annotate macros.xml @ 7:5b097fde95dd draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw commit 4048394d36408ccfeca401a84c4909a6c023e30e

<macros>
    <token name="@TOOL_VERSION@">2.1</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">
                clustal2
            </xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">clustalw</requirement>
        </requirements>
    </xml>
    <xml name="macro_options" token_algorithm="" token_multiple="" token_label="" token_default="">
        <conditional name="algorithm_conditional">
            <param name="selector" type="select" label="Algorithm for the alignment guide tree" help="Default: slow">
                <option value="">Slow: dynamic programming (accurate)</option>
                <option value="-QUICKTREE">Fast: method of Wilbur and Lipman (approximate)</option>
            </param>
            <when value="">
                <section name="slow_pairwise_alignments" title="Slow pairwise alignments options">
                    <param argument="-@ALGORITHM@" type="select" label="@LABEL@ weigth matrix" help="Default: @DEFAULT@">
                        <yield/>
                    </param>
                    <param argument="-PWGAPOPEN" type="integer" min="0" optional="true" label="Gap opening penalty" help="Default: 10" />
                    <param argument="-PWGAPEXT" type="float" min="0" optional="true" label="Gap extension penalty" help="Default: 0.1" />
                </section>
            </when>
            <when value="-QUICKTREE">
                <section name="fast_pairwise_alignments" title="Fast pairwise alignments options">
                    <param argument="-KTUPLE" type="integer" min="0" optional="true" label="Word size" 
                        help="Size of exactly matching fragment that is used. Increase for speed, decrease for sensitivity. Maximum value for proteins is 2, and for DNA 4.Default: 1" />
                    <param argument="-TOPDIAGS" type="integer" min="0" optional="true" label="Number of best diagonals" 
                        help="Number of k-tuple matches on each diagonal. Decrease for speed; increase for sensitivity. Default: 5" />
                    <param argument="-WINDOW" type="integer" min="0" optional="true" label="Window length"
                        help="This is the number of diagonals around each of the best diagonals that will be used. Decrease for speed; increase for sensitivity. Default: 5" />
                    <param argument="-PAIRGAP" type="integer" min="0" optional="true" label="Gap penalty" 
                        help="Fast pairwise alignment gap penalty for each gap created. Default: 3" />
                    <param argument="-SCORE" type="select" label="Score type" help="Score type to output. Default: percent">
                        <option value="PERCENT">Percent</option>
                        <option value="ABSOLUTE">Absolute</option>
                    </param>
                </section>
            </when>
        </conditional>
        <section name="multiple_alignments" title="Multiple alignments options">
            <param argument="-@MULTIPLE@" type="select" label="@LABEL@ weigth matrix" help="Default: @DEFAULT@">
                <yield/>
            </param>
            <param argument="-GAPOPEN" type="integer" min="0" optional="true" label="Gap opening penalty" help="Default: 10" />
            <param argument="-GAPEXT" type="float" min="0" optional="true" label="Gap extension penalty" help="Default: 0.2" />
            <param argument="-ENDGAPS" type="boolean" truevalue="-ENDGAPS" falsevalue="" checked="false" label="End gap separation penalty" 
                help="End gap separation treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close. If you turn this off, end gaps will be ignored for this purpose. 
                    This is useful when you wish to align fragments where the end gaps are not biologically meaningful" />
            <param argument="-GAPDIST" type="integer" min="0" optional="true" label="Gap separation penalty range" 
                help="Gap separation distance tries to decrease the chances of gaps being too close to each other. Gaps that are less than this distance apart are penalised more than other gaps. 
                    This does not prevent close gaps; it makes them less frequent, promoting a block-like appearance of the alignment" />
            <param argument="-NOPGAP" type="boolean" truevalue="-NOPGAP" falsevalue="" checked="false" label="Residue specific penalties" 
                help="Residue specific penalties are amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence. As an example, 
                    positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine" />
            <param argument="-NOHGAP" type="boolean" truevalue="-NOHGAP" falsevalue="" checked="false" label="Hydrophilic gaps" help="Hydrophilic gap penalties are used to increase the chances of a gap 
                within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common" />
            <param argument="-MAXDIV" type="integer" min="0" max="100" optional="true" label="Delay divergent sequences" help="Percentage identity for delay" />
            <param argument="-NEGATIVE" type="boolean" truevalue="-NEGATIVE" falsevalue="" checked="false" label="Negative values in matrix" help="Delays the alignment of the most distantly related sequences 
                until after the most closely related sequences have been aligned. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical 
                than this level to any other sequences will be aligned later" />
            <param argument="-TRANSWEIGHT" type="float" min="0" max="1" optional="true" label="Transition weight" help="The transition weight option for aligning nucleotide sequences has been changed in version 
                1.7 from an on/off toggle to a weight between 0 and 1. A weight of zero means that the transitions are scored as mismatches; a weight of 1 gives transitions the full match score. For distantly 
                related DNA sequences, the weight should be near to zero; for closely related sequences it can be useful to assign a higher score" />
        </section>
    </xml>
    <token name="@SLOW_PAIRWISE_ALIGNMENTS@"><![CDATA[
        #if str($type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN)
            -PWGAPOPEN=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN
        #end if
        #if str($type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT)
            -PWGAPEXT=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT
        #end ifx
    ]]></token>
    <token name="@FAST_PAIRWISE_ALIGNMENTS@"><![CDATA[
        #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE)
        -KTUPLE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE
        #end if
        #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS)
            -TOPDIAGS=$type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS
        #end if
        #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW)
            -WINDOW=$type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW
        #end if
        #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP)
            -PAIRGAP=$type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP
        #end if
        -SCORE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.SCORE
    ]]></token>
    <token name="@MULTIPLE_ALIGNMENTS@"><![CDATA[
        #if str($type_conditional.multiple_alignments.GAPOPEN)
            -GAPOPEN=$type_conditional.multiple_alignments.GAPOPEN
        #end if
        #if str($type_conditional.multiple_alignments.GAPEXT)
            -GAPEXT=$type_conditional.multiple_alignments.GAPEXT
        #end if
        $type_conditional.multiple_alignments.ENDGAPS
        #if str($type_conditional.multiple_alignments.GAPDIST)
            -GAPDIST=$type_conditional.multiple_alignments.GAPDIST
        #end if
        $type_conditional.multiple_alignments.NOPGAP
        $type_conditional.multiple_alignments.NOHGAP
        #if str($type_conditional.multiple_alignments.MAXDIV)
            -MAXDIV=$type_conditional.multiple_alignments.MAXDIV
        #end if
        $type_conditional.multiple_alignments.NEGATIVE
        #if str($type_conditional.multiple_alignments.TRANSWEIGHT)
            -TRANSWEIGHT=$type_conditional.multiple_alignments.TRANSWEIGHT
        #end if
    ]]></token>

</macros>