comparison bowtie2_wrapper.xml @ 11:b4e9cf5f2ae8 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd

10:a9d4f71dbfb0

<tool id="bowtie2" name="Bowtie2" version="2.2.6.2">
    <description>- map reads against reference genome</description>
    <macros>
        <import>read_group_macros.xml</import>
    </macros>
    <version_command>bowtie2 --version</version_command>
    <requirements>
        <requirement type="package" version="2.2.6">bowtie2</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <command>
        ## prepare bowtie2 index
        #set index_path = ''
        #if str($reference_genome.source) == "history":
            bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
            ln -s "$reference_genome.own_file" genome.fa &amp;&amp;
            #set index_path = 'genome'
        #else:
            #set index_path = $reference_genome.index.fields.path
        #end if

        ## execute bowtie2

        bowtie2

        ## number of threads
        -p \${GALAXY_SLOTS:-4}

        ## index file path
        -x $index_path

        ## Fastq inputs
        #if str( $library.type ) == "single":
            -U "${library.input_1}"
            #if str( $library.unaligned_file ) == "true":
                --un $output_unaligned_reads_l
            #end if
            #if str( $library.aligned_file ) == "true":
                --al $output_aligned_reads_l
            #end if
        #elif str( $library.type ) == "paired":
            -1 "${library.input_1}"
            -2 "${library.input_2}"
            #if str( $library.paired_options.paired_options_selector ) == "yes":
                -I "${library.paired_options.I}"
                -X "${library.paired_options.X}"
                ${library.paired_options.fr_rf_ff}
                ${library.paired_options.no_mixed}

                ${library.paired_options.dovetail}
                ${library.paired_options.no_contain}
                ${library.paired_options.no_overlap}
            #end if
            #if str( $library.unaligned_file ) == "true":
                --un-conc $output_unaligned_reads_l
            #end if
        #end if

        ## Read group information.
        @define_read_group_helpers@

            ${analysis_type.cline}
        #end if

        ## mapping stats (i.e. stderr from bowtie2)
        #if $save_mapping_stats
	  2> "$mapping_stats"
        #end if

        ## output file
        #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
          | samtools view -Su - | samtools sort -o - - > $output
        #else
          > $output_sam
        #end if

        ## rename unaligned sequence files
        #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
            #from os.path import splitext
            #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
            && mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }"
            && mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }"
        #end if
        #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
            #from os.path import splitext
            #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
            && mv "${ _aligned_root }.1${_aligned_ext}" "${ output_aligned_reads_l }"
            && mv "${ _aligned_root }.2${_aligned_ext}" "${ output_aligned_reads_r }"
        #end if

    </command>
    <!-- basic error handling -->
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>

    <inputs>
        <!-- single/paired -->
        <conditional name="library">
            <param name="type" type="select" label="Is this single or paired library">
              <option value="single">Single-end</option>

                        <!-- do nothing -->
                    </when>
                </conditional>
            </when>
        </conditional>
            
        <!-- reference genome -->
        <conditional name="reference_genome">
          <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
            <option value="indexed">Use a built-in genome index</option>
            <option value="history">Use a genome from the history and build index</option>

                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
              </options>
            </param>
          </when>
          <when value="history">
            <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />
          </when>
        </conditional>
        
        <!-- read group settings -->
        <expand macro="read_group_conditional" />
        <conditional name="analysis_type">
            <param name="analysis_type_selector" type="select" label="Select analysis mode">
                <option value="simple">1: Default setting only</option>

                        <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/>
                        <param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
                        <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/>
                        <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/>
                        <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/>
                        <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" selected="False" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/>
                        <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" selected="False" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
                        <param name="norc" type="boolean" truevalue="--norc" falsevalue="" selected="False" label="Do not attempt to align unpaired reads to the reverse (Crick) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
                        <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" selected="False" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic.  Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments.  However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`.  For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported.  This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/>
                        <conditional name="align_mode">
                            <param name="align_mode_selector" type="select" display="radio" label="Select between `--local` and `--end-to-end` alignment modes" help="--local and --end-to-end; see help below for detailed explanation; default=--end-to-end">
                                <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
                                <option value="local">Local (--local)</option>
                            </param>

                    </when>
                    <when value="no">
                        <!-- do nothing -->
                    </when>
                </conditional>
                
                <conditional name="sam_options">
                    <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
                        <option value="yes">Yes</option>
                        <option value="no" selected="true">No</option>
                    </param>

        </conditional>
        <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
    </inputs>

    <!-- define outputs -->
    
    <outputs>
    
        <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
            <filter>library['unaligned_file'] is True</filter>
            <actions>
                <conditional name="library.type">
                    <when value="single">

                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        
        <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
          <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
          <actions>
            <conditional name="reference_genome.source">
              <when value="indexed">

            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
            <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/>
        </test>
    </tests>

    <help>
        
**Bowtie2 Overview**
    
Bowtie2_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site.
Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.

.. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
.. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

**Selecting reference genomes for Bowtie2**

Galaxy wrapper for Bowtie2 allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:

    1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bowtie2-build utility and are ready to be mapped against.  
    2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using bowtie2-build command, and then run mapping with bowtie2.
    
If your genome of interest is not listed here you have two choices:

    1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
    2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.

------

**Input options**::

    -s/--skip <int>
            Skip (i.e. do not align) the first `<int>` reads or pairs in the input.

    -u/--qupto <int>
            Align the first `<int>` reads or read pairs from the input (after the
            `-s`/`--skip` reads or pairs have been skipped), then stop.  Default: no limit.

    -5/--trim5 <int>
            Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).

    -3/--trim3 <int>
            Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).

    --phred33
            Input qualities are ASCII chars equal to the Phred quality plus 33.  This is
            also called the "Phred+33" encoding, which is used by the very latest Illumina
            pipelines.

    --int-quals
            Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
            Integers are treated as being on the Phred quality scale unless
            `--solexa-quals` is also specified. Default: off.
                        
------

**Presets in `--end-to-end` mode**::

    --very-fast
            Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`

    --fast
            Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
    
    --sensitive
            Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)

    --very-sensitive
            Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`

    --sensitive-local
            Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)

    --very-sensitive-local
            Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
    
------

**Alignment options**::

    -N <int>
            Sets the number of mismatches to allowed in a seed alignment during multiseed
            alignment.  Can be set to 0 or 1. Setting this higher makes alignment slower
            (often much slower) but increases sensitivity.  Default: 0.

    -L <int>
            Sets the length of the seed substrings to align during multiseed alignment.
            Smaller values make alignment slower but more sensitive. Default: the
            `--sensitive` preset is used by default, which sets `-L` to 22 in
            `--end-to-end` mode and to 20 in `--local` mode.

    -i <func>
            Sets a function governing the interval between seed substrings to use during
            multiseed alignment.  For instance, if the read has 30 characers, and seed
            length is 10, and the seed interval is 6, the seeds extracted will be:

    Read:      TAGCTACGCTCTACGCTATCATGCATAAAC

    If the function returns a result less than
    1, it is rounded up to 1. Default: the `--sensitive` preset is used by
    default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
    in `--local` mode.

    --n-ceil <func>
            Sets a function governing the maximum number of ambiguous characters (usually
            `N`s and/or `.`s) allowed in a read as a function of read length.  For instance,
            specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
            where x is the read length.  Reads exceeding this ceiling are filtered out.
            Default: `L,0,0.15`.

    --dpad <int>
            "Pads" dynamic programming problems by `<int>` columns on either side to allow
            gaps.  Default: 15.

    --gbar <int>
            Disallow gaps within `<int>` positions of the beginning or end of the read. 
            Default: 4.

    --ignore-quals
            When calculating a mismatch penalty, always consider the quality value at the
            mismatched position to be the highest possible, regardless of the actual value. 
            I.e. input is treated as though all quality values are high.  This is also the
            default behavior when the input doesn't specify quality values (e.g. in `-f`,
            `-r`, or `-c` modes).

    --nofw/--norc

            the forward (Watson) reference strand.  If `--norc` is specified, `bowtie2` will
            not attempt to align unpaired reads against the reverse-complement (Crick)
            reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
            fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
            paired-end configurations corresponding to fragments from the reverse-complement
            (Crick) strand.  Default: both strands enabled. 

    --no-1mm-upfront
            By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
            end-to-end alignment for the read *before* trying the multiseed heuristic.  Such
            alignments can be found very quickly, and many short read alignments have exact or

            `--ma` is used in this mode, and the best possible alignment score is equal to
            the match bonus (`--ma`) times the length of the read.  Specifying `--local`
            and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
            the local version of the preset (`--very-fast-local`).  This is mutually
            exclusive with `--end-to-end`.  `--end-to-end` is the default mode.
                            
-----

**Scoring options**::

    --ma <int>
            Sets the match bonus.  In `--local` mode `<int>` is added to the alignment
            score for each position where a read character aligns to a reference character
            and the characters match.  Not used in `--end-to-end` mode.  Default: 2.

    --mp MX,MN
            Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers.  A

            aligns to a reference character, the characters do not match, and neither is an
            `N`.  If `--ignore-quals` is specified, the number subtracted quals `MX`.
            Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
            where Q is the Phred quality value.  Default: `MX` = 6, `MN` = 2.

    --np <int>
            Sets penalty for positions where the read, reference, or both, contain an
            ambiguous character such as `N`.  Default: 1.

    --rdg <int1>,<int2>
            Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties.  A read gap of
            length N gets a penalty of `<int1>` + N * `<int2>`.  Default: 5, 3.

    --rfg <int1>,<int2>
            Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties.  A
            reference gap of length N gets a penalty of `<int1>` + N * `<int2>`.  Default:
            5, 3.

    --score-min <func>
            Sets a function governing the minimum alignment score needed for an alignment to
            be considered "valid" (i.e. good enough to report).  This is a function of read
            length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
            to `f(x) = 0 + -0.6 * x`, where `x` is the read length.  The default in `--end-to-end` mode is `L,-0.6,-0.6` and
            the default in `--local` mode is `G,20,8`.
                                        
-----                                        

**Reporting options**::

    -k <int>
            By default, `bowtie2` searches for distinct, valid alignments for each read.
            When it finds a valid alignment, it continues looking for alignments that are
            nearly as good or better.  The best alignment found is reported (randomly
            selected from among best if tied).  Information about the best alignments is
            used to estimate mapping quality and to set SAM optional fields, such as
            `AS:i` and `XS:i`.

    When `-k` is specified, however, `bowtie2` behaves differently.  Instead, it
    searches for at most `<int>` distinct, valid alignments for each read.  The
    search terminates when it can't find more distinct valid alignments, or when it
    finds `<int>`, whichever happens first.  All alignments found are reported in
    descending order by alignment score. The alignment score for a paired-end
    alignment equals the sum of the alignment scores of the individual mates. Each
    reported read or pair alignment beyond the first has the SAM 'secondary' bit
    (which equals 256) set in its FLAGS field.  For reads that have more than
    `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
    `<int>` alignments reported are the best possible in terms of alignment score. 
    `-k` is mutually exclusive with `-a`.

    Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
    aligning reads to long, repetitive genomes large `-k` can be very, very slow.

            Like `-k` but with no upper limit on number of alignments to search for.  `-a`
            is mutually exclusive with `-k`.

    Note: Bowtie 2 is not designed with `-a` mode in mind, and when
    aligning reads to long, repetitive genomes this mode can be very, very slow.
    
-----

**Effort options**::

    -D <int>
            Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
            moves on, using the alignments found so far.  A seed extension "fails" if it
            does not yield a new best or a new second-best alignment.  This limit is
            automatically adjusted up when -k or -a are specified.  Default: 15.

    -R <int>
            `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
            repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
            (same length, same number of mismatches allowed) at different offsets and
            searches for more alignments.  A read is considered to have repetitive seeds if
            the total number of seed hits divided by the number of seeds that aligned at
            least once is greater than 300.  Default: 2.
                        
-----

**Paired-end options**::

    -I/--minins <int>
            The minimum fragment length 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

            run.  This is because larger differences bewteen `-I` and `-X` require that
            Bowtie 2 scan a larger window to determine if a concordant alignment exists.
            For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
            efficient.

            Default: 0 (essentially imposing no minimum) 

    -X/--maxins <int>
            The maximum fragment length 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`

            Default: a mate can contain the other in a concordant alignment.

    --no-overlap
            If one mate alignment overlaps the other at all, consider that to be
            non-concordant.  Default: mates can overlap in a concordant alignment.
                                
------

**SAM options**::

    --rg-id <text>
            Set the read group ID to `<text>`.  This causes the SAM `@RG` header line to be
            printed, with `<text>` as the value associated with the `ID:` tag.  It also
            causes the `RG:Z:` extra field to be attached to each SAM output record, with
            value set to `<text>`.

    --rg <text>
            Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
            `@RG` header line.  Note: in order for the `@RG` line to appear, `--rg-id`
            must also be specified.  This is because the `ID` tag is required by the SAM
            Specification.  Specify `--rg` multiple times to set multiple fields.  See the
            SAM Specification for details about what fields are legal.

    --omit-sec-seq
            When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
            and `QUAL` strings.  Specifying this option causes Bowtie 2 to print an asterix
            in those fields instead.
            
-----

**Other options**::

    --reorder

            than 1.  Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
            2 to run somewhat slower and use somewhat more memory then if `--reorder` were
            not specified.  Has no effect if `-p` is set to 1, since output order will
            naturally correspond to input order in that case.

    --seed <int>
            Use `<int>` as the seed for pseudo-random number generator.  Default: 0.

    --non-deterministic
            Normally, Bowtie 2 re-initializes its pseudo-random generator for each read.  It
            seeds the generator with a number derived from (a) the read name, (b) the
            nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`

            current time.  This means that Bowtie 2 will not necessarily report the same
            alignment for two identical reads.  This is counter-intuitive for some users,
            but might be more appropriate in situations where the input consists of many
            identical reads.

    </help>
    <citations>
    <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
    <citation type="doi">10.1038/nmeth.1923</citation>
  </citations>
</tool>

11:b4e9cf5f2ae8

<tool id="bowtie2" name="Bowtie2" version="2.2.8">
    <description>- map reads against reference genome</description>
    <macros>
        <import>read_group_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.2.8">bowtie2</requirement>
        <requirement type="package" version="1.3.1">samtools</requirement>
    </requirements>
    <version_command>bowtie2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        ## prepare bowtie2 index
        #set index_path = ''
        #if str($reference_genome.source) == "history":
            bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
            ln -s -f '$reference_genome.own_file' genome.fa &&
            #set index_path = 'genome'
        #else:
            #set index_path = '$reference_genome.index.fields.path'
        #end if

        ## execute bowtie2

        bowtie2

        ## number of threads
        -p \${GALAXY_SLOTS:-4}

        ## index file path
        -x '$index_path'

        ## Fastq inputs
        #if str( $library.type ) == "single":
            -U '${library.input_1}'
            #if str( $library.unaligned_file ) == "true":
                --un '$output_unaligned_reads_l'
            #end if
            #if str( $library.aligned_file ) == "true":
                --al '$output_aligned_reads_l'
            #end if
        #elif str( $library.type ) == "paired":
            -1 '${library.input_1}'
            -2 '${library.input_2}'
            #if str( $library.paired_options.paired_options_selector ) == "yes":
                -I "${library.paired_options.I}"
                -X "${library.paired_options.X}"
                ${library.paired_options.fr_rf_ff}
                ${library.paired_options.no_mixed}

                ${library.paired_options.dovetail}
                ${library.paired_options.no_contain}
                ${library.paired_options.no_overlap}
            #end if
            #if str( $library.unaligned_file ) == "true":
                --un-conc '$output_unaligned_reads_l'
            #end if
        #end if

        ## Read group information.
        @define_read_group_helpers@

            ${analysis_type.cline}
        #end if

        ## mapping stats (i.e. stderr from bowtie2)
        #if $save_mapping_stats
            2> '$mapping_stats'
        #end if

        ## output file
        #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
            | samtools sort -O bam -o '$output'
        #else
            > '$output_sam'
        #end if

        ## rename unaligned sequence files
        #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
            #from os.path import splitext
            #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
            && mv "${ _unaligned_root }.1${_unaligned_ext}" '$output_unaligned_reads_l'
            && mv "${ _unaligned_root }.2${_unaligned_ext}" '$output_unaligned_reads_r'
        #end if
        #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
            #from os.path import splitext
            #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
            && mv "${ _aligned_root }.1${_aligned_ext}" '$output_aligned_reads_l'
            && mv "${ _aligned_root }.2${_aligned_ext}" '$output_aligned_reads_r'
        #end if

        ]]></command>
    <inputs>
        <!-- single/paired -->
        <conditional name="library">
            <param name="type" type="select" label="Is this single or paired library">
              <option value="single">Single-end</option>

                        <!-- do nothing -->
                    </when>
                </conditional>
            </when>
        </conditional>

        <!-- reference genome -->
        <conditional name="reference_genome">
          <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
            <option value="indexed">Use a built-in genome index</option>
            <option value="history">Use a genome from the history and build index</option>

                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
              </options>
            </param>
          </when>
          <when value="history">
            <param name="own_file" type="data" format="fasta" label="Select reference genome" />
          </when>
        </conditional>

        <!-- read group settings -->
        <expand macro="read_group_conditional" />
        <conditional name="analysis_type">
            <param name="analysis_type_selector" type="select" label="Select analysis mode">
                <option value="simple">1: Default setting only</option>

                        <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/>
                        <param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
                        <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/>
                        <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/>
                        <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/>
                        <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/>
                        <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
                        <param name="norc" type="boolean" truevalue="--norc" falsevalue="" label="Do not attempt to align unpaired reads to the reverse (Crick) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
                        <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic.  Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments.  However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`.  For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported.  This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/>
                        <conditional name="align_mode">
                            <param name="align_mode_selector" type="select" display="radio" label="Select between `--local` and `--end-to-end` alignment modes" help="--local and --end-to-end; see help below for detailed explanation; default=--end-to-end">
                                <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
                                <option value="local">Local (--local)</option>
                            </param>

                    </when>
                    <when value="no">
                        <!-- do nothing -->
                    </when>
                </conditional>

                <conditional name="sam_options">
                    <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
                        <option value="yes">Yes</option>
                        <option value="no" selected="true">No</option>
                    </param>

        </conditional>
        <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
    </inputs>

    <!-- define outputs -->

    <outputs>

        <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
            <filter>library['unaligned_file'] is True</filter>
            <actions>
                <conditional name="library.type">
                    <when value="single">

                        </action>
                    </when>
                </conditional>
            </actions>
        </data>

        <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
          <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
          <actions>
            <conditional name="reference_genome.source">
              <when value="indexed">

            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
            <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/>
        </test>
    </tests>

    <help><![CDATA[

**Bowtie2 Overview**

Bowtie2_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site.
Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.

.. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
.. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

**Selecting reference genomes for Bowtie2**

Galaxy wrapper for Bowtie2 allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:

    1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bowtie2-build utility and are ready to be mapped against.
    2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using bowtie2-build command, and then run mapping with bowtie2.

If your genome of interest is not listed here you have two choices:

    1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
    2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.

------

**Input options**::

    -s/--skip <int>
            Skip (i.e. do not align) the first `<int>` reads or pairs in the input.

    -u/--qupto <int>
            Align the first `<int>` reads or read pairs from the input (after the
            `-s`/`--skip` reads or pairs have been skipped), then stop.  Default: no limit.

    -5/--trim5 <int>
            Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).

    -3/--trim3 <int>
            Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).

    --phred33
            Input qualities are ASCII chars equal to the Phred quality plus 33.  This is
            also called the "Phred+33" encoding, which is used by the very latest Illumina
            pipelines.

    --int-quals
            Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
            Integers are treated as being on the Phred quality scale unless
            `--solexa-quals` is also specified. Default: off.

------

**Presets in `--end-to-end` mode**::

    --very-fast
            Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`

    --fast
            Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`

    --sensitive
            Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)

    --very-sensitive
            Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`

    --sensitive-local
            Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)

    --very-sensitive-local
            Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`

------

**Alignment options**::

    -N <int>
            Sets the number of mismatches to allowed in a seed alignment during multiseed
            alignment.  Can be set to 0 or 1. Setting this higher makes alignment slower
            (often much slower) but increases sensitivity.  Default: 0.

    -L <int>
            Sets the length of the seed substrings to align during multiseed alignment.
            Smaller values make alignment slower but more sensitive. Default: the
            `--sensitive` preset is used by default, which sets `-L` to 22 in
            `--end-to-end` mode and to 20 in `--local` mode.

    -i <func>
            Sets a function governing the interval between seed substrings to use during
            multiseed alignment.  For instance, if the read has 30 characers, and seed
            length is 10, and the seed interval is 6, the seeds extracted will be:

    Read:      TAGCTACGCTCTACGCTATCATGCATAAAC

    If the function returns a result less than
    1, it is rounded up to 1. Default: the `--sensitive` preset is used by
    default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
    in `--local` mode.

    --n-ceil <func>
            Sets a function governing the maximum number of ambiguous characters (usually
            `N`s and/or `.`s) allowed in a read as a function of read length.  For instance,
            specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
            where x is the read length.  Reads exceeding this ceiling are filtered out.
            Default: `L,0,0.15`.

    --dpad <int>
            "Pads" dynamic programming problems by `<int>` columns on either side to allow
            gaps.  Default: 15.

    --gbar <int>
            Disallow gaps within `<int>` positions of the beginning or end of the read.
            Default: 4.

    --ignore-quals
            When calculating a mismatch penalty, always consider the quality value at the
            mismatched position to be the highest possible, regardless of the actual value.
            I.e. input is treated as though all quality values are high.  This is also the
            default behavior when the input doesn't specify quality values (e.g. in `-f`,
            `-r`, or `-c` modes).

    --nofw/--norc

            the forward (Watson) reference strand.  If `--norc` is specified, `bowtie2` will
            not attempt to align unpaired reads against the reverse-complement (Crick)
            reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
            fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
            paired-end configurations corresponding to fragments from the reverse-complement
            (Crick) strand.  Default: both strands enabled.

    --no-1mm-upfront
            By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
            end-to-end alignment for the read *before* trying the multiseed heuristic.  Such
            alignments can be found very quickly, and many short read alignments have exact or

            `--ma` is used in this mode, and the best possible alignment score is equal to
            the match bonus (`--ma`) times the length of the read.  Specifying `--local`
            and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
            the local version of the preset (`--very-fast-local`).  This is mutually
            exclusive with `--end-to-end`.  `--end-to-end` is the default mode.

-----

**Scoring options**::

    --ma <int>
            Sets the match bonus.  In `--local` mode `<int>` is added to the alignment
            score for each position where a read character aligns to a reference character
            and the characters match.  Not used in `--end-to-end` mode.  Default: 2.

    --mp MX,MN
            Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers.  A

            aligns to a reference character, the characters do not match, and neither is an
            `N`.  If `--ignore-quals` is specified, the number subtracted quals `MX`.
            Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
            where Q is the Phred quality value.  Default: `MX` = 6, `MN` = 2.

    --np <int>
            Sets penalty for positions where the read, reference, or both, contain an
            ambiguous character such as `N`.  Default: 1.

    --rdg <int1>,<int2>
            Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties.  A read gap of
            length N gets a penalty of `<int1>` + N * `<int2>`.  Default: 5, 3.

    --rfg <int1>,<int2>
            Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties.  A
            reference gap of length N gets a penalty of `<int1>` + N * `<int2>`.  Default:
            5, 3.

    --score-min <func>
            Sets a function governing the minimum alignment score needed for an alignment to
            be considered "valid" (i.e. good enough to report).  This is a function of read
            length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
            to `f(x) = 0 + -0.6 * x`, where `x` is the read length.  The default in `--end-to-end` mode is `L,-0.6,-0.6` and
            the default in `--local` mode is `G,20,8`.

-----

**Reporting options**::

    -k <int>
            By default, `bowtie2` searches for distinct, valid alignments for each read.
            When it finds a valid alignment, it continues looking for alignments that are
            nearly as good or better.  The best alignment found is reported (randomly
            selected from among best if tied).  Information about the best alignments is
            used to estimate mapping quality and to set SAM optional fields, such as
            `AS:i` and `XS:i`.

    When `-k` is specified, however, `bowtie2` behaves differently.  Instead, it
    searches for at most `<int>` distinct, valid alignments for each read.  The
    search terminates when it can't find more distinct valid alignments, or when it
    finds `<int>`, whichever happens first.  All alignments found are reported in
    descending order by alignment score. The alignment score for a paired-end
    alignment equals the sum of the alignment scores of the individual mates. Each
    reported read or pair alignment beyond the first has the SAM 'secondary' bit
    (which equals 256) set in its FLAGS field.  For reads that have more than
    `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
    `<int>` alignments reported are the best possible in terms of alignment score.
    `-k` is mutually exclusive with `-a`.

    Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
    aligning reads to long, repetitive genomes large `-k` can be very, very slow.

            Like `-k` but with no upper limit on number of alignments to search for.  `-a`
            is mutually exclusive with `-k`.

    Note: Bowtie 2 is not designed with `-a` mode in mind, and when
    aligning reads to long, repetitive genomes this mode can be very, very slow.

-----

**Effort options**::

    -D <int>
            Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
            moves on, using the alignments found so far.  A seed extension "fails" if it
            does not yield a new best or a new second-best alignment.  This limit is
            automatically adjusted up when -k or -a are specified.  Default: 15.

    -R <int>
            `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
            repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
            (same length, same number of mismatches allowed) at different offsets and
            searches for more alignments.  A read is considered to have repetitive seeds if
            the total number of seed hits divided by the number of seeds that aligned at
            least once is greater than 300.  Default: 2.

-----

**Paired-end options**::

    -I/--minins <int>
            The minimum fragment length 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

            run.  This is because larger differences bewteen `-I` and `-X` require that
            Bowtie 2 scan a larger window to determine if a concordant alignment exists.
            For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
            efficient.

            Default: 0 (essentially imposing no minimum)

    -X/--maxins <int>
            The maximum fragment length 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`

            Default: a mate can contain the other in a concordant alignment.

    --no-overlap
            If one mate alignment overlaps the other at all, consider that to be
            non-concordant.  Default: mates can overlap in a concordant alignment.

------

**SAM options**::

    --rg-id <text>
            Set the read group ID to `<text>`.  This causes the SAM `@RG` header line to be
            printed, with `<text>` as the value associated with the `ID:` tag.  It also
            causes the `RG:Z:` extra field to be attached to each SAM output record, with
            value set to `<text>`.

    --rg <text>
            Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
            `@RG` header line.  Note: in order for the `@RG` line to appear, `--rg-id`
            must also be specified.  This is because the `ID` tag is required by the SAM
            Specification.  Specify `--rg` multiple times to set multiple fields.  See the
            SAM Specification for details about what fields are legal.

    --omit-sec-seq
            When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
            and `QUAL` strings.  Specifying this option causes Bowtie 2 to print an asterix
            in those fields instead.

-----

**Other options**::

    --reorder

            than 1.  Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
            2 to run somewhat slower and use somewhat more memory then if `--reorder` were
            not specified.  Has no effect if `-p` is set to 1, since output order will
            naturally correspond to input order in that case.

    --seed <int>
            Use `<int>` as the seed for pseudo-random number generator.  Default: 0.

    --non-deterministic
            Normally, Bowtie 2 re-initializes its pseudo-random generator for each read.  It
            seeds the generator with a number derived from (a) the read name, (b) the
            nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`

            current time.  This means that Bowtie 2 will not necessarily report the same
            alignment for two identical reads.  This is counter-intuitive for some users,
            but might be more appropriate in situations where the input consists of many
            identical reads.

    ]]></help>
    <citations>
    <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
    <citation type="doi">10.1038/nmeth.1923</citation>
  </citations>
</tool>