comparison ivar_trim.xml @ 13:f0cc9cf99407 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a16957b7f6cb8687daafb005c0036abebce59b26

12:e3bb03cf207a

<tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@">
    <description>Trim reads in aligned BAM</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&

        ivar trim
        -i sorted.bam
        -b bed.bed
        #if $amplicons.filter_by == 'yes'
            -f amplicon_info.tsv
        #end if
        -x $primer_pos_wiggle
        $inc_primers
        -m $min_len

        <param name="primer_pos_wiggle" argument="-x" type="integer" min="0" value="0"
        label="Wiggling room for read ends relative to primer binding sites"
        help="Reads that occur at the specified offset positions relative to primer positions (as annotated in the primer information dataset) will also be trimmed (default: 0)" />
        <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads not ending in any primer binding sites?"/>
        <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/>
        <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/>
        <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/>
    </inputs>
    <outputs>
        <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Trimmed bam" from_work_dir="trimmed.sorted.bam"/>
    </outputs>
    <tests>

13:f0cc9cf99407

<tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy6" profile="@PROFILE@">
    <description>Trim reads in aligned BAM</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&

        ivar trim
        -i sorted.bam
        -b bed.bed
        #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_compute'
            -f amplicon_info.tsv
        #end if
        -x $primer_pos_wiggle
        $inc_primers
        -m $min_len

        <param name="primer_pos_wiggle" argument="-x" type="integer" min="0" value="0"
        label="Wiggling room for read ends relative to primer binding sites"
        help="Reads that occur at the specified offset positions relative to primer positions (as annotated in the primer information dataset) will also be trimmed (default: 0)" />
        <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads not ending in any primer binding sites?"/>
        <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/>
        <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality threshold for sliding window to pass"/>
        <param name="window_width" argument="-s" type="integer" min="0" max="255" value="4" label="Width of sliding window"/>
    </inputs>
    <outputs>
        <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Trimmed bam" from_work_dir="trimmed.sorted.bam"/>
    </outputs>
    <tests>