comparison bowtie2_wrapper.xml @ 7:4f92dccc808a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7

6:e23b0cdeeba6

    <requirements>
        <requirement type="package" version="2.2.4">bowtie2</requirement>
        <requirement type="package" version="0.1.18">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.unaligned_file ) == "true":
                --un-conc $output_unaligned_reads_l
            #end if
        #end if
        
        ## Read group information.
        @define_read_group_helpers@
        #if str( $library.type ) == "single":
            #set $rg_auto_name = $read_group_name_default($library.input_1)
        #elif str( $library.type ) == "paired":

          $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
          $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
          $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
          $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
        #end if
        
        ## Analysis type
        #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
            $analysis_type.presets
        #elif str( $analysis_type.analysis_type_selector ) == "full":
            #if str( $analysis_type.input_options.input_options_selector ) == "yes":

                --trim3 "${analysis_type.input_options.trim3}"
                ${analysis_type.input_options.qv_encoding}
                ${analysis_type.input_options.solexa_quals}
                ${analysis_type.input_options.int_quals}
            #end if
            
            #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
                -N "${analysis_type.alignment_options.N}"
                -L "${analysis_type.alignment_options.L}"
                -i "${analysis_type.alignment_options.i}"
                --n-ceil "${analysis_type.alignment_options.n_ceil}"

                #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
                    --local
                    --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"
                #end if
            #end if
            
            #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
                #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
                    --ma "${analysis_type.scoring_options.ma}"
                #end if
                --mp "${analysis_type.scoring_options.mp}"
                --np "${analysis_type.scoring_options.np}"
                --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"
                --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}"
            #end if
            
            #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
                -k "${analysis_type.reporting_options.k}"
            #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
                -a
            #end if
            
            #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
                -D "${analysis_type.effort_options.D}"
                -R "${analysis_type.effort_options.R}"
            #end if
            
            #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
                ${analysis_type.sam_options.no_unal}
                ${analysis_type.sam_options.omit_sec_seq}
            #end if
            
            #if str( $analysis_type.other_options.other_options_selector ) == "yes":
                ${analysis_type.other_options.non_deterministic}
                --seed "${analysis_type.other_options.seed}"
            #end if
        
        #elif str( $analysis_type.analysis_type_selector ) == "cline":
            ${analysis_type.cline}
        #end if
        
        -S "galaxy_bowtie_2_output.sam" &&

        ## view/sort and output BAM file
        ( samtools view -Su "galaxy_bowtie_2_output.sam" | samtools sort -o - - > $output )

        ## 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
        
    </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>
              <option value="paired">Paired-end</option>
              <option value="paired_collection">Paired-end Dataset Collection</option>
            </param>

            <when value="single">
                <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
            </when>
            <when value="paired">
                <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                <param name="input_2" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
                <conditional name="paired_options">
                    <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>

                            <option value="--ff">--ff</option>
                        </param>
                        <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
                        <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
                        <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
                        <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Allow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
                        <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Allow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
                    </when>
                    <when value="no">
                        <!-- do nothing -->
                    </when>
                </conditional>
            </when>
            <when value="paired_collection">
                <param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
                <conditional name="paired_options">
                    <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>

                            <option value="--ff">--ff</option>
                        </param>
                        <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
                        <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
                        <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
                        <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Allow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
                        <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Allow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
                    </when>
                    <when value="no">
                        <!-- do nothing -->
                    </when>
                </conditional>

                        <option value="no" selected="true">No</option>
                    </param>
                    <when value="yes">
                        <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/>
                        <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" size="10" 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"/>

                        <option value="yes">Yes</option>
                        <option value="no" selected="true">No</option>
                    </param>
                    <when value="yes">
                        <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma;  In `--local` mode match bonus 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"/>
                        <param name="mp" type="text" size="10" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character 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=6,2"/>
                        <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/>
                        <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/>
                        <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/>
                        <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/>
                        <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/>

                    <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
                        <option value="yes">Yes</option>
                        <option value="no" selected="true">No</option>
                    </param>
                    <when value="yes">
                        <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
                        <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
                    </when>
                    <when value="no">
                        <!-- do nothing -->
                    </when>
                </conditional>
            </when>
        </conditional>
    </inputs>

    <!-- define outputs -->

    <outputs>
    
        <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
            <filter>library['unaligned_file'] is True</filter>
            <actions>
                <action type="format">
                    <option type="from_param" name="library.input_1" param_attribute="ext" />
                </action>
            </actions>
        </data>
        <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
            <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
            <actions>
                <action type="format">
                    <option type="from_param" name="library.input_1" param_attribute="ext" />
                </action>
            </actions>
        </data>
        
        <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
          <actions>
            <conditional name="reference_genome.source">
              <when value="indexed">
                <action type="metadata" name="dbkey">
                  <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">

7:4f92dccc808a

    <requirements>
        <requirement type="package" version="2.2.4">bowtie2</requirement>
        <requirement type="package" version="0.1.18">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.unaligned_file ) == "true":
                --un-conc $output_unaligned_reads_l
            #end if
        #end if

        ## Read group information.
        @define_read_group_helpers@
        #if str( $library.type ) == "single":
            #set $rg_auto_name = $read_group_name_default($library.input_1)
        #elif str( $library.type ) == "paired":

          $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
          $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
          $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
          $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
        #end if

        ## Analysis type
        #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
            $analysis_type.presets
        #elif str( $analysis_type.analysis_type_selector ) == "full":
            #if str( $analysis_type.input_options.input_options_selector ) == "yes":

                --trim3 "${analysis_type.input_options.trim3}"
                ${analysis_type.input_options.qv_encoding}
                ${analysis_type.input_options.solexa_quals}
                ${analysis_type.input_options.int_quals}
            #end if

            #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
                -N "${analysis_type.alignment_options.N}"
                -L "${analysis_type.alignment_options.L}"
                -i "${analysis_type.alignment_options.i}"
                --n-ceil "${analysis_type.alignment_options.n_ceil}"

                #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
                    --local
                    --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"
                #end if
            #end if

            #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
                #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
                    --ma "${analysis_type.scoring_options.ma}"
                #end if
                --mp "${analysis_type.scoring_options.mp}"
                --np "${analysis_type.scoring_options.np}"
                --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"
                --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}"
            #end if

            #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
                -k "${analysis_type.reporting_options.k}"
            #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
                -a
            #end if

            #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
                -D "${analysis_type.effort_options.D}"
                -R "${analysis_type.effort_options.R}"
            #end if

            #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
                ${analysis_type.sam_options.no_unal}
                ${analysis_type.sam_options.omit_sec_seq}
            #end if

            #if str( $analysis_type.other_options.other_options_selector ) == "yes":
                ${analysis_type.other_options.reorder}
                ${analysis_type.other_options.non_deterministic}
                --seed "${analysis_type.other_options.seed}"
            #end if

        #elif str( $analysis_type.analysis_type_selector ) == "cline":
            ${analysis_type.cline}
        #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

    </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>
              <option value="paired">Paired-end</option>
              <option value="paired_collection">Paired-end Dataset Collection</option>
            </param>

            <when value="single">
                <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
            </when>
            <when value="paired">
                <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
                <conditional name="paired_options">
                    <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>

                            <option value="--ff">--ff</option>
                        </param>
                        <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
                        <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
                        <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
                        <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
                        <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
                    </when>
                    <when value="no">
                        <!-- do nothing -->
                    </when>
                </conditional>
            </when>
            <when value="paired_collection">
                <param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
                <conditional name="paired_options">
                    <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>

                            <option value="--ff">--ff</option>
                        </param>
                        <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
                        <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
                        <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
                        <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
                        <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
                    </when>
                    <when value="no">
                        <!-- do nothing -->
                    </when>
                </conditional>

                        <option value="no" selected="true">No</option>
                    </param>
                    <when value="yes">
                        <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/>
                        <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"/>

                        <option value="yes">Yes</option>
                        <option value="no" selected="true">No</option>
                    </param>
                    <when value="yes">
                        <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma;  In `--local` mode match bonus 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"/>
                        <param name="mp" type="text" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character 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=6,2"/>
                        <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/>
                        <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/>
                        <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/>
                        <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/>
                        <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/>

                    <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
                        <option value="yes">Yes</option>
                        <option value="no" selected="true">No</option>
                    </param>
                    <when value="yes">
                        <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file" help="--reorder; Default=False"/>
                        <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
                        <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
                    </when>
                    <when value="no">
                        <!-- do nothing -->
                    </when>
                </conditional>
                <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
            </when>
        </conditional>
    </inputs>

    <!-- define outputs -->

    <outputs>
    
        <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
            <filter>library['unaligned_file'] is True</filter>
            <actions>
                <conditional name="library.type">
                    <when value="single">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
            <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
            <actions>
                <conditional name="library.type">
                    <when value="paired">
                        <action type="format">
                            <option type="from_param" name="library.input_2" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
                        </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">
                <action type="metadata" name="dbkey">
                  <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
                    <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                    <filter type="param_value" ref="reference_genome.index" column="0"/>
                  </option>
                </action>
              </when>
              <when value="history">
                <action type="metadata" name="dbkey">
                  <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
                </action>
              </when>
            </conditional>
          </actions>
        </data>

        <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
          <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
          <actions>
            <conditional name="reference_genome.source">
              <when value="indexed">
                <action type="metadata" name="dbkey">
                  <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">