comparison hisat2.xml @ 28:d4b55e2beb12 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"

27:a86e80d3c09c

<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy5" profile="17.01">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>

        -X ${adv.spliced_options.no_spliced_alignment_options.maxins}
    #end if
    --min-intronlen ${adv.spliced_options.min_intron}
    --max-intronlen ${adv.spliced_options.max_intron}
    ${adv.spliced_options.tma}
	
    #if str($adv.spliced_options.novel_splicesite_outfile) == "true":
       --novel-splicesite-outfile '$novel_splicesite_output'
    #end if
	
    #if str($adv.spliced_options.notmplen):
        ${adv.spliced_options.notmplen}
    #end if
#end if

                    <option value="defaults">Use default values</option>
                    <option value="advanced">Specify alignment options</option>
                </param>
                <when value="defaults" />
                <when value="advanced">
                    <param name="function_type" argument="--n-ceil" type="select" display="radio" label="Function governing the maximum number of ambiguous characters (usually Ns and/or .s) allowed in a read as a function of read length" help="Reads exceeding this ceiling are filtered out">
                        <option value="C">Constant [f(x) = B]</option>
                        <option value="L" selected="true">Linear [f(x) = B + A * x]</option>
                        <option value="S">Square root [f(x) = B + A * x&#178;]</option>
                        <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option>
                    </param>
                    <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
                    <param name="coefficient" type="float" value="0.15" label="Coefficient (A)" help="Coefficient for the above function" />
                    <param argument="--ignore-quals" name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="Ignore quality values" help="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" />
                    <param argument="--nofw" name="skip_forward" type="boolean" truevalue="--nofw" falsevalue="" label="Skip forward strand of reference" help="If --nofw is specified, HISAT2 will not attempt to align unpaired reads to the forward (Watson) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes HISAT2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" />
                    <param argument="--norc" name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reverse strand of reference" help="If --norc is specified, HISAT2 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 --norc causes HISAT2 to explore only those paired-end configurations corresponding to fragments from the forward-complement (Watson) strand" />

                    <param argument="--np" name="ambiguous_penalty" type="integer" value="1" min="0" label="Ambiguous read penalty" help="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N" />
                    <param argument="--rdg" name="read_open_penalty" type="integer" value="5" min="0" label="Read gap open penalty" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
                    <param argument="--rdg" name="read_extend_penalty" type="integer" value="3" min="0" label="Read gap extend penalty" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
                    <param argument="--rfg" name="ref_open_penalty" type="integer" value="5" min="0" label="Reference gap open penalty" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
                    <param argument="--rfg" name="ref_extend_penalty" type="integer" value="3" min="0" label="Reference gap extend penalty" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
                    <param name="function_type" argument="--score-min" type="select" display="radio" label="Function governing the minimum alignment score needed for an alignment to be considered &quot;valid&quot; (i.e. good enough to report)" help="This is a function of read length">
                        <option value="C">Constant [f(x) = B]</option>
                        <option value="L" selected="true">Linear [f(x) = B + A * x]</option>
                        <option value="S">Square root [f(x) = B + A * x&#178;]</option>
                        <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option>
                    </param>
                </when>
            </conditional>

            <conditional name="spliced_options">
                <param name="spliced_options_selector" type="select" label="Spliced alignment options">

                </param>
                <when value="defaults" />
                <when value="advanced">
                    <param name="canonical_penalty" argument="--pen-cansplice" type="integer" value="0" min="0" label="Penalty for canonical splice sites" />
                    <param name="noncanonical_penalty" argument="--pen-noncansplice" type="integer" value="12" min="0" label="Penalty for non-canonical splice sites" />
                    <param name="function_type" argument="--pen-canintronlen" type="select" display="radio" label="Penalty function for long introns with canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones">
                        <option value="C">Constant [f(x) = B]</option>
                        <option value="L">Linear [f(x) = B + A * x]</option>
                        <option value="S">Square root [f(x) = B + A * x&#178;]</option>
                        <option value="G" selected="true">Natural logarithm [f(x) = B + A * log(x)]</option>
                    </param>
                    <param name="constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
                    <param name="coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
                    <param name="nc_function_type" argument="--pen-noncanintronlen" type="select" display="radio" label="Penalty function for long introns with non-canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones">
                        <option value="C">Constant [f(x) = B]</option>
                        <option value="L">Linear [f(x) = B + A * x]</option>
                        <option value="S">Square root [f(x) = B + A * x&#178;]</option>
                        <option value="G" selected="true">Natural logarithm [f(x) = B + A * log(x)]</option>
                    </param>
                    <param name="nc_constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
                    <param name="nc_coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
                    <param name="min_intron" type="integer" value="20" min="0" label="Minimum intron length" />
                    <param name="max_intron" type="integer" value="500000" min="0" label="Maximum intron length" />
                    <conditional name="no_spliced_alignment_options">

    --dta-cufflinks
            Report alignments tailored specifically for Cufflinks. In addition to what HISAT2 does with the above option (--dta), With this option, HISAT2 looks for novel splice sites with three signals (GT/AG, GC/AG, AT/AC), but all user-provided splice sites are used irrespective of their signals. HISAT2 produces an optional field, XS:A:[+-], for every spliced alignment.

    --no-templatelen-adjustment
            Disables template length adjustment for RNA-seq reads.
    
    --novel-splicesite-outfile
			In this mode, HISAT2 reports a list of splice sites in the file :
				chromosome name <tab> genomic position of the flanking base on the left side of an intron <tab> genomic position of the flanking base on the right <tab> strand (+, -, and .) '.' indicates an unknown strand for non-canonical splice sites.

-----

28:d4b55e2beb12

<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy6" profile="17.01">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>

        -X ${adv.spliced_options.no_spliced_alignment_options.maxins}
    #end if
    --min-intronlen ${adv.spliced_options.min_intron}
    --max-intronlen ${adv.spliced_options.max_intron}
    ${adv.spliced_options.tma}

    #if str($adv.spliced_options.novel_splicesite_outfile) == "true":
       --novel-splicesite-outfile '$novel_splicesite_output'
    #end if

    #if str($adv.spliced_options.notmplen):
        ${adv.spliced_options.notmplen}
    #end if
#end if

                    <option value="defaults">Use default values</option>
                    <option value="advanced">Specify alignment options</option>
                </param>
                <when value="defaults" />
                <when value="advanced">
                    <expand macro="nc_function" name="function_type" argument="--n-ceil" label="Function governing the maximum number of ambiguous characters (usually Ns and/or .s) allowed in a read as a function of read length" help="Reads exceeding this ceiling are filtered out" lselected="true"/>
                    <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
                    <param name="coefficient" type="float" value="0.15" label="Coefficient (A)" help="Coefficient for the above function" />
                    <param argument="--ignore-quals" name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="Ignore quality values" help="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" />
                    <param argument="--nofw" name="skip_forward" type="boolean" truevalue="--nofw" falsevalue="" label="Skip forward strand of reference" help="If --nofw is specified, HISAT2 will not attempt to align unpaired reads to the forward (Watson) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes HISAT2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" />
                    <param argument="--norc" name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reverse strand of reference" help="If --norc is specified, HISAT2 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 --norc causes HISAT2 to explore only those paired-end configurations corresponding to fragments from the forward-complement (Watson) strand" />

                    <param argument="--np" name="ambiguous_penalty" type="integer" value="1" min="0" label="Ambiguous read penalty" help="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N" />
                    <param argument="--rdg" name="read_open_penalty" type="integer" value="5" min="0" label="Read gap open penalty" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
                    <param argument="--rdg" name="read_extend_penalty" type="integer" value="3" min="0" label="Read gap extend penalty" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
                    <param argument="--rfg" name="ref_open_penalty" type="integer" value="5" min="0" label="Reference gap open penalty" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
                    <param argument="--rfg" name="ref_extend_penalty" type="integer" value="3" min="0" label="Reference gap extend penalty" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
                    <expand macro="nc_function" name="function_type" argument="--score-min" label="Function governing the minimum alignment score needed for an alignment to be considered &quot;valid&quot; (i.e. good enough to report)" help="This is a function of read length" lselected="true"/>
                </when>
            </conditional>

            <conditional name="spliced_options">
                <param name="spliced_options_selector" type="select" label="Spliced alignment options">

                </param>
                <when value="defaults" />
                <when value="advanced">
                    <param name="canonical_penalty" argument="--pen-cansplice" type="integer" value="0" min="0" label="Penalty for canonical splice sites" />
                    <param name="noncanonical_penalty" argument="--pen-noncansplice" type="integer" value="12" min="0" label="Penalty for non-canonical splice sites" />
                    <expand macro="nc_function" name="function_type" argument="--pen-canintronlen" label="Penalty function for long introns with canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones" gselected="true"/>
                    <param name="constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
                    <param name="coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
                    <expand macro="nc_function" name="nc_function_type" argument="--pen-noncanintronlen" label="Penalty function for long introns with non-canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones" gselected="true"/>
                    <param name="nc_constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
                    <param name="nc_coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
                    <param name="min_intron" type="integer" value="20" min="0" label="Minimum intron length" />
                    <param name="max_intron" type="integer" value="500000" min="0" label="Maximum intron length" />
                    <conditional name="no_spliced_alignment_options">

    --dta-cufflinks
            Report alignments tailored specifically for Cufflinks. In addition to what HISAT2 does with the above option (--dta), With this option, HISAT2 looks for novel splice sites with three signals (GT/AG, GC/AG, AT/AC), but all user-provided splice sites are used irrespective of their signals. HISAT2 produces an optional field, XS:A:[+-], for every spliced alignment.

    --no-templatelen-adjustment
            Disables template length adjustment for RNA-seq reads.

    --novel-splicesite-outfile
			In this mode, HISAT2 reports a list of splice sites in the file :
				chromosome name <tab> genomic position of the flanking base on the left side of an intron <tab> genomic position of the flanking base on the right <tab> strand (+, -, and .) '.' indicates an unknown strand for non-canonical splice sites.

-----