bowtie_0.12.7.yaml

!mobyle/program
name: bowtie
version: 0.12.7
title: Bowtie
description: Bowtie is an ultrafast and memory-efficient alignment of short DNA sequences
    to the reference genome sequence.
authors: Langmead B. & Trapnell C.
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        prompt: Input
        name: input_args
        children:
        - !mobyle/inputprogramparameter
            comment: '-If the query input files are FASTQ (usually having extension
                .fq or .fastq), this is the default.If the query input files are FASTA
                files (usually having extension .fa, .mfa, .fna or similar), all quality
                values are assumed to be 40 on the Phred quality scale.If the query
                input files are Raw files (one sequence per line, without quality
                values or names), all quality values are assumed to be 40 on the Phred
                quality scale.If the query input file is a comma-separated list of
                files containing a mix of unpaired and paired-end reads in Tab-delimited
                format, quality values can be expressed using any of the scales supported
                in FASTQ files. Tab-delimited format is a 1-read-per-line format where
                unpaired reads consist of a read name, sequence and quality string
                each separated by tabs. A paired-end read consists of a read name,
                sequence of the #1 mate, quality values of the #1 mate, sequence of
                the #2 mate, and quality values of the #2 mate separated by tabs.
                Q Reads may be a mix of different lengths and paired-end and unpaired
                reads may be intermingled in the same file. If - is specified, bowtie
                will read the Tab-delimited reads from the "standard in" filehandle.'
            prompt: 'Data format (-f or -q or -C or -r or --12) :'
            format: ("", " " + str(value))[value != vdef]
            simple: true
            mandatory: true
            name: input_data_format
            command: false
            type: !mobyle/stringtype
                default: -q
                options:
                - {label: FASTQ (-q), value: -q}
                - {label: FASTA (-f), value: -f}
                - {label: CSFASTA (-C), value: -C}
                - {label: raw (-r), value: -r}
                - {label: tab-delimited (--12), value: --12}
        - !mobyle/inputprogramparameter
            prompt: Select a reference genome
            format: (""," " + str( value ))[value != vdef and value != "upload"]
            simple: true
            argpos: 100
            mandatory: true
            name: opt_selrefgen
            precond:
                input_data_format: {'#ne': -C}
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choose a database, value: 'null'}
        - !mobyle/inputprogramparameter
            prompt: Upload a custom reference genome
            format: (""," " + str( value ))[value is not None]
            simple: true
            argpos: 100
            name: custom_ref_genome
            precond:
                '#and':
                - {opt_selrefgen: upload}
                -   input_data_format: {'#ne': -C}
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: If uploading a custom genome, please load a single zip file containing
                the index and the FASTA file.
            prompt: 'Select a reference genome:'
            format: (""," " + str( value ))[value != vdef and value != "upload"]
            simple: true
            argpos: 50
            mandatory: true
            name: color_ref_genome
            precond: {input_data_format: -C}
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choose a database, value: 'null'}
        - !mobyle/inputprogramparameter
            prompt: Upload a custom colorspace reference genome
            format: (""," " + str( value ))[value is not None]
            simple: true
            argpos: 50
            name: custom_color_genome
            precond:
                '#and':
                - {color_ref_genome: upload}
                - {input_data_format: -C}
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: The flag is required on the command line when running colorspace.
            prompt: required flag
            format: ('', ' -f')[color_ref_genome is not None]
            name: colorspace_flag
            command: false
            hidden: true
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            prompt: Data type
            simple: true
            mandatory: true
            name: input_data_type
            command: false
            type: !mobyle/stringtype
                default: single_end
                options:
                - {label: Single-end, value: single_end}
                - {label: Paired-end, value: paired_end}
                - {label: Mixed, value: mixed}
        - !mobyle/inputprogramparameter {prompt: The tab-delimited (--12) format is
                the only format for the Mixed (mix of unpaired and paired-end reads)
                data format, simple: true, name: help_string, command: false}
        - !mobyle/inputprogramparameter
            prompt: 'Quality score type (only valid for FASTQ format):'
            format: ("", " " + str(value))[value != vdef]
            name: input_quality_score_type
            precond: {input_data_format: -q}
            command: false
            type: !mobyle/stringtype
                default: --phred33-quals
                options:
                - {label: 'Phred +33 (Sanger, Illumina 1.8+)', value: --phred33-quals}
                - {label: Phred +64 (Illumina 1.3-1.7) or Solexa (Illumina > 1.3),
                    value: --phred64-quals}
                - {label: Solexa (Illumina < 1.3), value: --solexa-quals}
        - !mobyle/inputprogramparameter
            comment: Represent quality values in the read input file as space-separated
                ASCII integers.Default is to represent quality values as ASCII characters.
            prompt: Specify qualities as space separated integers? (--integer-quals)
            format: ("", " --integer-quals")[value]
            name: quality_scores_integer
            precond: {input_data_format: -q}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Please upload a zip or tar.gz file containing all the input data
            prompt: Input data
            format: (" ", " -1 ")[input_data_type == "paired_end"] + str(value)
            simple: true
            argpos: 101
            mandatory: true
            name: first_files
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: Currently multiple files upload is not supported. This will be
                implemented in future
            prompt: Second File (for "paired-end" library)
            format: (" ", " -2 ")[input_data_type == "paired_end"] + str(value)
            simple: true
            argpos: 102
            mandatory: true
            name: second_files
            precond: {input_data_type: paired_end}
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: List of files containing quality values for corresponding unpaired
                CSFASTA reads.
            prompt: QV file
            format: (" -Q ", " --Q1 ")[input_data_type == "paired_end"] + str(value)
            simple: true
            argpos: 110
            mandatory: true
            name: first_qual_file
            precond: {input_data_format: -C}
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: 'File containing quality values for corresponding CSFASTA #2
                mates.'
            prompt: Second QV file (for "paired-end" library)
            format: ("", " --Q2 ")[input_data_type == "paired_end"] + str(value)
            simple: true
            argpos: 111
            mandatory: true
            name: second_qual_file
            precond:
                '#and':
                - {input_data_format: -C}
                - {input_data_type: paired_end}
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            prompt: Skip the first n reads (-s or --skip)
            format: ("", " -s " + str(value))[value is not None and value != vdef
                ]
            name: skip_first_reads
            command: false
            type: !mobyle/integertype {default: 0}
        - !mobyle/inputprogramparameter
            comment: -1 for off
            prompt: Only align the first n reads (-u or --qupto)
            format: ("", " -u " + str(value))[value is not None and value != vdef
                ]
            name: align_only_first_reads
            command: false
            type: !mobyle/integertype {default: -1}
        - !mobyle/inputprogramparameter
            prompt: Trim n bases from high-quality (left) end of each read before
                alignment (-5 or trim5)
            format: ("", " -5 " + str(value))[value is not None and value != vdef
                ]
            name: trim5
            command: false
            type: !mobyle/integertype {default: 0}
        - !mobyle/inputprogramparameter
            prompt: Trim n bases from low-quality (right) end of each read before
                alignment (-3 or --trim3)
            format: ("", " -3 " + str(value))[value is not None and value != vdef
                ]
            name: trim3
            command: false
            type: !mobyle/integertype {default: 0}
    - !mobyle/inputprogramparagraph
        prompt: Alignment Options
        name: alignment_para
        children:
        - !mobyle/inputprogramparameter
            prompt: Use seed options?
            name: use_seed_opts
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: 'Seed Options:'
            name: seed_opts_text
            precond: {use_seed_opts: '1'}
            command: false
        - !mobyle/inputprogramparameter
            comment: Maximum number of mismatches permitted in the "seed", i.e. the
                first L base pairs of the read (where L is set with -l/--seedlen).
                This may be 0, 1, 2 or 3 and the default is 2. This option is mutually
                exclusive with the -v option.
            prompt: 'Maximum number of mismatches permitted in the seed: (-n or --seedmms)'
            format: ("", " -n " + str(value))[value is not None and value != vdef
                ]
            name: seed_opts_max_mismatches
            precond: {use_seed_opts: '1'}
            command: false
            type: !mobyle/integertype {default: 2}
        - !mobyle/inputprogramparameter
            comment: Maximum permitted total of quality values at all mismatched read
                positions throughout the entire alignment, not just in the "seed".
                The default is 70. Like Maq, bowtie rounds quality values to the nearest
                10 and saturates at 30; rounding can be disabled with --nomaqround.
            prompt: 'Maximum permitted total of quality values: (-e)'
            format: ("", " -e " + str(value))[value is not None and value != vdef
                ]
            name: max_quality_across_align
            precond: {use_seed_opts: '1'}
            command: false
            type: !mobyle/integertype {default: 70}
        - !mobyle/inputprogramparameter
            prompt: 'Seed length: (-l or --seedlen)'
            format: ("", " -l " + str(value))[value is not None and value != vdef
                ]
            name: seed_opts_length
            precond: {use_seed_opts: '1'}
            command: false
            type: !mobyle/integertype {default: 28}
        - !mobyle/inputprogramparameter
            comment: Maq accepts quality values in the Phred quality scale, but internally
                rounds values to the nearest 10, with a maximum of 30. By default,
                bowtie also rounds this way. --nomaqround prevents this rounding in
                bowtie.
            prompt: Prevent rounding? (-nomaqround)
            format: ("", " --nomaqround" )[value]
            name: prevent_quality_score_rounding
            precond: {use_seed_opts: '1'}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: 'If not using seed options, specify v:'
            name: v_option_text
            precond: {use_seed_opts: '0'}
            command: false
        - !mobyle/inputprogramparameter
            prompt: 'Number of mismatches allowed: (-v)'
            format: ("", " -v " + str(value))[value is not None]
            name: mismatches
            precond: {use_seed_opts: '0'}
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: If --nofw is specified, bowtie will not attempt to align against
                the forward reference strand. If --norc is specified, bowtie will
                not attempt to align against the reverse-complement reference strand.
                For paired-end reads using --fr or --rf modes, --nofw and --norc apply
                to the forward and reverse-complement pair orientations. I.e. specifying
                --nofw and --fr will only find reads in the R/F orientation where
                mate 2 occurs upstream of mate 1 with respect to the forward reference
                strand.
            prompt: 'Reference strand alignment options: (-nofw, -norc)'
            format: ("", " " + str(value))[value is not None and value != vdef ]
            name: reference_strand_options
            command: false
            type: !mobyle/stringtype
                default: both
                options:
                - {label: Both forward and reverse strand, value: both}
                - {label: Not forward strand, value: --nofw}
                - {label: Not reverse strand, value: --norc}
        - !mobyle/inputprogramparameter
            comment: 'The maximum number of backtracks permitted when aligning a read
                in -n 2 or -n 3 mode (default: 125 without --best, 800 with --best).
                A "backtrack" is the introduction of a speculative substitution into
                the alignment. Without this limit, the default parameters will sometimes
                require that bowtie try 100s or 1,000s of backtracks to align a read,
                especially if the read has many low-quality bases and/or has no valid
                alignments, slowing bowtie down significantly. However, this limit
                may cause some valid alignments to be missed. Higher limits yield
                greater sensitivity at the expensive of longer running times.'
            prompt: 'Maximum number of backtracks: (--maxbts)'
            format: ("", " --maxbts " + str(value))[value is not None and value !=
                vdef ]
            name: max_backtracks
            precond:
                '#and':
                - {use_seed_opts: '1'}
                -   seed_opts_max_mismatches: {'#gte': '2'}
                - {best_opts: '1'}
            command: false
            type: !mobyle/integertype {default: 125}
        - !mobyle/inputprogramparameter
            comment: Try as hard as possible to find valid alignments when they exist,
                including paired-end alignments. This is equivalent to specifying
                very high values for the --maxbts and --pairtries options. This mode
                is generally much slower than the default settings, but can be useful
                for certain problems. This mode is slower when (a) the reference is
                very repetitive, (b) the reads are low quality, or (c) not many reads
                have valid alignments.
            prompt: Try as hard as possible to find valid alignments? (-y or --tryhard)
            format: (""," -y ")[value]
            name: try_hard
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: 'The number of megabytes of memory a given thread is given to
                store path descriptors in --best mode. Best-first search must keep
                track of many paths at once to ensure it is always extending the path
                with the lowest cumulative cost. Bowtie tries to minimize the memory
                impact of the descriptors, but they can still grow very large in some
                cases. If you receive an error message saying that chunk memory has
                been exhausted in --best mode, try adjusting this parameter up to
                dedicate more memory to the descriptors. Default: 64.'
            prompt: 'Number of megabytes of memory a given thread is given to store
                path descriptors: (--chunkmbs)'
            format: ("", " --chunkmbs " + str(value))[value is not None and value
                != vdef ]
            name: chunk_megabytes
            command: false
            type: !mobyle/integertype {default: 64}
    - !mobyle/inputprogramparagraph
        prompt: Paired-end Options
        name: paired_end_para
        precond: {input_data_type: paired_end}
        children:
        - !mobyle/inputprogramparameter
            comment: 'The upstream/downstream mate orientations for a valid paired-end
                alignment against the forward reference strand. E.g., if --fr is specified
                and there is a candidate paired-end alignment where mate1 appears
                upstream of the reverse complement of mate2 and the insert length
                constraints are met, that alignment is valid. Also, if mate2 appears
                upstream of the reverse complement of mate1 and all other constraints
                are met, that too is valid. --rf likewise requires that an upstream
                mate1 be reverse-complemented and a downstream mate2 be forward-oriented.
                --ff requires both an upstream mate1 and a downstream mate2 to be
                forward-oriented. Default: --fr when -C (colorspace alignment) is
                not specified, --ff when -C is specified.'
            prompt: 'Paired-end alignment options: (-fr, -rf, -ff, -nofr)'
            format: ("", " " + str(value))[value is not None and value != vdef ]
            name: paired_end_align_options
            command: false
            type: !mobyle/stringtype
                default: --fr
                options:
                - {label: 'Illumina paired-end : forward/reverse strands alignment(--fr)',
                    value: --fr}
                - {label: 'Illumina mate-pair : reverse/forward strands alignment(--rf)',
                    value: --rf}
                - {label: 'Same strand : forward/forward strands alignment(--ff)',
                    value: --ff}
        - !mobyle/inputprogramparameter
            comment: 'The minimum insert size for valid paired-end alignments. E.g.
                if -I 60 is specified and a paired-end alignment consists of two 20-bp
                alignments in the appropriate orientation with a 20-bp gap between
                them, that alignment is considered valid (as long as -X is also satisfied).
                A 19-bp gap would not be valid in that case. If trimming options -3
                or -5 are also used, the -I constraint is applied with respect to
                the untrimmed mates. Default: 0.'
            prompt: 'Minimum insert size for valid paired-end alignments: (-I or --minins)'
            format: ("", " --minins " + str(value))[value is not None and value !=
                vdef ]
            name: paired_end_min_insert_size
            command: false
            type: !mobyle/integertype {default: 0}
        - !mobyle/inputprogramparameter
            comment: 'The maximum insert size for valid paired-end alignments. E.g.
                if -X 100 is specified and a paired-end alignment consists of two
                20-bp alignments in the proper orientation with a 60-bp gap between
                them, that alignment is considered valid (as long as -I is also satisfied).
                A 61-bp gap would not be valid in that case. If trimming options -3
                or -5 are also used, the -X constraint is applied with respect to
                the untrimmed mates, not the trimmed mates. Default: 250.'
            prompt: 'Maximum insert size for valid paired-end alignments: (-X or --maxins)'
            format: ("", " --maxins " + str(value))[value is not None and value !=
                vdef ]
            name: paired_end_max_insert_size
            command: false
            type: !mobyle/integertype {default: 250}
        - !mobyle/inputprogramparameter
            comment: For paired-end alignment, this is the maximum number of attempts
                bowtie will make to match an alignment for one mate up with an alignment
                for the opposite mate. Most paired-end alignments require only a few
                such attempts, but pairs where both mates occur in highly repetitive
                regions of the reference can require significantly more. Setting this
                to a higher number allows bowtie to find more paired- end alignments
                for repetitive pairs at the expense of speed. The default is 100.
            prompt: 'Maximum number of alignment matching attempts: (--pairtries)'
            format: ("", " --pairtries " + str(value))[value is not None and value
                != vdef ]
            name: pair_tries
            command: false
            type: !mobyle/integertype {default: 100}
    - !mobyle/inputprogramparagraph
        prompt: Reporting Options
        name: reporting_para
        children:
        - !mobyle/inputprogramparameter
            comment: Report up to <int> valid alignments per read or pair. If no value
                is specified then all the alignments will be reported.Validity of
                alignments is determined by the alignment policy (combined effects
                of -n, -v, -l, and -e). If more than one valid alignment exists and
                the --best and --strata options are specified, then only those alignments
                belonging to the best alignment "stratum" will be reported. Bowtie
                is designed to be very fast for small -k but bowtie can become significantly
                slower as -k increases.
            prompt: 'Report up to k valid alignments per read or pair: (-k)'
            format: ("", " -k " + str(value))[value is not None and value != vdef
                ]
            name: report_upto
            command: false
            type: !mobyle/integertype {default: 1}
        - !mobyle/inputprogramparameter
            comment: 'Suppress all alignments for a particular read or pair if more
                than <int> reportable alignments exist for it. Reportable alignments
                are those that would be reported given the -n, -v, -l, -e, -k, -a,
                --best, and --strata options. Default: no limit. Bowtie is designed
                to be very fast for small -m but bowtie can become significantly slower
                for larger values of -m.'
            prompt: 'Suppress all alignments for a particular read or pair if more
                than m reportable alignments exist for it: (-m)'
            format: ("", " -m " + str(value))[value is not None and value != vdef
                ]
            name: suppress_align_if_contains
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: Behaves like -m except that if a read has more than <int> reportable
                alignments, one is reported at random. In default output mode, the
                selected alignment's 7th column is set to <int>+1 to indicate the
                read has at least <int>+1 valid alignments. In -S/--sam mode, the
                selected alignment is given a MAPQ (mapping quality) of 0 and the
                XM:I field is set to <int>+1. This option requires --best; if specified
                without --best, --best is enabled automatically.
            prompt: If a read has more than M reportable alignments, report one at
                random. (-M). By default the "--best" option is used
            format: ("", " -M " + str(value))[value is not None and value != vdef
                ]
            name: report_random_align_if_contains
            precond: {best_opts: '1'}
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: Guaranteed best stratum; ties broken by quality.
            prompt: Report hits guaranteed best stratum (--best)
            format: ("", " --best")[value]
            name: best_opts
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Hits in sub-optimal strata aren't reported (requires --best).
                If many valid alignments exist and are reportable (e.g. are not disallowed
                via the -k option) and they fall into more than one alignment "stratum",
                report only those alignments that fall into the best stratum. By default,
                Bowtie reports all reportable alignments regardless of whether they
                fall into multiple strata. When --strata is specified, --best must
                also be specified.
            prompt: Do not report hits in sub-optimal strata(--strata)
            format: ("", " --strata")[value]
            name: strate_opts
            precond: {best_opts: '1'}
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Colorspace Options
        name: color_space_para
        precond: {input_data_format: -c}
        children:
        - !mobyle/inputprogramparameter
            prompt: SNP options
            name: colorspace_snps
            command: false
            type: !mobyle/stringtype
                default: penalty
                options:
                - {label: SNP Penalty, value: penalty}
                - {label: SNP Fraction, value: fraction}
        - !mobyle/inputprogramparameter
            comment: When decoding colorspace alignments, use <int> as the SNP penalty.
                This should be set to the user's best guess of the true ratio of SNPs
                per base in the subject genome, converted to the Phred quality scale.
                E.g., if the user expects about 1 SNP every 1,000 positions, --snpphred
                should be set to 30 (which is also the default). To specify the directly,
                use --snpfrac.
            prompt: 'SNP penalty: (-snpphred)'
            format: ("", " --snpphred " + str(value))[ value is not None and value
                != vdef]
            name: cs_snps_penalty
            precond: {colorspace_snps: penalty}
            command: false
            type: !mobyle/integertype {default: 30}
        - !mobyle/inputprogramparameter
            comment: 'When decoding colorspace alignments, use <dec> as the estimated
                ratio of SNPs per base. For best decoding results, this should be
                set to the user''s best guess of the true ratio. bowtie internally
                converts the ratio to a Phred quality, and behaves as if that quality
                had been set via the --snpphred option. Default: 0.001.'
            prompt: 'Estimated fractions of SNP''s per base: (-snpfrac)'
            format: ("", " --snpfrac " + str(value))[ value is not None and value
                != vdef]
            name: cs_snps_fraction
            precond: {colorspace_snps: fraction}
            command: false
            type: !mobyle/floattype {default: 0.001}
        - !mobyle/inputprogramparameter
            comment: If reads are in colorspace and the default output mode is active,
                --col-cseq causes the reads' color sequence to appear in the read-sequence
                column (column 5) instead of the decoded nucleotide sequence. See
                the Decoding colorspace alignments section for details about decoding.
                This option is ignored in -S/--sam mode.
            prompt: Do you want the color sequence to appear in the read-sequence
                column? (-col-cseq)
            format: ("", " --col-cseq")[value]
            name: print_color_seq
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: If reads are in colorspace and the default output mode is active,
                --col-cqual causes the reads' original (color) quality sequence to
                appear in the quality column (column 6) instead of the decoded qualities.
                See the Colorspace alignment section for details about decoding. This
                option is ignored in -S/--sam mode.
            prompt: Do you want the reads to appear in the quality column instead
                of the decoded qualitites? (-col-cqual)
            format: ("", " --col-cqual")[value]
            name: print_color_quals
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: When decoding colorpsace alignments, bowtie trims off a nucleotide
                and quality from the left and right edges of the alignment. This is
                because those nucleotides are supported by only one color, in contrast
                to the middle nucleotides which are supported by two. Specify --col-keepends
                to keep the extreme-end nucleotides and qualities.
            prompt: Do you want to keep extreme-end nucleotides and qualities? (-col-keepends)
            format: ("", " --col-keepends")[value]
            name: cs_keep_extreme_end_nucl
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Output
        name: output_param
        children:
        - !mobyle/inputprogramparameter
            comment: When outputting alignments, number the first base of a reference
                sequence as 'int'.
            prompt: 'Number the first base of a reference sequence as: (-B or --offbase)'
            format: ("", " --offbase " + str(value))[value is not None and value !=
                vdef]
            name: ref_offset_value
            command: false
            type: !mobyle/integertype {default: 0}
        - !mobyle/inputprogramparameter
            comment: Write alignments to a set of files named refXXXXX.map, where
                XXXXX is the 0-padded index of the reference sequence aligned to.
                This can be a useful way to break up work for downstream analyses
                when dealing with, for example, large numbers of reads aligned to
                the assembled human genome. If <hits> is also specified, it will be
                ignored.
            prompt: Write alignments to a set of files named refXXXXX.map? (--refout)
            format: ("", " --refout")[value]
            name: write_alignments
            precond: {out_format: txt}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: When a reference sequence is referred to in a reported alignment,
                refer to it by 0-based index (its offset into the list of references
                that were indexed) rather than by name.
            prompt: Refer reference sequence to a 0-based index if it is referred
                to in a reported alignment? (-refidx)
            format: ("", " --refidx")[value]
            name: zero_based_idx
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: 'Write all reads for which at least one alignment was reported
                to a file with name <filename>. Written reads will appear as they
                did in the input, without any of the trimming or translation of quality
                values that may have taken place within bowtie. Paired-end reads will
                be written to two parallel files with _1 and _2 inserted in the filename,
                e.g., if <filename> is aligned.fq, the #1 and #2 mates that fail to
                align will be written to aligned_1.fq and aligned_2.fq respectively.'
            prompt: Prefix of the file name to write all reads for which at least
                one alignment(--al)
            format: ("", " --al " + str(value) + "_aligned_reads.fq")[value is not
                None]
            name: write_aligned
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: 'Write all reads that could not be aligned to a file with name
                <filename>. Written reads will appear as they did in the input, without
                any of the trimming or translation of quality values that may have
                taken place within Bowtie. Paired-end reads will be written to two
                parallel files with _1 and _2 inserted in the filename, e.g., if <filename>
                is unaligned.fq, the #1 and #2 mates that fail to align will be written
                to unaligned_1.fq and unaligned_2.fq respectively. Unless --max is
                also specified, reads with a number of valid alignments exceeding
                the limit set with the -m option are also written to <filename>.'
            prompt: Write all reads that could not be aligned to a file (--un)?
            format: ("", " --un " + str(value) + "_unaligned_reads.fq")[value is not
                None]
            name: write_unaligned
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: 'Write all reads with a number of valid alignments exceeding
                the limit set with the -m option to a file with name <filename>. Written
                reads will appear as they did in the input, without any of the trimming
                or translation of quality values that may have taken place within
                bowtie. Paired-end reads will be written to two parallel files with
                _1 and _2 inserted in the filename, e.g., if <filename> is max.fq,
                the #1 and #2 mates that exceed the -m limit will be written to max_1.fq
                and max_2.fq respectively. These reads are not written to the file
                specified with --un.'
            prompt: Write all reads with a number of valid alignments exceeding the
                limit set with the -m option to a file (--max)
            format: ("", " --max " + str(value) + "_aligned_reads.fq" )[value is not
                None]
            name: write_align_with_n
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: Suppress columns of output in the default output mode. E.g. if
                --suppress 1,5,6 is specified, the read name, read sequence, and read
                quality fields will be omitted. See Default Bowtie output for field
                descriptions. This option is ignored if the output mode is -S/--sam.
            prompt: Suppress columns of output in the default output mode? (--suppress)
            format: ("", " --suppress " + str(value) )[value is not None]
            name: columns_to_suppress
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: Print the full reference sequence name, including whitespace,
                in alignment output. By default bowtie prints everything up to but
                not including the first whitespace.
            prompt: Print full reference sequence name? (--fullref)
            format: ("", " --fullref")[value]
            name: write_full_alignment
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: 'Job description:'
            simple: true
            mandatory: true
            name: output_file
            command: false
            type: !mobyle/stringtype {default: bowtie_alignment}
        - !mobyle/inputprogramparameter
            comment: 'Default output: One alignment per line. Each line is a collection
                of 8 fields separated by tabs - refer Bowtie manual for detailsSAM
                format : Print alignments in SAM format. See the SAM output section
                of the manual for details. To suppress all SAM headers, use --sam-nohead
                in addition to -S/--sam. To suppress just the @SQ headers (e.g. if
                the alignment is against a very large number of reference sequences),
                use --sam-nosq in addition to -S/--sam. bowtie does not write BAM
                files directly, but SAM output can be converted to BAM on the fly
                by piping bowtie''s output to samtools view. -S/--sam is not compatible
                with --refout.BAM format: The bowtie SAM file is converted to sorted
                BAM file using SAMTools package.'
            prompt: Output formats
            format: (" " , ( " -S | samtools view -bS - | samtools sort - ", " -S
                " )[value == "sam"] )[value != "txt"] + str(output_file)
            simple: true
            argpos: 104
            name: out_format
            command: false
            type: !mobyle/stringtype
                default: sam
                options:
                - {label: Default hit file, value: txt}
                - {label: SAM, value: sam}
                - {label: BAM, value: bam}
    - !mobyle/inputprogramparagraph
        prompt: SAM Options
        name: sam_options_para
        precond: {out_format: sam}
        children:
        - !mobyle/inputprogramparameter
            prompt: 'If an alignment is non-repetitive, set the MAPQ field to this
                value: (-mapq)'
            format: ("", " --mapq " + str(value))[value is not None and value !=vdef]
            name: mapq_quality
            precond: {out_format: sam}
            command: false
            type: !mobyle/integertype {default: 255}
        - !mobyle/inputprogramparameter
            comment: Suppress header lines (starting with @) when output is -S/--sam.
                This must be specified in addition to -S/--sam. --sam-nohead is ignored
                unless -S/--sam is also specified.
            prompt: Suppress @ header lines when output is SAM? (-sam-nohead)
            format: ("", " --sam-nohead ")[value]
            name: suppress_header
            precond: {out_format: sam}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Suppress @SQ header lines when output is -S/--sam. This must
                be specified in addition to -S/--sam. --sam-nosq is ignored unless
                -S/--sam is also specified.
            prompt: Supress @SQ header lines when output is SAM? (sam-nosq)
            format: ("", " --sam-nosq ")[value]
            name: suppress_sq
            precond: {out_format: sam}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Add text (usually of the form TAG:VAL, e.g. ID:IL7LANE2) as a
                field on the @RG header line. Specify --sam-RG multiple times to set
                multiple fields. See the SAM Spec for details about what fields are
                legal. Note that, if any @RG fields are set using this option, the
                ID and SM fields must both be among them to make the @RG line legal
                according to the SAM Spec. --sam-RG is ignored unless -S/--sam is
                also specified.
            prompt: 'Add ''text'' as a field on the @RG header line: (-sam-RG)'
            format: ("", " --sam-RG " + str(value) )[value is not None]
            name: add_rg
            precond: {out_format: sam}
            command: false
            type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output
        name: output_param
        children:
        - !mobyle/outputprogramparameter
            prompt: Bowtie Alignments
            filenames: '"*.bam"'
            name: bamout
            precond: {out_format: bam}
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/outputprogramparameter
            prompt: Bowtie Alignments - SAM
            filenames: '"*.sam"'
            name: samout
            precond: {out_format: sam}
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/outputprogramparameter
            prompt: Bowtie Alignments - Text output
            filenames: '"*.txt"'
            name: text_out
            precond: {out_format: txt}
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
        - !mobyle/outputprogramparameter
            prompt: Multiple files - Text output
            filenames: '"*.map"'
            name: mapfiles
            precond: {write_alignments: '1'}
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
        - !mobyle/outputprogramparameter
            prompt: Aligned reads
            filenames: write_aligned + "_aligned_reads*.fq"
            name: aligned_reads
            precond:
                write_aligned: {'#ne': None}
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/outputprogramparameter
            prompt: Unaligned reads
            filenames: write_unaligned + "_unaligned_reads*.fq"
            name: unaligned_reads
            precond:
                write_unaligned: {'#ne': None}
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/outputprogramparameter
            prompt: Aligned reads
            filenames: write_align_with_n + "_aligned_reads*.fq"
            name: reads
            precond:
                write_align_with_n: {'#ne': None}
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"bowtie.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"bowtie.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0523', 'EDAM_operation:2520']
topics: ['EDAM_topic:0102', 'EDAM_topic:0196']
command: bowtie
env: {}