comparison hisat2.xml @ 2:c37b4554f794 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit a2aaa7c9fe7b343f95450ec428250317696a9fb7

1:6d4d39720545

<?xml version="1.0"?>
<tool id="hisat2" name="HISAT2" version="1.0.0">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>

            --sp ${scoring_options.soft_clip_penalty_max},${scoring_options.soft_clip_penalty_min}
            --score-min ${scoring_options.function_type},${scoring_options.constant_term},${scoring_options.coefficient}
        #end if
        #if str($alignment_options.alignment_options_selector) == "advanced":
            --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient}
            ${alignment_options.skip_forward} ${alignment_options.skip_reverse}
        #end if
        #if str($spliced_options.spliced_options_selector) == "advanced":
            --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty}
            --pen-canintronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient}
            --pen-noncanintronlen ${spliced_options.nc_function_type},${spliced_options.nc_constant_term},${spliced_options.nc_coefficient}

                    help="'F' means a read corresponds to a transcript. 'R' means a read corresponds to the reverse complemented counterpart of a transcript.">
                    <option value="">FR Unstranded</option>
                    <option value="R">First Strand (R/RF)</option>
                    <option value="F">Second Strand (F/FR)</option>
                </param>
                <param argument="--no-spliced-alignment" name="ignore_quals" type="boolean" truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced alignment" />
                <param format="gtf" label="GTF file with known splice sites" name="known_splice_gtf" optional="True" type="data" />
                <param display="radio" label="Transcriptome assembly reporting" name="tma" type="select">
                    <option value="">Use default reporting.</option>
                    <option value="--tmo">Report only those alignments within known transcripts.</option>
                    <option value="--dta">Report alignments tailored for transcript assemblers including StringTie.</option>

2:c37b4554f794

<?xml version="1.0"?>
<tool id="hisat2" name="HISAT2" version="1.0.1">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>

            --sp ${scoring_options.soft_clip_penalty_max},${scoring_options.soft_clip_penalty_min}
            --score-min ${scoring_options.function_type},${scoring_options.constant_term},${scoring_options.coefficient}
        #end if
        #if str($alignment_options.alignment_options_selector) == "advanced":
            --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient}
            ${alignment_options.skip_forward} ${alignment_options.skip_reverse} ${alignment_options.ignore_quals}
        #end if
        #if str($spliced_options.spliced_options_selector) == "advanced":
            --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty}
            --pen-canintronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient}
            --pen-noncanintronlen ${spliced_options.nc_function_type},${spliced_options.nc_constant_term},${spliced_options.nc_coefficient}

                    help="'F' means a read corresponds to a transcript. 'R' means a read corresponds to the reverse complemented counterpart of a transcript.">
                    <option value="">FR Unstranded</option>
                    <option value="R">First Strand (R/RF)</option>
                    <option value="F">Second Strand (F/FR)</option>
                </param>
                <param argument="--no-spliced-alignment" name="no_spliced_alignment" type="boolean" truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced alignment" />
                <param format="gtf" label="GTF file with known splice sites" name="known_splice_gtf" optional="True" type="data" />
                <param display="radio" label="Transcriptome assembly reporting" name="tma" type="select">
                    <option value="">Use default reporting.</option>
                    <option value="--tmo">Report only those alignments within known transcripts.</option>
                    <option value="--dta">Report alignments tailored for transcript assemblers including StringTie.</option>