comparison bam_readtagger.xml @ 29:2c62ca47c455 draft

planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty

28:be95c9c82937

<tool id="bam_readtagger" name="Tag alignment files" version="0.3.22">
    <description>from multiple bam files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.3.22">readtagger</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        readtagger -t '$tag_file' -s
        #for $element in $alignment_series
            '$element.annotate_with':$element.r_tag:$element.m_tag
        #end for
        $allow_dovetailing
        $discard_suboptimal
        $discarded
        $verified
        $discard_proper_pairs

            </param>
            <param type="select" name="m_tag" label="First letter to use for mate tag" value="B">
                <expand macro="tag_options"/>
            </param>
        </repeat>
        <param argument="--allow_dovetailing" type="boolean" truevalue="--allow_dovetailing" falsevalue="--no_allow_dovetailing" checked="True" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/>
        <param argument="--discard_suboptimal_alternate_tags" name="discard_suboptimal" type="boolean" checked="True" truevalue="--discard_suboptimal_alternate_tags" falsevalue="--no_discard_suboptimal" label="Discard suboptimal alternative tags" help="Check this to discard alternative tags that cannot explain the current read cigar"/>
        <param argument="--discard_if_proper_pair" name="discard_proper_pairs" type="boolean" truevalue="--discard_if_proper_pair" falsevalue="--no_discard_if_proper_pair" label="Discard alternative tags for proper pairs" checked="True" help="Check this to discard alternative tags for reads in proper pairs"/>
        <param argument="--discarded_path" name="discarded" type="boolean" truevalue="--discarded_path discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/>
        <param argument="--verified_path" name="verified" type="boolean" truevalue="--verified_path verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/>

29:2c62ca47c455

<tool id="bam_readtagger" name="Tag alignment files" version="0.3.23">
    <description>from multiple bam files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.3.23">readtagger</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        readtagger -t '$tag_file' -s
        #for $element in $alignment_series
            '$element.annotate_with':$element.r_tag:$element.m_tag
        #end for
        #if $reference_fasta:
            --reference_fasta '$reference_fasta'
        #end if
        $allow_dovetailing
        $discard_suboptimal
        $discarded
        $verified
        $discard_proper_pairs

            </param>
            <param type="select" name="m_tag" label="First letter to use for mate tag" value="B">
                <expand macro="tag_options"/>
            </param>
        </repeat>
        <param argument="--reference_fasta" type="data" format="fasta" label="Reference fasta for realigning clipped reads" optional="True" help="This file is optional. If you provide it, clipped sequences are extracted and aligned against this fasta file."/>
        <param argument="--allow_dovetailing" type="boolean" truevalue="--allow_dovetailing" falsevalue="--no_allow_dovetailing" checked="True" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/>
        <param argument="--discard_suboptimal_alternate_tags" name="discard_suboptimal" type="boolean" checked="True" truevalue="--discard_suboptimal_alternate_tags" falsevalue="--no_discard_suboptimal" label="Discard suboptimal alternative tags" help="Check this to discard alternative tags that cannot explain the current read cigar"/>
        <param argument="--discard_if_proper_pair" name="discard_proper_pairs" type="boolean" truevalue="--discard_if_proper_pair" falsevalue="--no_discard_if_proper_pair" label="Discard alternative tags for proper pairs" checked="True" help="Check this to discard alternative tags for reads in proper pairs"/>
        <param argument="--discarded_path" name="discarded" type="boolean" truevalue="--discarded_path discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/>
        <param argument="--verified_path" name="verified" type="boolean" truevalue="--verified_path verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/>