comparison bam_readtagger.xml @ 28:be95c9c82937 draft

planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty

27:9f7737be4732

<tool id="bam_readtagger" name="Tag alignment files" version="0.3.21">
    <description>from multiple bam files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.3.21">readtagger</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        readtagger -t '$tag_file' -a
        #for $element in $alignment_series
            '$element.annotate_with':$element.r_tag:$element.m_tag
        #end for
        $allow_dovetailing
        $keep_suboptimal
        $discarded
        $verified
        $discard_proper_pairs
        --cores "\${GALAXY_SLOTS:-2}"
        -o '$tagged_file'

            </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="-d" falsevalue="" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/>
        <param argument="-k" name="keep_suboptimal" type="boolean" truevalue="-k" falsevalue="" label="Keep suboptimal alternative tags" help="Check this to also keep alternative tags that cannot explain the current read cigar"/>
        <param argument="-dp" name="discard_proper_pairs" type="boolean" truevalue="-dp" falsevalue="" label="Discard alternative tags for proper pairs" help="Check this to discard alternative tags for reads in proper pairs"/>
        <param argument="-wd" name="discarded" type="boolean" truevalue="-wd discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/>
        <param argument="-wv" name="verified" type="boolean" truevalue="-wv verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/>
    </inputs>
    <outputs>
        <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>
        <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string">
            <filter>verified is True</filter>

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
        $discard_proper_pairs
        --cores "\${GALAXY_SLOTS:-2}"
        -o '$tagged_file'

            </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"/>
    </inputs>
    <outputs>
        <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>
        <data name="verified_file" format="bam" from_work_dir="verified.bam" label="Verified reads/tags on $on_string">
            <filter>verified is True</filter>