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bowtie-build_0.12.7.yaml
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bowtie-build_0.12.7.yaml
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!mobyle/program
name: bowtie-build
version: 0.12.7
title: 'Bowtie: build'
description: The Bowtie index is based on the FM Index of Ferragina and Manzini, which
in turn is based on the Burrows-Wheeler transform. The algorithm used to build
the index is based on the [blockwise algorithm] of Karkkainen.
authors: Langmead B. & Trapnell C.
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparagraph
prompt: Input
name: input
children:
- !mobyle/inputprogramparameter
comment: comma-separated list of files with ref sequences
prompt: 'Upload reference sequence:'
format: '" " + str(value)'
simple: true
argpos: 25
mandatory: true
name: ref_seqfile
command: false
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparagraph
prompt: Options
name: options
children:
- !mobyle/inputprogramparameter
comment: To be queried using bowtie -C.
prompt: Build a colorspace index (-C/--color)
format: ('',' -C ')[value]
simple: true
name: build_colorspace
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Build both letter- and color-space indexes (-B)
format: ('',' -B ')[value]
name: build_both
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: 'Disable use of the difference-cover sample. Suffix sorting becomes
quadratic-time in the worst case (where the worst case is an extremely
repetitive reference). Default: off.'
prompt: Disable diff-cover [algorithm becomes quadratic] (--nodc)
format: ('',' --nodc')[value]
name: disable_diff_cover
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: Do not build the NAME.3.ebwt and NAME.4.ebwt portions of the
index, which contain a bitpacked version of the reference sequences
and are used for paired-end alignment.
prompt: Don't build .3/.4.ebwt (packed reference) portion (-r/--noref)
format: ('',' -r ')[value]
name: donotbuild_3_4_ebwt
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: Build only the NAME.3.ebwt and NAME.4.ebwt portions of the index,
which contain a bitpacked version of the reference sequences and are
used for paired-end alignment.
prompt: Just build .3/.4.ebwt (packed reference) portion (-3/--justref)
format: ('',' -3 ')[value]
name: justbuild_3_4_ebwt
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: 'SA is sampled every 2^offRate BWT chars [default: 5]. To map
alignments back to positions on the reference sequences, it''s necessary
to annotate ("mark") some or all of the Burrows-Wheeler rows with
their corresponding location on the genome. -o/--offrate governs how
many rows get marked: the indexer will mark every 2^<int> rows. Marking
more rows makes reference-position lookups faster, but requires more
memory to hold the annotations at runtime. The default is 5 (every
32nd row is marked; for human genome, annotations occupy about 340
megabytes).'
prompt: 'SA sample offrate: (-o/--offrate)'
format: ("", " -o " + str(value))[value is not None and value != vdef]
name: SA_sampled
command: false
type: !mobyle/integertype {default: 5}
- !mobyle/inputprogramparameter
comment: The ftab is the lookup table used to calculate an initial Burrows-Wheeler
range with respect to the first <int> characters of the query. A larger
<int> yields a larger lookup table but faster query times. The ftab
has size 4^(<int>+1) bytes. The default setting is 10 (ftab is 4MB).
prompt: Number of characters consumed in initial lookup (-t/--ftabchars)
format: ("", " -t " + str(value))[value is not None and value != vdef]
name: num_chars_consumed
command: false
type: !mobyle/integertype {default: 10}
- !mobyle/inputprogramparameter
comment: Convert Ns in the reference sequence to As before building the
index. By default, Ns are simply excluded from the index and bowtie
will not report alignments that overlap them.
prompt: Convert Ns in reference to As (--ntoa)
format: ('',' -n ')[value]
name: convert_ns_ref_as
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: Use <int> as the seed for pseudo-random number generator.
prompt: Seed for random number generator (--seed)
format: ("", " --seed " + str(value))[value is not None]
name: seed_random_number
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparagraph
prompt: Advanced Options
name: AdvancedOptions
children:
- !mobyle/inputprogramparameter
comment: Disable the default behavior whereby bowtie-build automatically
selects values for the --bmax, --dcv and --packed parameters according
to available memory. Instead, user may specify values for those parameters.
If memory is exhausted during indexing, an error message will be printed;
it is up to the user to try new parameters.
prompt: Disable automatic -p/--bmax/--dcv memory-fitting (-a/--noauto)
format: ('',' -a')[value]
name: memory_fitting
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: 'Use a packed (2-bits-per-nucleotide) representation for DNA
strings. This saves memory but makes indexing 2-3 times slower. Default:
off. This is configured automatically by default; use -a/--noauto
to configure manually.'
prompt: Use packed strings internally; slower, uses less memory. (-p/--packed)
format: ('',' -p')[value]
name: packed_strings
precond: {memory_fitting: '1'}
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
comment: The maximum number of suffixes allowed in a block. Allowing more
suffixes per block makes indexing faster, but increases peak memory
usage. Setting this option overrides any previous setting for --bmax,
or --bmaxdivn. Default (in terms of the --bmaxdivn parameter) is --bmaxdivn
4. This is configured automatically by default; use -a/--noauto to
configure manually.
prompt: Max bucket size for blockwise suffix-array builder (--bmax)
format: ('', ' -bmax ' + str(value))[value is not None]
name: max_bucket_size
precond: {memory_fitting: '1'}
command: false
type: !mobyle/integertype {}
- !mobyle/inputprogramparameter
comment: 'The maximum number of suffixes allowed in a block, expressed
as a fraction of the length of the reference. Setting this option
overrides any previous setting for --bmax, or --bmaxdivn. Default:
--bmaxdivn 4. This is configured automatically by default; use -a/--noauto
to configure manually.'
prompt: 'Max bucket size as divisor of ref len [default: 4] (--bmaxdivn)'
format: ( "" , " --bmaxdivn " +str(value) )[value is not None and value
!= vdef]
name: fraction_reference
command: false
type: !mobyle/integertype {default: 4}
- !mobyle/inputprogramparameter
comment: 'Use <int> as the period for the difference-cover sample. A larger
period yields less memory overhead, but may make suffix sorting slower,
especially if repeats are present. Must be a power of 2 no greater
than 4096. Default: 1024. This is configured automatically by default;
use -a/--noauto to configure manually.'
prompt: 'Diff-cover period for blockwise [default: 1024] (--dcv)'
format: ('', ' --dcv ' + str(value))[value is not None and value != vdef]
name: difference_cover
precond: {memory_fitting: '1'}
command: false
type: !mobyle/integertype {default: 1024}
- !mobyle/inputprogramparagraph
prompt: Output
name: output_params
children:
- !mobyle/inputprogramparameter
comment: write Ebwt data to files with this basename
prompt: 'Ebwt file name:'
format: '" " + ( str(vdef) ,str(value) )[value is not None and value !=
vdef]'
simple: true
argpos: 30
mandatory: true
name: ebwt_base
command: false
type: !mobyle/stringtype {default: my_bowtie}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparagraph
prompt: Output
name: output_params
children:
- !mobyle/outputprogramparameter
prompt: Report
filenames: str(ebwt_base) +".1.ebwt"
name: Ebwt_file_one
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Report
filenames: str(ebwt_base) +".2.ebwt"
name: Ebwt_file_two
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Report
filenames: str(ebwt_base) +".3.ebwt"
name: Ebwt_file_three
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Report
filenames: str(ebwt_base) +".4.ebwt"
name: Ebwt_file_four
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Report
filenames: str(ebwt_base) +".rev.1.ebwt"
name: Ebwt_file_rev
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Report
filenames: str(ebwt_base) + ".rev.2.ebwt"
name: Ebwt_file_rev_two
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"bowtie-build.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"bowtie-build.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0227']
topics: ['EDAM_topic:0102', 'EDAM_topic:0196']
command: bowtie-build
env: {}