inputs.output_filename)"
stdout: stdout
stderr: stderr
stdout: samtools-view-stdout.log
stderr: samtools-view-stderr.log
|
